Starting phenix.real_space_refine
on Sun Jun 15 02:59:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r1f_18809/06_2025/8r1f_18809.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r1f_18809/06_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_18809/06_2025/8r1f_18809.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r1f_18809/06_2025/8r1f_18809.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r1f_18809/06_2025/8r1f_18809.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r1f_18809/06_2025/8r1f_18809.cif"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.23, per 1000 atoms: 0.49
  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: 4.35
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  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: 1.61
  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: 6.42

  Time building geometry restraints manager: 5.31 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:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.270
  Extract box with map and model:          0.720
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     44.810
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.110
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.019   0.004   TRP A 791 
 HIS   0.013   0.003   HIS C 233 
 PHE   0.051   0.005   PHE A 256 
 TYR   0.030   0.004   TYR A 494 
 ARG   0.037   0.001   ARG A 500 

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

*********************** 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  : 1.264 
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: symmetry clash
REVERT: A  303 GLU cc_start: 0.6539 (tt0) cc_final: 0.6319 (tp30)
REVERT: A  313 MET cc_start: 0.7243 (ttm) cc_final: 0.6893 (ttm)
REVERT: A  389 ASP cc_start: 0.6868 (m-30) cc_final: 0.5336 (p0)
REVERT: A  415 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6837 (mp0)
REVERT: A  470 GLU cc_start: 0.5170 (tt0) cc_final: 0.4952 (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: 0.6009 (m-80)
REVERT: A  591 THR cc_start: 0.5311 (p) cc_final: 0.4542 (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: 0.6122 (tm-30)
REVERT: A  757 LEU cc_start: 0.6630 (mt) cc_final: 0.6278 (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: 0.6222 (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: 0.4625 (mp)
REVERT: B  129 LYS cc_start: 0.7730 (mttt) cc_final: 0.6998 (mmmt)
REVERT: C  100 GLN cc_start: 0.7958 (pt0) cc_final: 0.7682 (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: 0.4259 (m-80)
REVERT: C  165 GLN cc_start: 0.8806 (mt0) cc_final: 0.8296 (mt0)
REVERT: C  196 ARG cc_start: 0.7032 (mtt180) cc_final: 0.6282 (ttp-110)
REVERT: C  271 GLU cc_start: 0.7220 (tt0) cc_final: 0.6909 (tt0)
  outliers start: 2
  outliers final: 1
  residues processed: 256
  average time/residue: 0.5729
  time to fit residues: 188.5252
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  : 1.249 
-------------------------------------------------------------------------------
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 86 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0980
   chunk 26 optimal weight:    0.0970
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 795 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.223821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.187591 restraints weight = 38955.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.194591 restraints weight = 19605.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.198411 restraints weight = 12683.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.4499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.3351

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     :  0.601   7.354  11556  Z= 0.313
  Chirality :  0.040   0.140   1260
  Planarity :  0.005   0.046   1501
  Dihedral  :  4.699  56.088   1146
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  8.09 %
    Favored  : 90.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1017
  helix:  0.75 (0.23), residues: 484
  sheet: -0.12 (0.47), residues: 120
  loop :  0.39 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 791 
 HIS   0.006   0.001   HIS C 168 
 PHE   0.019   0.002   PHE A 730 
 TYR   0.016   0.002   TYR A 624 
 ARG   0.008   0.001   ARG A 500 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04812 (  422)
  hydrogen bonds       : angle       5.49585 ( 1176)
  metal coordination   : bond        0.01174 (   12)
  metal coordination   : angle       3.66121 (   15)
  covalent geometry    : bond        0.00299 ( 8540)
  covalent geometry    : angle       0.58661 (11541)

