Starting phenix.real_space_refine
on Fri Jun  6 14:34:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hr5_34958/06_2025/8hr5_34958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hr5_34958/06_2025/8hr5_34958.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hr5_34958/06_2025/8hr5_34958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hr5_34958/06_2025/8hr5_34958.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hr5_34958/06_2025/8hr5_34958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hr5_34958/06_2025/8hr5_34958.cif"
  }
  resolution = 3.73
  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=  -0.000 sd=   0.037
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: 5
    Type Number    sf(0)   Gaussians
     P     123      5.49       5
     S      17      5.16       5
     C    4339      2.51       5
     N    1351      2.21       5
     O    1765      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7595
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 466, 3327
          Classifications: {'peptide': 466}
          Incomplete info: {'truncation_to_alanine': 135}
          Link IDs: {'PTRANS': 5, 'TRANS': 460}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 531
          Unresolved non-hydrogen angles: 628
          Unresolved non-hydrogen dihedrals: 452
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 11, 'GLU:plan': 25, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 286
    Chain: "B"
      Number of atoms: 1660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1660
          Classifications: {'peptide': 245}
          Incomplete info: {'truncation_to_alanine': 110}
          Link IDs: {'PTRANS': 3, 'TRANS': 241}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 400
          Unresolved non-hydrogen angles: 479
          Unresolved non-hydrogen dihedrals: 332
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 200
    Chain: "C"
      Number of atoms: 2163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 2163
          Classifications: {'RNA': 101}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 50, 'rna3p_pyr': 41}
          Link IDs: {'rna2p': 10, 'rna3p': 90}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 345
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "E"
      Number of atoms: 100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 100
          Classifications: {'DNA': 5}
          Link IDs: {'rna3p': 4}
  Time building chain proxies: 7.97, per 1000 atoms: 1.05
  Number of scatterers: 7595
  At special positions: 0
  Unit cell: (80.36, 117.26, 113.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      17     16.00
     P     123     15.00
     O    1765      8.00
     N    1351      7.00
     C    4339      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.97
  Conformation dependent library (CDL) restraints added in 737.7 milliseconds
  

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1364

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 5 sheets defined
      55.3% alpha, 12.2% beta
      42 base pairs and 67 stacking pairs defined.
    Time for finding SS restraints: 3.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 53
      removed outlier: 3.616A  pdb=" N   ARG A  18 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ASN A  19 " --> pdb=" O   LYS A  15 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER A  20 " --> pdb=" O   ASP A  16 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ASN A  37 " --> pdb=" O   TYR A  33 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   MET A  51 " --> pdb=" O   ASP A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 81
      removed outlier: 3.974A  pdb=" N   GLU A  57 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 131
    Processing helix  chain 'A' and resid 136 through 145
    Processing helix  chain 'A' and resid 148 through 153
    Processing helix  chain 'A' and resid 154 through 156
      No H-bonds generated for 'chain 'A' and resid 154 through 156'
    Processing helix  chain 'A' and resid 162 through 182
      removed outlier: 4.218A  pdb=" N   LEU A 166 " --> pdb=" O   ASP A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 206
      removed outlier: 3.672A  pdb=" N   ASP A 205 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU A 206 " --> pdb=" O   GLY A 203 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 206'
    Processing helix  chain 'A' and resid 237 through 249
      removed outlier: 3.620A  pdb=" N   ARG A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 340
      removed outlier: 3.517A  pdb=" N   PHE A 319 " --> pdb=" O   ARG A 315 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   LYS A 321 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   THR A 324 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLN A 325 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 344
      removed outlier: 4.045A  pdb=" N   LYS A 344 " --> pdb=" O   LYS A 341 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 341 through 344'
    Processing helix  chain 'A' and resid 345 through 382
      removed outlier: 3.618A  pdb=" N   ASN A 382 " --> pdb=" O   PHE A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 422
      removed outlier: 3.646A  pdb=" N   LEU A 411 " --> pdb=" O   SER A 407 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU A 416 " --> pdb=" O   GLN A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 477
    Processing helix  chain 'B' and resid 14 through 52
      removed outlier: 3.546A  pdb=" N   TYR B  50 " --> pdb=" O   ASN B  46 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   MET B  51 " --> pdb=" O   ASP B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 79
      removed outlier: 3.944A  pdb=" N   ILE B  58 " --> pdb=" O   SER B  54 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASP B  63 " --> pdb=" O   ARG B  59 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLU B  79 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 148
      removed outlier: 4.314A  pdb=" N   VAL B 146 " --> pdb=" O   LYS B 142 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASP B 147 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 181
      removed outlier: 4.384A  pdb=" N   SER B 165 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LYS B 176 " --> pdb=" O   LYS B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 206
      removed outlier: 3.792A  pdb=" N   LEU B 206 " --> pdb=" O   GLY B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 249
      removed outlier: 3.855A  pdb=" N   HIS B 242 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 201
      removed outlier: 3.617A  pdb=" N   THR A 201 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER A 257 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   SER A 258 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   LEU A 267 " --> pdb=" O   LEU A   9 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   ILE A 216 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LYS A 207 " --> pdb=" O   LYS A 219 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201
      removed outlier: 3.617A  pdb=" N   THR A 201 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER A 257 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   SER A 258 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LYS A 253 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 302
      removed outlier: 5.400A  pdb=" N   VAL A 289 " --> pdb=" O   ASN A 388 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   GLU A 390 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   VAL A 291 " --> pdb=" O   GLU A 390 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 456
    Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 201
      removed outlier: 3.521A  pdb=" N   THR B 201 " --> pdb=" O   SER B 257 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER B 257 " --> pdb=" O   THR B 201 " (cutoff:3.500A)

