Starting phenix.real_space_refine
on Wed Sep 17 16:26:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ge7_51292/09_2025/9ge7_51292.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ge7_51292/09_2025/9ge7_51292.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ge7_51292/09_2025/9ge7_51292.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ge7_51292/09_2025/9ge7_51292.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ge7_51292/09_2025/9ge7_51292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ge7_51292/09_2025/9ge7_51292.map"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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
     P       6      5.49       5
     Mg      2      5.21       5
     S      42      5.16       5
     C    6219      2.51       5
     N    1725      2.21       5
     O    1779      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9773
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 804, 6295
          Classifications: {'peptide': 804}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 40, 'TRANS': 760}
    Chain: "B"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1707
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 219}
    Chain: "C"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1707
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 219}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.41, per 1000 atoms: 0.25
  Number of scatterers: 9773
  At special positions: 0
  Unit cell: (139.445, 88.51, 106.88, 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)
     S      42     16.00
     P       6     15.00
     Mg      2     11.99
     O    1779      8.00
     N    1725      7.00
     C    6219      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: 0.95
  Conformation dependent library (CDL) restraints added in 376.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2300

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      55.9% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 11
    Processing helix  chain 'A' and resid 12 through 49
      removed outlier: 3.677A  pdb=" N   GLU A  49 " --> pdb=" O   GLN A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 74
      removed outlier: 4.208A  pdb=" N   LEU A  68 " --> pdb=" O   PRO A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 137
      removed outlier: 3.520A  pdb=" N   MET A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 185
      removed outlier: 4.965A  pdb=" N   ASP A 182 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS A 183 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 214
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 233 through 280
      removed outlier: 3.863A  pdb=" N   MET A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   TYR A 271 " --> pdb=" O   CYS A 267 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   ASP A 272 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   LEU A 273 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 321
    Processing helix  chain 'A' and resid 334 through 361
      removed outlier: 3.735A  pdb=" N   LEU A 338 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   THR A 343 " --> pdb=" O   TRP A 339 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   ARG A 354 " --> pdb=" O   LEU A 350 " (cutoff:3.500A)
      Proline residue:  A 355  - end of helix
    Processing helix  chain 'A' and resid 363 through 369
    Processing helix  chain 'A' and resid 378 through 399
      Proline residue:  A 384  - end of helix
    Processing helix  chain 'A' and resid 401 through 430
      removed outlier: 3.575A  pdb=" N   TRP A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
      removed outlier: 4.050A  pdb=" N   GLN A 449 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 485
    Processing helix  chain 'A' and resid 498 through 500
      No H-bonds generated for 'chain 'A' and resid 498 through 500'
    Processing helix  chain 'A' and resid 501 through 512
      removed outlier: 3.521A  pdb=" N   LEU A 505 " --> pdb=" O   GLN A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 584
    Processing helix  chain 'A' and resid 645 through 655
    Processing helix  chain 'A' and resid 663 through 707
      removed outlier: 3.540A  pdb=" N   GLN A 672 " --> pdb=" O   LYS A 668 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL A 673 " --> pdb=" O   GLN A 669 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ARG A 707 " --> pdb=" O   GLY A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 718
    Processing helix  chain 'A' and resid 720 through 758
      removed outlier: 3.652A  pdb=" N   ILE A 745 " --> pdb=" O   LEU A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 794
      removed outlier: 3.515A  pdb=" N   TRP A 770 " --> pdb=" O   ASP A 766 " (cutoff:3.500A)
      Proline residue:  A 774  - end of helix
      removed outlier: 3.509A  pdb=" N   LYS A 794 " --> pdb=" O   ALA A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 804
      removed outlier: 3.922A  pdb=" N   ALA A 803 " --> pdb=" O   ARG A 800 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 22
    Processing helix  chain 'B' and resid 48 through 57
    Processing helix  chain 'B' and resid 73 through 77
    Processing helix  chain 'B' and resid 78 through 89
    Processing helix  chain 'B' and resid 104 through 116
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'B' and resid 119 through 134
    Processing helix  chain 'B' and resid 143 through 147
    Processing helix  chain 'B' and resid 148 through 163
      removed outlier: 4.410A  pdb=" N   GLY B 163 " --> pdb=" O   ARG B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 197
    Processing helix  chain 'B' and resid 206 through 213
    Processing helix  chain 'C' and resid 18 through 22
    Processing helix  chain 'C' and resid 48 through 57
    Processing helix  chain 'C' and resid 73 through 77
      removed outlier: 4.260A  pdb=" N   MET C  77 " --> pdb=" O   LEU C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 89
    Processing helix  chain 'C' and resid 104 through 117
      Proline residue:  C 112  - end of helix
    Processing helix  chain 'C' and resid 119 through 135
    Processing helix  chain 'C' and resid 148 through 164
      removed outlier: 3.637A  pdb=" N   ARG C 164 " --> pdb=" O   ALA C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 197
    Processing helix  chain 'C' and resid 206 through 213
      removed outlier: 3.519A  pdb=" N   ALA C 210 " --> pdb=" O   ASP C 206 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81
    Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89
      removed outlier: 8.702A  pdb=" N   LEU A 174 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ASN A  98 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   MET A 176 " --> pdb=" O   ASN A  98 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   LYS A 100 " --> pdb=" O   MET A 176 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   ASN A 177 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 8.431A  pdb=" N   SER A 125 " --> pdb=" O   ASN A 177 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   LEU A 128 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   GLU A 156 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 497
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 492 through 497
    current: chain 'A' and resid 533 through 534
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 533 through 534
    current: chain 'A' and resid 600 through 608
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 16
      removed outlier: 6.360A  pdb=" N   LEU B  12 " --> pdb=" O   THR B  27 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   THR B  27 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LYS B  14 " --> pdb=" O   ILE B  25 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 91
      removed outlier: 6.467A  pdb=" N   GLY B  91 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   ASP B 171 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE B  39 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   CYS B 216 " --> pdb=" O   GLU B 227 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 23 through 33
      removed outlier: 6.308A  pdb=" N   LYS C  14 " --> pdb=" O   ILE C  25 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   THR C  27 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU C  12 " --> pdb=" O   THR C  27 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   VAL C  29 " --> pdb=" O   HIS C  10 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   HIS C  10 " --> pdb=" O   VAL C  29 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   LEU C  31 " --> pdb=" O   GLU C   8 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLU C   8 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   VAL C   9 " --> pdb=" O   SER C  68 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   SER C  68 " --> pdb=" O   VAL C   9 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   HIS C  11 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLU C  66 " --> pdb=" O   HIS C  11 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 90 through 93
      removed outlier: 6.392A  pdb=" N   GLY C  91 " --> pdb=" O   PHE C 169 " (cutoff:3.500A)
      removed outlier: 8.194A  pdb=" N   ASP C 171 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   VAL C  93 " --> pdb=" O   ASP C 171 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   LEU C 168 " --> pdb=" O   ILE C 201 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   VAL C 203 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ALA C 170 " --> pdb=" O   VAL C 203 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   CYS C 216 " --> pdb=" O   GLU C 227 " (cutoff:3.500A)