*********************** 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
  172 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 161
  time to evaluate  : 1.284 
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: A  239 ILE cc_start: 0.7114 (mm) cc_final: 0.6761 (mt)
REVERT: A  511 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6685 (t80)
REVERT: A  556 TYR cc_start: 0.6379 (t80) cc_final: 0.6043 (t80)
REVERT: A  559 PHE cc_start: 0.7528 (m-80) cc_final: 0.7256 (m-80)
REVERT: A  591 THR cc_start: 0.7485 (p) cc_final: 0.6125 (m)
REVERT: A  757 LEU cc_start: 0.8472 (mt) cc_final: 0.7805 (tt)
REVERT: B   18 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7529 (mmmt)
REVERT: B   58 CYS cc_start: 0.7954 (m) cc_final: 0.7358 (t)
REVERT: B  127 ASP cc_start: 0.7116 (m-30) cc_final: 0.6877 (m-30)
REVERT: C  287 GLU cc_start: 0.7419 (pt0) cc_final: 0.7198 (pt0)
  outliers start: 11
  outliers final: 8
  residues processed: 166
  average time/residue: 0.5134
  time to fit residues: 113.9074
Evaluate side-chains
  141 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  285 ASN
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  739 MET
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 84 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 76 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.4689 r_free = 0.4689 target = 0.219030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.184867 restraints weight = 38535.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.192065 restraints weight = 20627.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.194247 restraints weight = 12071.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.4456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6684
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8552  Z= 0.166
  Angle     :  0.580   6.772  11556  Z= 0.302
  Chirality :  0.039   0.148   1260
  Planarity :  0.005   0.051   1501
  Dihedral  :  4.677  58.026   1146
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.12 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.26), residues: 1017
  helix:  0.80 (0.23), residues: 487
  sheet: -0.30 (0.47), residues: 120
  loop :  0.47 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 791 
 HIS   0.005   0.001   HIS C 168 
 PHE   0.022   0.002   PHE A 467 
 TYR   0.019   0.002   TYR B  86 
 ARG   0.006   0.001   ARG A 500 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04385 (  422)
  hydrogen bonds       : angle       5.24522 ( 1176)
  metal coordination   : bond        0.00868 (   12)
  metal coordination   : angle       3.76265 (   15)
  covalent geometry    : bond        0.00375 ( 8540)
  covalent geometry    : angle       0.56481 (11541)

*********************** 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
  155 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 1.344 
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: 0.7337 (OUTLIER) cc_final: 0.6653 (t80)
REVERT: A  591 THR cc_start: 0.7601 (p) cc_final: 0.6009 (m)
REVERT: A  757 LEU cc_start: 0.8533 (mt) cc_final: 0.7930 (tt)
REVERT: B   58 CYS cc_start: 0.7877 (m) cc_final: 0.7142 (t)
REVERT: B  127 ASP cc_start: 0.6792 (m-30) cc_final: 0.6457 (m-30)
REVERT: C  160 MET cc_start: 0.7276 (ttp) cc_final: 0.7063 (ttp)
REVERT: C  206 LEU cc_start: 0.4658 (mp) cc_final: 0.3970 (tt)
  outliers start: 16
  outliers final: 10
  residues processed: 148
  average time/residue: 0.5376
  time to fit residues: 108.5116
Evaluate side-chains
  130 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  450 ILE
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  739 MET
Chi-restraints excluded: chain B residue   78 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 29 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 93 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 11 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.4674 r_free = 0.4674 target = 0.217296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.183995 restraints weight = 38455.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.186981 restraints weight = 21611.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.189876 restraints weight = 14715.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.4662

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= 0.142
  Angle     :  0.544   6.871  11556  Z= 0.280
  Chirality :  0.039   0.138   1260
  Planarity :  0.005   0.045   1501
  Dihedral  :  4.581  58.854   1146
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 10.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.26), residues: 1017
  helix:  0.89 (0.23), residues: 487
  sheet: -0.27 (0.48), residues: 116
  loop :  0.56 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 139 
 HIS   0.004   0.001   HIS C 233 
 PHE   0.018   0.002   PHE A 467 
 TYR   0.016   0.001   TYR B  86 
 ARG   0.005   0.000   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03945 (  422)
  hydrogen bonds       : angle       5.03084 ( 1176)
  metal coordination   : bond        0.00716 (   12)
  metal coordination   : angle       3.36693 (   15)
  covalent geometry    : bond        0.00319 ( 8540)
  covalent geometry    : angle       0.53046 (11541)