    345 hydrogen bonds defined for protein.
    999 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      100 hydrogen bonds
      184 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      67 stacking parallelities
  Total time for adding SS restraints: 3.13

  Time building geometry restraints manager: 3.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1314
        1.33 -     1.45: 2528
        1.45 -     1.57: 3856
        1.57 -     1.69: 239
        1.69 -     1.81: 27
  Bond restraints: 7964
  Sorted by residual:
  bond pdb=" O3'   A C  79 "
       pdb=" P     U C  80 "
    ideal  model  delta    sigma   weight residual
    1.607  1.546  0.061 1.50e-02 4.44e+03 1.63e+01
  bond pdb=" O3'   G C  99 "
       pdb=" P     A C 100 "
    ideal  model  delta    sigma   weight residual
    1.607  1.660 -0.053 1.50e-02 4.44e+03 1.25e+01
  bond pdb=" N   VAL A   4 "
       pdb=" CA  VAL A   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.19e-02 7.06e+03 8.11e+00
  bond pdb=" N   ILE A 113 "
       pdb=" CA  ILE A 113 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 8.08e+00
  bond pdb=" N   ILE A 120 "
       pdb=" CA  ILE A 120 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.82e+00
  ... (remaining 7959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 10921
        1.57 -     3.14: 422
        3.14 -     4.71: 43
        4.71 -     6.28: 10
        6.28 -     7.85: 2
  Bond angle restraints: 11398
  Sorted by residual:
  angle pdb=" N   GLY A  55 "
        pdb=" CA  GLY A  55 "
        pdb=" C   GLY A  55 "
      ideal   model   delta    sigma   weight residual
     113.24  107.38    5.86 1.31e+00 5.83e-01 2.00e+01
  angle pdb=" N   MET A 221 "
        pdb=" CA  MET A 221 "
        pdb=" C   MET A 221 "
      ideal   model   delta    sigma   weight residual
     110.80  118.65   -7.85 2.13e+00 2.20e-01 1.36e+01
  angle pdb=" C3'   G C  91 "
        pdb=" O3'   G C  91 "
        pdb=" P     U C  92 "
      ideal   model   delta    sigma   weight residual
     120.20  125.26   -5.06 1.50e+00 4.44e-01 1.14e+01
  angle pdb=" N   GLU A 222 "
        pdb=" CA  GLU A 222 "
        pdb=" C   GLU A 222 "
      ideal   model   delta    sigma   weight residual
     111.39  115.89   -4.50 1.38e+00 5.25e-01 1.06e+01
  angle pdb=" CA  THR A  10 "
        pdb=" C   THR A  10 "
        pdb=" O   THR A  10 "
      ideal   model   delta    sigma   weight residual
     121.33  117.96    3.37 1.08e+00 8.57e-01 9.72e+00
  ... (remaining 11393 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.63: 4377
       35.63 -    71.25: 405
       71.25 -   106.88: 27
      106.88 -   142.51: 2
      142.51 -   178.13: 5
  Dihedral angle restraints: 4816
    sinusoidal: 2720
      harmonic: 2096
  Sorted by residual:
  dihedral pdb=" O4'   U C  94 "
           pdb=" C1'   U C  94 "
           pdb=" N1    U C  94 "
           pdb=" C2    U C  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   29.81  170.19     1      1.50e+01 4.44e-03 8.47e+01
  dihedral pdb=" O4'   U C  77 "
           pdb=" C1'   U C  77 "
           pdb=" N1    U C  77 "
           pdb=" C2    U C  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   41.62  158.38     1      1.50e+01 4.44e-03 8.23e+01
  dihedral pdb=" O4'   U C  76 "
           pdb=" C1'   U C  76 "
           pdb=" N1    U C  76 "
           pdb=" C2    U C  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   61.11  170.89     1      1.70e+01 3.46e-03 6.60e+01
  ... (remaining 4813 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1153
       0.048 -    0.097: 186
       0.097 -    0.145: 49
       0.145 -    0.193: 41
       0.193 -    0.241: 5
  Chirality restraints: 1434
  Sorted by residual:
  chirality pdb=" CA  MET A 221 "
            pdb=" N   MET A 221 "
            pdb=" C   MET A 221 "
            pdb=" CB  MET A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" C3'   G C  91 "
            pdb=" C4'   G C  91 "
            pdb=" O3'   G C  91 "
            pdb=" C2'   G C  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.54   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" C3'   A C 207 "
            pdb=" C4'   A C 207 "
            pdb=" O3'   A C 207 "
            pdb=" C2'   A C 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.69    0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 1431 not shown)