    565 hydrogen bonds defined for protein.
    1614 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.56

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3270
        1.34 -     1.46: 2054
        1.46 -     1.58: 4548
        1.58 -     1.70: 8
        1.70 -     1.82: 76
  Bond restraints: 9956
  Sorted by residual:
  bond pdb=" CB  MET A  51 "
       pdb=" CG  MET A  51 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.32e+00
  bond pdb=" CB  TRP A 481 "
       pdb=" CG  TRP A 481 "
    ideal  model  delta    sigma   weight residual
    1.498  1.467  0.031 3.10e-02 1.04e+03 1.02e+00
  bond pdb=" CA  VAL A 259 "
       pdb=" C   VAL A 259 "
    ideal  model  delta    sigma   weight residual
    1.524  1.511  0.012 1.22e-02 6.72e+03 9.97e-01
  bond pdb=" CA  PRO B  73 "
       pdb=" C   PRO B  73 "
    ideal  model  delta    sigma   weight residual
    1.527  1.517  0.010 1.07e-02 8.73e+03 9.49e-01
  bond pdb=" CB  TRP A 337 "
       pdb=" CG  TRP A 337 "
    ideal  model  delta    sigma   weight residual
    1.498  1.469  0.029 3.10e-02 1.04e+03 8.88e-01
  ... (remaining 9951 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 13268
        2.04 -     4.07: 215
        4.07 -     6.11: 35
        6.11 -     8.15: 5
        8.15 -    10.19: 3
  Bond angle restraints: 13526
  Sorted by residual:
  angle pdb=" CB  LYS A 100 "
        pdb=" CG  LYS A 100 "
        pdb=" CD  LYS A 100 "
      ideal   model   delta    sigma   weight residual
     111.30  118.71   -7.41 2.30e+00 1.89e-01 1.04e+01
  angle pdb=" CA  LEU A 426 "
        pdb=" CB  LEU A 426 "
        pdb=" CG  LEU A 426 "
      ideal   model   delta    sigma   weight residual
     116.30  126.49  -10.19 3.50e+00 8.16e-02 8.47e+00
  angle pdb=" CA  GLU A  40 "
        pdb=" CB  GLU A  40 "
        pdb=" CG  GLU A  40 "
      ideal   model   delta    sigma   weight residual
     114.10  119.89   -5.79 2.00e+00 2.50e-01 8.38e+00
  angle pdb=" CB  MET A 432 "
        pdb=" CG  MET A 432 "
        pdb=" SD  MET A 432 "
      ideal   model   delta    sigma   weight residual
     112.70  121.22   -8.52 3.00e+00 1.11e-01 8.07e+00
  angle pdb=" CA  LYS C 184 "
        pdb=" CB  LYS C 184 "
        pdb=" CG  LYS C 184 "
      ideal   model   delta    sigma   weight residual
     114.10  119.78   -5.68 2.00e+00 2.50e-01 8.07e+00
  ... (remaining 13521 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 5234
       16.91 -    33.82: 603
       33.82 -    50.73: 138
       50.73 -    67.64: 39
       67.64 -    84.54: 4
  Dihedral angle restraints: 6018
    sinusoidal: 2453
      harmonic: 3565
  Sorted by residual:
  dihedral pdb=" CA  HIS C  89 "
           pdb=" C   HIS C  89 "
           pdb=" N   VAL C  90 "
           pdb=" CA  VAL C  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.78  -17.22     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  LYS B  88 "
           pdb=" C   LYS B  88 "
           pdb=" N   HIS B  89 "
           pdb=" CA  HIS B  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.36  -16.64     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  ASP C 183 "
           pdb=" CB  ASP C 183 "
           pdb=" CG  ASP C 183 "
           pdb=" OD1 ASP C 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.50   54.50     1      2.00e+01 2.50e-03 1.01e+01
  ... (remaining 6015 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1036
       0.031 -    0.061: 367
       0.061 -    0.092: 97
       0.092 -    0.122: 60
       0.122 -    0.153: 5
  Chirality restraints: 1565
  Sorted by residual:
  chirality pdb=" CA  ILE C 201 "
            pdb=" N   ILE C 201 "
            pdb=" C   ILE C 201 "
            pdb=" CB  ILE C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.82e-01
  chirality pdb=" CA  TRP A 335 "
            pdb=" N   TRP A 335 "
            pdb=" C   TRP A 335 "
            pdb=" CB  TRP A 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  PRO A 450 "
            pdb=" N   PRO A 450 "
            pdb=" C   PRO A 450 "
            pdb=" CB  PRO A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 1562 not shown)