*********************** 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
  146 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 1.482 
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: 0.7365 (OUTLIER) cc_final: 0.6613 (t80)
REVERT: A  591 THR cc_start: 0.7621 (p) cc_final: 0.6058 (m)
REVERT: A  757 LEU cc_start: 0.8581 (mt) cc_final: 0.7974 (tt)
REVERT: B   58 CYS cc_start: 0.7929 (m) cc_final: 0.7250 (t)
REVERT: B  127 ASP cc_start: 0.6855 (m-30) cc_final: 0.6465 (m-30)
REVERT: C  140 THR cc_start: 0.6297 (OUTLIER) cc_final: 0.5673 (t)
REVERT: C  206 LEU cc_start: 0.4644 (mp) cc_final: 0.3882 (tt)
  outliers start: 19
  outliers final: 14
  residues processed: 140
  average time/residue: 0.4932
  time to fit residues: 94.2160
Evaluate side-chains
  134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 1.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  456 GLU
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  739 MET
Chi-restraints excluded: chain B residue   78 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
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 62 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 68 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    8.9990
   chunk 60 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0370
   overall best weight:    0.8460

-------------------------------------------------------------------------------
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 = 0.4670 r_free = 0.4670 target = 0.216567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.182991 restraints weight = 38601.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.188107 restraints weight = 21421.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.190305 restraints weight = 13901.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.4396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8552  Z= 0.143
  Angle     :  0.537   7.286  11556  Z= 0.274
  Chirality :  0.039   0.162   1260
  Planarity :  0.004   0.045   1501
  Dihedral  :  4.520  59.361   1146
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 11.18 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.26), residues: 1017
  helix:  0.96 (0.23), residues: 487
  sheet: -0.25 (0.49), residues: 116
  loop :  0.59 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 139 
 HIS   0.003   0.001   HIS A 392 
 PHE   0.018   0.002   PHE A 467 
 TYR   0.017   0.001   TYR B  86 
 ARG   0.005   0.000   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03733 (  422)
  hydrogen bonds       : angle       4.92023 ( 1176)
  metal coordination   : bond        0.00773 (   12)
  metal coordination   : angle       3.36215 (   15)
  covalent geometry    : bond        0.00325 ( 8540)
  covalent geometry    : angle       0.52344 (11541)

*********************** 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
  146 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 1.387 
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  456 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7411 (mm-30)
REVERT: A  470 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.5473 (mp0)
REVERT: A  511 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6579 (t80)
REVERT: A  591 THR cc_start: 0.7535 (p) cc_final: 0.6060 (m)
REVERT: A  757 LEU cc_start: 0.8525 (mt) cc_final: 0.8020 (tt)
REVERT: B   58 CYS cc_start: 0.8045 (m) cc_final: 0.7236 (t)
REVERT: C  200 ASN cc_start: 0.6994 (m110) cc_final: 0.6690 (m-40)
REVERT: C  206 LEU cc_start: 0.4448 (mp) cc_final: 0.3619 (tt)
REVERT: C  287 GLU cc_start: 0.7045 (pt0) cc_final: 0.6768 (pt0)
  outliers start: 20
  outliers final: 14
  residues processed: 137
  average time/residue: 0.4812
  time to fit residues: 90.5090
Evaluate side-chains
  135 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  456 GLU
Chi-restraints excluded: chain A residue  470 GLU
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  739 MET
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  125 HIS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 95 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0020
   chunk 85 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0030
   chunk 34 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 94 optimal weight:    6.9990
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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 = 0.4676 r_free = 0.4676 target = 0.217211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.183250 restraints weight = 38532.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.186919 restraints weight = 21920.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.189887 restraints weight = 14822.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.5255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8552  Z= 0.112
  Angle     :  0.500   5.811  11556  Z= 0.255
  Chirality :  0.038   0.131   1260
  Planarity :  0.004   0.040   1501
  Dihedral  :  4.375  59.734   1146
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.71 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.27), residues: 1017
  helix:  1.24 (0.24), residues: 487
  sheet: -0.31 (0.49), residues: 116
  loop :  0.62 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 139 
 HIS   0.006   0.001   HIS C 233 
 PHE   0.013   0.001   PHE A 730 
 TYR   0.012   0.001   TYR B  86 
 ARG   0.003   0.000   ARG A 500 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  422)
  hydrogen bonds       : angle       4.75227 ( 1176)
  metal coordination   : bond        0.00552 (   12)
  metal coordination   : angle       2.95501 (   15)
  covalent geometry    : bond        0.00250 ( 8540)
  covalent geometry    : angle       0.48914 (11541)