  Planarity restraints: 1009
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  27 "   -0.027 2.00e-02 2.50e+03   1.21e-02 4.41e+00
        pdb=" N9    G C  27 "    0.030 2.00e-02 2.50e+03
        pdb=" C8    G C  27 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G C  27 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    G C  27 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    G C  27 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6    G C  27 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G C  27 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G C  27 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G C  27 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    G C  27 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G C  27 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C  40 "    0.022 2.00e-02 2.50e+03   1.18e-02 3.13e+00
        pdb=" N1    C C  40 "   -0.025 2.00e-02 2.50e+03
        pdb=" C2    C C  40 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2    C C  40 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    C C  40 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    C C  40 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C C  40 "    0.008 2.00e-02 2.50e+03
        pdb=" C5    C C  40 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6    C C  40 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C  90 "   -0.011 2.00e-02 2.50e+03   1.06e-02 2.52e+00
        pdb=" N1    U C  90 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    U C  90 "    0.005 2.00e-02 2.50e+03
        pdb=" O2    U C  90 "    0.007 2.00e-02 2.50e+03
        pdb=" N3    U C  90 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4    U C  90 "   -0.010 2.00e-02 2.50e+03
        pdb=" O4    U C  90 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    U C  90 "   -0.011 2.00e-02 2.50e+03
        pdb=" C6    U C  90 "    0.023 2.00e-02 2.50e+03
  ... (remaining 1006 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 687
        2.73 -     3.27: 7314
        3.27 -     3.82: 13145
        3.82 -     4.36: 14335
        4.36 -     4.90: 22495
  Nonbonded interactions: 57976
  Sorted by model distance:
  nonbonded pdb=" O2'   G C  74 "
            pdb=" O4'   G C  75 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O2'   A C  71 "
            pdb=" O4'   A C  72 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   LEU A 320 "
            pdb=" OG1 THR A 324 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O2    U C  87 "
            pdb=" O6    G C  99 "
     model   vdw
     2.246 2.432
  nonbonded pdb=" O4    U C  47 "
            pdb=" O6    G C  68 "
     model   vdw
     2.246 2.432
  ... (remaining 57971 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:             3.960
  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:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     28.870
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:3.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
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      :  0.004   0.061   7964  Z= 0.264
  Angle     :  0.673   7.848  11398  Z= 0.420
  Chirality :  0.048   0.241   1434
  Planarity :  0.003   0.040   1009
  Dihedral  : 22.930 178.134   3452
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  :  2.16 %
    Favored  : 94.47 %
  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:  0.07 (0.32), residues: 699
  helix:  1.21 (0.27), residues: 352
  sheet: -1.12 (0.55), residues: 90
  loop : -1.10 (0.39), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  24 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.013   0.002   PHE A 370 
 TYR   0.018   0.002   TYR A 150 
 ARG   0.002   0.000   ARG A 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18117 (  440)
  hydrogen bonds       : angle       6.44768 ( 1183)
  covalent geometry    : bond        0.00438 ( 7964)
  covalent geometry    : angle       0.67269 (11398)