  Planarity restraints: 1728
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 261 "   -0.011 2.00e-02 2.50e+03   2.19e-02 4.80e+00
        pdb=" C   VAL A 261 "    0.038 2.00e-02 2.50e+03
        pdb=" O   VAL A 261 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA A 262 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 259 "    0.011 2.00e-02 2.50e+03   2.10e-02 4.39e+00
        pdb=" C   VAL A 259 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL A 259 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA A 260 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 257 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.03e+00
        pdb=" C   ALA A 257 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ALA A 257 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A 258 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1725 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.43: 78
        2.43 -     3.05: 6779
        3.05 -     3.67: 15532
        3.67 -     4.28: 21398
        4.28 -     4.90: 35763
  Nonbonded interactions: 79550
  Sorted by model distance:
  nonbonded pdb=" O1G ANP B 301 "
            pdb="MG    MG B 302 "
     model   vdw
     1.817 2.170
  nonbonded pdb=" O2B ANP B 301 "
            pdb="MG    MG B 302 "
     model   vdw
     1.831 2.170
  nonbonded pdb=" O1G ANP C 301 "
            pdb="MG    MG C 302 "
     model   vdw
     1.876 2.170
  nonbonded pdb=" OG  SER C  50 "
            pdb="MG    MG C 302 "
     model   vdw
     1.913 2.170
  nonbonded pdb=" OG  SER B  50 "
            pdb="MG    MG B 302 "
     model   vdw
     1.920 2.170
  ... (remaining 79545 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