*********************** 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
  142 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 1.254 
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  470 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.5432 (mp0)
REVERT: A  511 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6509 (t80)
REVERT: A  537 LEU cc_start: 0.4822 (tt) cc_final: 0.4468 (tt)
REVERT: A  552 LYS cc_start: 0.7762 (mttp) cc_final: 0.7509 (mmtm)
REVERT: A  572 LYS cc_start: 0.7610 (tttt) cc_final: 0.7300 (tptp)
REVERT: A  591 THR cc_start: 0.7568 (p) cc_final: 0.6068 (m)
REVERT: A  757 LEU cc_start: 0.8429 (mt) cc_final: 0.7895 (tt)
REVERT: B   58 CYS cc_start: 0.8004 (m) cc_final: 0.7239 (t)
REVERT: C  206 LEU cc_start: 0.4413 (mp) cc_final: 0.3549 (tt)
  outliers start: 16
  outliers final: 11
  residues processed: 135
  average time/residue: 0.4579
  time to fit residues: 85.2724
Evaluate side-chains
  131 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  470 GLU
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  739 MET
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
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 93 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.8386

-------------------------------------------------------------------------------
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 = 0.4659 r_free = 0.4659 target = 0.215370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.181221 restraints weight = 38271.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.184883 restraints weight = 21911.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.188091 restraints weight = 14873.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.5456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8552  Z= 0.141
  Angle     :  0.523   6.165  11556  Z= 0.268
  Chirality :  0.039   0.140   1260
  Planarity :  0.004   0.043   1501
  Dihedral  :  4.411  59.928   1146
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.71 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.27), residues: 1017
  helix:  1.19 (0.23), residues: 487
  sheet: -0.40 (0.49), residues: 116
  loop :  0.61 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 139 
 HIS   0.004   0.001   HIS A 392 
 PHE   0.019   0.002   PHE A 467 
 TYR   0.018   0.001   TYR C 103 
 ARG   0.004   0.000   ARG A 500 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  422)
  hydrogen bonds       : angle       4.80172 ( 1176)
  metal coordination   : bond        0.00716 (   12)
  metal coordination   : angle       3.09781 (   15)
  covalent geometry    : bond        0.00322 ( 8540)
  covalent geometry    : angle       0.51145 (11541)

*********************** 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
  137 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 1.290 
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  470 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.5473 (mp0)
REVERT: A  511 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6480 (t80)
REVERT: A  537 LEU cc_start: 0.5258 (tt) cc_final: 0.4909 (tt)
REVERT: A  552 LYS cc_start: 0.7586 (mttp) cc_final: 0.7385 (mmtm)
REVERT: A  572 LYS cc_start: 0.7648 (tttt) cc_final: 0.7190 (tptp)
REVERT: A  591 THR cc_start: 0.7522 (p) cc_final: 0.6131 (m)
REVERT: B   58 CYS cc_start: 0.8046 (m) cc_final: 0.7244 (t)
REVERT: C  206 LEU cc_start: 0.4442 (mp) cc_final: 0.3603 (tt)
  outliers start: 18
  outliers final: 12
  residues processed: 129
  average time/residue: 0.4802
  time to fit residues: 84.8830
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  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  470 GLU
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  739 MET
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain C residue  147 VAL
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 101 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0000
   chunk 31 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 64 optimal weight:   10.0000
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 100 ASN
C 193 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.216308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.182217 restraints weight = 38265.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.185089 restraints weight = 21901.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.188724 restraints weight = 15303.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.5588