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.802 
Fit side-chains
REVERT: B   52 ASN cc_start: 0.8797 (t0) cc_final: 0.8536 (t0)
REVERT: B   63 ASP cc_start: 0.5379 (t0) cc_final: 0.5051 (t0)
REVERT: B  147 ASP cc_start: 0.8139 (t70) cc_final: 0.7926 (t0)
  outliers start: 14
  outliers final: 1
  residues processed: 102
  average time/residue: 0.2522
  time to fit residues: 33.9525
Evaluate side-chains
  71 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 47 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   overall best weight:    1.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.180269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.146062 restraints weight = 11409.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.145915 restraints weight = 16724.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.147285 restraints weight = 13872.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7964  Z= 0.194
  Angle     :  0.645   9.566  11398  Z= 0.336
  Chirality :  0.037   0.183   1434
  Planarity :  0.004   0.041   1009
  Dihedral  : 23.687 172.644   2548
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.42 %
    Favored  : 83.41 %
  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:  1.05 (0.32), residues: 699
  helix:  2.39 (0.27), residues: 356
  sheet: -0.91 (0.50), residues: 103
  loop : -1.21 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  24 
 HIS   0.005   0.001   HIS A 160 
 PHE   0.020   0.003   PHE A 370 
 TYR   0.023   0.002   TYR A 150 
 ARG   0.007   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05784 (  440)
  hydrogen bonds       : angle       3.84491 ( 1183)
  covalent geometry    : bond        0.00421 ( 7964)
  covalent geometry    : angle       0.64479 (11398)

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.634 
Fit side-chains
REVERT: B   63 ASP cc_start: 0.6182 (t0) cc_final: 0.5939 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 83
  average time/residue: 0.1493
  time to fit residues: 18.1370
Evaluate side-chains
  73 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  156 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0870
   chunk 45 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 27 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 54 optimal weight:   50.0000
   overall best weight:    1.1162

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.180934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.148416 restraints weight = 11558.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.147921 restraints weight = 16795.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.148555 restraints weight = 14503.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7964  Z= 0.170
  Angle     :  0.592   8.578  11398  Z= 0.311
  Chirality :  0.036   0.196   1434
  Planarity :  0.004   0.037   1009
  Dihedral  : 23.484 174.604   2547
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.51 %
    Favored  : 78.37 %
  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:  1.50 (0.32), residues: 699
  helix:  2.88 (0.27), residues: 358
  sheet: -0.97 (0.52), residues: 102
  loop : -1.11 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 220 
 HIS   0.005   0.001   HIS A 160 
 PHE   0.016   0.002   PHE A 370 
 TYR   0.018   0.002   TYR A 150 
 ARG   0.008   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05503 (  440)
  hydrogen bonds       : angle       3.62580 ( 1183)
  covalent geometry    : bond        0.00363 ( 7964)
  covalent geometry    : angle       0.59237 (11398)

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.690 
Fit side-chains
REVERT: B   63 ASP cc_start: 0.6189 (t0) cc_final: 0.5980 (t0)
  outliers start: 13
  outliers final: 11
  residues processed: 79
  average time/residue: 0.1526
  time to fit residues: 17.8778
Evaluate side-chains
  76 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  156 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.171760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.135695 restraints weight = 12019.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.136015 restraints weight = 13387.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.136489 restraints weight = 11346.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7964  Z= 0.187
  Angle     :  0.610   7.120  11398  Z= 0.321
  Chirality :  0.036   0.205   1434
  Planarity :  0.004   0.038   1009
  Dihedral  : 23.387 176.206   2547
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 20.91 %
    Favored  : 74.76 %
  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:  1.37 (0.33), residues: 699
  helix:  2.94 (0.27), residues: 359
  sheet: -1.11 (0.49), residues: 114
  loop : -1.45 (0.38), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  24 
 HIS   0.005   0.001   HIS A 160 
 PHE   0.017   0.002   PHE A 370 
 TYR   0.021   0.002   TYR A 150 
 ARG   0.004   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05707 (  440)
  hydrogen bonds       : angle       3.55946 ( 1183)
  covalent geometry    : bond        0.00404 ( 7964)
  covalent geometry    : angle       0.60972 (11398)