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= 0.116
  Angle     :  0.504   5.163  11556  Z= 0.258
  Chirality :  0.038   0.139   1260
  Planarity :  0.004   0.040   1501
  Dihedral  :  4.316  59.950   1146
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.25 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.27), residues: 1017
  helix:  1.33 (0.24), residues: 487
  sheet: -0.38 (0.49), residues: 116
  loop :  0.67 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 139 
 HIS   0.004   0.001   HIS A 392 
 PHE   0.013   0.001   PHE A 730 
 TYR   0.016   0.001   TYR C 103 
 ARG   0.004   0.000   ARG A 500 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03353 (  422)
  hydrogen bonds       : angle       4.68928 ( 1176)
  metal coordination   : bond        0.00548 (   12)
  metal coordination   : angle       2.74128 (   15)
  covalent geometry    : bond        0.00262 ( 8540)
  covalent geometry    : angle       0.49467 (11541)

*********************** 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
  134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 1.422 
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  470 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.5444 (mp0)
REVERT: A  511 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6464 (t80)
REVERT: A  537 LEU cc_start: 0.5272 (tt) cc_final: 0.4896 (tt)
REVERT: A  552 LYS cc_start: 0.7863 (mttp) cc_final: 0.7650 (mmtm)
REVERT: A  572 LYS cc_start: 0.7582 (tttt) cc_final: 0.7189 (tptp)
REVERT: B   58 CYS cc_start: 0.8043 (m) cc_final: 0.7279 (t)
REVERT: C  206 LEU cc_start: 0.4356 (mp) cc_final: 0.3482 (tt)
  outliers start: 14
  outliers final: 11
  residues processed: 128
  average time/residue: 0.4898
  time to fit residues: 85.8149
Evaluate side-chains
  129 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  470 GLU
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  739 MET
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
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 68 optimal weight:    0.0970
   chunk 36 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.6978

-------------------------------------------------------------------------------
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 = 0.215230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.180256 restraints weight = 38335.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.184992 restraints weight = 20771.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.187766 restraints weight = 14034.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.4379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.5705

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= 0.125
  Angle     :  0.513   5.175  11556  Z= 0.263
  Chirality :  0.038   0.140   1260
  Planarity :  0.004   0.053   1501
  Dihedral  :  4.311  59.819   1146
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.89 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.27), residues: 1017
  helix:  1.41 (0.24), residues: 481
  sheet: -0.33 (0.49), residues: 115
  loop :  0.70 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 139 
 HIS   0.004   0.001   HIS A 392 
 PHE   0.015   0.002   PHE A 467 
 TYR   0.017   0.001   TYR C 103 
 ARG   0.008   0.000   ARG C 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03388 (  422)
  hydrogen bonds       : angle       4.67720 ( 1176)
  metal coordination   : bond        0.00608 (   12)
  metal coordination   : angle       2.56656 (   15)
  covalent geometry    : bond        0.00286 ( 8540)
  covalent geometry    : angle       0.50472 (11541)