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.625 
Fit side-chains
  outliers start: 18
  outliers final: 15
  residues processed: 84
  average time/residue: 0.1338
  time to fit residues: 17.1265
Evaluate side-chains
  79 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  256 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 6 optimal weight:    0.6980
   chunk 69 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    1.0586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.172841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.136413 restraints weight = 12023.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.138232 restraints weight = 12250.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.138456 restraints weight = 9488.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7964  Z= 0.162
  Angle     :  0.575   6.728  11398  Z= 0.305
  Chirality :  0.036   0.208   1434
  Planarity :  0.003   0.036   1009
  Dihedral  : 23.342 176.490   2547
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 21.39 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.56 (0.33), residues: 699
  helix:  3.11 (0.27), residues: 358
  sheet: -1.19 (0.51), residues: 102
  loop : -1.28 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  24 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.013   0.002   PHE A 370 
 TYR   0.016   0.002   TYR A 150 
 ARG   0.004   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05325 (  440)
  hydrogen bonds       : angle       3.44649 ( 1183)
  covalent geometry    : bond        0.00348 ( 7964)
  covalent geometry    : angle       0.57501 (11398)

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.686 
Fit side-chains
  outliers start: 22
  outliers final: 16
  residues processed: 84
  average time/residue: 0.1314
  time to fit residues: 17.0784
Evaluate side-chains
  80 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  256 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 17 optimal weight:    0.1980
   chunk 76 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   chunk 22 optimal weight:    0.4980
   chunk 20 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.4380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.177493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.139875 restraints weight = 11958.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.142215 restraints weight = 10233.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.142653 restraints weight = 7328.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7964  Z= 0.111
  Angle     :  0.504   6.139  11398  Z= 0.272
  Chirality :  0.034   0.203   1434
  Planarity :  0.003   0.033   1009
  Dihedral  : 23.189 177.162   2547
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.80 %
    Favored  : 72.36 %
  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:  1.97 (0.33), residues: 699
  helix:  3.49 (0.26), residues: 357
  sheet: -1.04 (0.51), residues: 102
  loop : -1.12 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  24 
 HIS   0.002   0.001   HIS A 160 
 PHE   0.018   0.001   PHE A 319 
 TYR   0.014   0.001   TYR A 367 
 ARG   0.003   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04147 (  440)
  hydrogen bonds       : angle       3.12142 ( 1183)
  covalent geometry    : bond        0.00219 ( 7964)
  covalent geometry    : angle       0.50405 (11398)

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.724 
Fit side-chains
  outliers start: 16
  outliers final: 13
  residues processed: 81
  average time/residue: 0.1298
  time to fit residues: 16.8432
Evaluate side-chains
  78 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  256 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0370
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.9660

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.173960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.138617 restraints weight = 11922.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.138223 restraints weight = 11331.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.139331 restraints weight = 11482.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7964  Z= 0.151
  Angle     :  0.550   7.031  11398  Z= 0.292
  Chirality :  0.035   0.178   1434
  Planarity :  0.003   0.033   1009
  Dihedral  : 23.184 177.890   2547
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 24.76 %
    Favored  : 70.43 %
  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:  1.81 (0.33), residues: 699
  helix:  3.39 (0.26), residues: 360
  sheet: -1.16 (0.50), residues: 108
  loop : -1.30 (0.38), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  24 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.019   0.002   PHE A 319 
 TYR   0.016   0.002   TYR A 150 
 ARG   0.003   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05040 (  440)
  hydrogen bonds       : angle       3.24986 ( 1183)
  covalent geometry    : bond        0.00322 ( 7964)
  covalent geometry    : angle       0.54954 (11398)