*********************** 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
  136 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 1.446 
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: symmetry clash
   revert: symmetry clash
REVERT: A  470 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.5431 (mp0)
REVERT: A  511 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6400 (t80)
REVERT: A  537 LEU cc_start: 0.5350 (tt) cc_final: 0.4951 (tt)
REVERT: A  572 LYS cc_start: 0.7529 (tttt) cc_final: 0.7158 (tptp)
REVERT: A  591 THR cc_start: 0.7404 (p) cc_final: 0.5917 (m)
REVERT: B   58 CYS cc_start: 0.8005 (m) cc_final: 0.7247 (t)
REVERT: C  206 LEU cc_start: 0.4364 (mp) cc_final: 0.3498 (tt)
  outliers start: 15
  outliers final: 12
  residues processed: 129
  average time/residue: 0.4686
  time to fit residues: 83.3273
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  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  470 GLU
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  739 MET
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain C residue  109 PHE
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 89 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 82 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 95 optimal weight:    0.1980
   chunk 32 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.4663 r_free = 0.4663 target = 0.215469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.180603 restraints weight = 38096.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.184539 restraints weight = 21330.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.188680 restraints weight = 14779.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.4389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6803
moved from start:          0.5823

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= 0.119
  Angle     :  0.509   5.177  11556  Z= 0.263
  Chirality :  0.038   0.140   1260
  Planarity :  0.004   0.051   1501
  Dihedral  :  4.271  59.982   1146
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.27), residues: 1017
  helix:  1.44 (0.24), residues: 481
  sheet: -0.29 (0.50), residues: 113
  loop :  0.77 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 139 
 HIS   0.004   0.001   HIS A 392 
 PHE   0.013   0.001   PHE A 467 
 TYR   0.018   0.001   TYR C 103 
 ARG   0.007   0.000   ARG C 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03356 (  422)
  hydrogen bonds       : angle       4.64992 ( 1176)
  metal coordination   : bond        0.00636 (   12)
  metal coordination   : angle       2.64039 (   15)
  covalent geometry    : bond        0.00272 ( 8540)
  covalent geometry    : angle       0.50032 (11541)

********************** 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
  136 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 1.396 
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  470 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.5415 (mp0)
REVERT: A  511 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6447 (t80)
REVERT: A  537 LEU cc_start: 0.5308 (tt) cc_final: 0.4946 (tt)
REVERT: A  572 LYS cc_start: 0.7560 (tttt) cc_final: 0.7130 (tptp)
REVERT: A  591 THR cc_start: 0.7345 (p) cc_final: 0.5924 (m)
REVERT: B   58 CYS cc_start: 0.8071 (m) cc_final: 0.7287 (t)
REVERT: C  206 LEU cc_start: 0.4351 (mp) cc_final: 0.3475 (tt)
  outliers start: 16
  outliers final: 12
  residues processed: 129
  average time/residue: 0.4535
  time to fit residues: 80.5313
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  : 1.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  470 GLU
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  739 MET
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  125 HIS
Chi-restraints excluded: chain C residue  109 PHE
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 81 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    0.2980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.214714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.179701 restraints weight = 38059.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.184177 restraints weight = 21492.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.187742 restraints weight = 14472.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.5923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8552  Z= 0.134
  Angle     :  0.519   5.549  11556  Z= 0.269
  Chirality :  0.038   0.141   1260
  Planarity :  0.004   0.052   1501
  Dihedral  :  4.300  59.889   1146
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.99 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.27), residues: 1017
  helix:  1.37 (0.24), residues: 481
  sheet: -0.29 (0.50), residues: 115
  loop :  0.79 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 139 
 HIS   0.004   0.001   HIS A 392 
 PHE   0.017   0.002   PHE A 467 
 TYR   0.016   0.001   TYR C 103 
 ARG   0.008   0.000   ARG C 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03445 (  422)
  hydrogen bonds       : angle       4.69031 ( 1176)
  metal coordination   : bond        0.00695 (   12)
  metal coordination   : angle       2.72942 (   15)
  covalent geometry    : bond        0.00306 ( 8540)
  covalent geometry    : angle       0.51035 (11541)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5610.29 seconds
wall clock time: 96 minutes 17.45 seconds (5777.45 seconds total)