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.638 
Fit side-chains
REVERT: A  327 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7750 (tm-30)
  outliers start: 20
  outliers final: 15
  residues processed: 79
  average time/residue: 0.1195
  time to fit residues: 14.9782
Evaluate side-chains
  79 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 73 optimal weight:    7.9990
   chunk 35 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.0382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.173571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.138042 restraints weight = 12134.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.139579 restraints weight = 12519.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.140037 restraints weight = 10897.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7964  Z= 0.157
  Angle     :  0.554   6.498  11398  Z= 0.294
  Chirality :  0.035   0.180   1434
  Planarity :  0.003   0.033   1009
  Dihedral  : 23.202 177.867   2547
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 25.00 %
    Favored  : 70.19 %
  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:  1.75 (0.33), residues: 699
  helix:  3.34 (0.26), residues: 360
  sheet: -1.16 (0.51), residues: 107
  loop : -1.33 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  24 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.020   0.002   PHE A 319 
 TYR   0.016   0.002   TYR A 367 
 ARG   0.003   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05105 (  440)
  hydrogen bonds       : angle       3.27239 ( 1183)
  covalent geometry    : bond        0.00338 ( 7964)
  covalent geometry    : angle       0.55384 (11398)

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.646 
Fit side-chains
  outliers start: 20
  outliers final: 17
  residues processed: 81
  average time/residue: 0.1206
  time to fit residues: 15.4627
Evaluate side-chains
  80 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.175676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.140428 restraints weight = 12112.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.140868 restraints weight = 12743.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.142338 restraints weight = 11313.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7964  Z= 0.125
  Angle     :  0.519   6.191  11398  Z= 0.278
  Chirality :  0.034   0.193   1434
  Planarity :  0.003   0.033   1009
  Dihedral  : 23.168 177.351   2547
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 24.76 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.95 (0.33), residues: 699
  helix:  3.49 (0.26), residues: 360
  sheet: -0.85 (0.51), residues: 110
  loop : -1.35 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  24 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.021   0.002   PHE A 319 
 TYR   0.016   0.001   TYR A 367 
 ARG   0.003   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04536 (  440)
  hydrogen bonds       : angle       3.07945 ( 1183)
  covalent geometry    : bond        0.00259 ( 7964)
  covalent geometry    : angle       0.51948 (11398)

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.712 
Fit side-chains
  outliers start: 19
  outliers final: 17
  residues processed: 83
  average time/residue: 0.1273
  time to fit residues: 16.5401
Evaluate side-chains
  83 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    1.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.172881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.137378 restraints weight = 11987.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.137838 restraints weight = 11915.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.138300 restraints weight = 11262.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7964  Z= 0.191
  Angle     :  0.595   6.786  11398  Z= 0.315
  Chirality :  0.036   0.179   1434
  Planarity :  0.003   0.033   1009
  Dihedral  : 23.266 178.041   2547
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 25.00 %
    Favored  : 69.95 %
  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:  1.71 (0.33), residues: 699
  helix:  3.29 (0.26), residues: 362
  sheet: -1.00 (0.49), residues: 116
  loop : -1.47 (0.39), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 220 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.021   0.002   PHE A 319 
 TYR   0.021   0.002   TYR A 150 
 ARG   0.002   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05674 (  440)
  hydrogen bonds       : angle       3.32834 ( 1183)
  covalent geometry    : bond        0.00420 ( 7964)
  covalent geometry    : angle       0.59470 (11398)

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.631 
Fit side-chains
  outliers start: 21
  outliers final: 17
  residues processed: 83
  average time/residue: 0.1240
  time to fit residues: 16.0922
Evaluate side-chains
  80 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 SER
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 60 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0770
   chunk 75 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 57 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:   40.0000
   chunk 56 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   overall best weight:    0.5938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.176459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.140985 restraints weight = 11885.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.140864 restraints weight = 12009.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.141565 restraints weight = 10519.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.3737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7964  Z= 0.125
  Angle     :  0.530   6.112  11398  Z= 0.284
  Chirality :  0.034   0.199   1434
  Planarity :  0.003   0.033   1009
  Dihedral  : 23.212 177.381   2547
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 26.44 %
    Favored  : 69.47 %
  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:  1.98 (0.33), residues: 699
  helix:  3.47 (0.26), residues: 362
  sheet: -0.81 (0.52), residues: 104
  loop : -1.31 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  24 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.019   0.001   PHE A 319 
 TYR   0.016   0.001   TYR A 367 
 ARG   0.003   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04589 (  440)
  hydrogen bonds       : angle       3.06109 ( 1183)
  covalent geometry    : bond        0.00257 ( 7964)
  covalent geometry    : angle       0.52993 (11398)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2310.91 seconds
wall clock time: 41 minutes 17.98 seconds (2477.98 seconds total)