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:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.380
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8857
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      :  0.005   0.035   9956  Z= 0.230
  Angle     :  0.642  10.187  13526  Z= 0.311
  Chirality :  0.038   0.153   1565
  Planarity :  0.004   0.032   1728
  Dihedral  : 15.241  84.544   3718
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.51 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.25), residues: 1250
  helix:  2.54 (0.21), residues: 638
  sheet:  0.04 (0.43), residues: 165
  loop : -0.62 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 445 
 TYR   0.007   0.001   TYR A 197 
 PHE   0.015   0.001   PHE A  50 
 TRP   0.011   0.001   TRP A 566 
 HIS   0.008   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 9956)
  covalent geometry    : angle       0.64239 (13526)
  hydrogen bonds       : bond        0.12094 (  565)
  hydrogen bonds       : angle       5.67272 ( 1614)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 62
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.9756 (mt) cc_final: 0.9433 (mt)
REVERT: A   87 MET cc_start: 0.9303 (tpp) cc_final: 0.9004 (tpp)
REVERT: A  175 MET cc_start: 0.9422 (mmt) cc_final: 0.9090 (mmm)
REVERT: A  176 MET cc_start: 0.8857 (ppp) cc_final: 0.8226 (ppp)
REVERT: A  312 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8984 (tt)
REVERT: A  348 SER cc_start: 0.9525 (t) cc_final: 0.9009 (p)
REVERT: A  398 MET cc_start: 0.8866 (tpp) cc_final: 0.8620 (tpp)
REVERT: A  402 MET cc_start: 0.8604 (mmt) cc_final: 0.8273 (mmm)
REVERT: A  424 MET cc_start: 0.8823 (tpp) cc_final: 0.8161 (tpp)
REVERT: A  575 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8873 (tmm)
REVERT: A  594 MET cc_start: 0.8516 (tpt) cc_final: 0.8268 (ppp)
REVERT: A  691 CYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8541 (t)
REVERT: A  771 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9123 (tp)
REVERT: B  118 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7830 (mp0)
REVERT: B  130 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9461 (tt)
REVERT: C  103 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9098 (pp)
  outliers start: 32
  outliers final: 22
  residues processed: 90
  average time/residue: 0.0849
  time to fit residues: 11.6686
Evaluate side-chains
  91 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 62
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  557 ASP
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  616 ARG
Chi-restraints excluded: chain A residue  629 ASP
Chi-restraints excluded: chain A residue  636 LEU
Chi-restraints excluded: chain A residue  691 CYS
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  118 GLU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  141 ASP
Chi-restraints excluded: chain C residue  204 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    0.4980
   chunk 53 optimal weight:   30.0000
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 123 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:   10.0000
   overall best weight:    5.2988

-------------------------------------------------------------------------------
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 = 0.3193 r_free = 0.3193 target = 0.054476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.037736 restraints weight = 46482.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.039147 restraints weight = 22391.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.040073 restraints weight = 14077.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.040677 restraints weight = 10316.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.041108 restraints weight = 8402.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.0637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   9956  Z= 0.265
  Angle     :  0.639   6.599  13526  Z= 0.314
  Chirality :  0.040   0.165   1565
  Planarity :  0.004   0.043   1728
  Dihedral  :  8.588  81.468   1467
  Min Nonbonded Distance : 1.824

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 20.64 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.25), residues: 1250
  helix:  2.84 (0.20), residues: 640
  sheet: -0.00 (0.43), residues: 167
  loop : -0.63 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 480 
 TYR   0.008   0.001   TYR A 209 
 PHE   0.012   0.001   PHE A  50 
 TRP   0.012   0.001   TRP A 451 
 HIS   0.006   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 ( 9956)
  covalent geometry    : angle       0.63874 (13526)
  hydrogen bonds       : bond        0.04976 (  565)
  hydrogen bonds       : angle       4.52237 ( 1614)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 62
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.9750 (mt) cc_final: 0.9404 (mt)
REVERT: A   87 MET cc_start: 0.9329 (tpp) cc_final: 0.9033 (tpp)
REVERT: A  175 MET cc_start: 0.9382 (mmt) cc_final: 0.8992 (mmm)
REVERT: A  312 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8985 (tt)
REVERT: A  398 MET cc_start: 0.8910 (tpp) cc_final: 0.8644 (tpp)
REVERT: A  402 MET cc_start: 0.8615 (mmt) cc_final: 0.8302 (mmm)
REVERT: A  424 MET cc_start: 0.8731 (tpp) cc_final: 0.8074 (tpp)
REVERT: A  575 MET cc_start: 0.9091 (tmm) cc_final: 0.8767 (tmm)
REVERT: A  594 MET cc_start: 0.8476 (tpt) cc_final: 0.8151 (ppp)
REVERT: A  691 CYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8436 (t)
REVERT: A  739 SER cc_start: 0.9399 (OUTLIER) cc_final: 0.9041 (p)
REVERT: C  103 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9100 (pp)
  outliers start: 41
  outliers final: 26
  residues processed: 100
  average time/residue: 0.0817
  time to fit residues: 12.4896
Evaluate side-chains
  89 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  616 ARG
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  691 CYS
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  749 THR
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  204 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 60 optimal weight:   40.0000
   chunk 95 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9980
   chunk 122 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 119 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 108 ASN
B 176 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.055640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.038482 restraints weight = 45578.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.039979 restraints weight = 21772.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.040963 restraints weight = 13521.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.041636 restraints weight = 9856.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.042036 restraints weight = 7955.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.0894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9956  Z= 0.134
  Angle     :  0.521   6.171  13526  Z= 0.263
  Chirality :  0.038   0.145   1565
  Planarity :  0.003   0.044   1728
  Dihedral  :  7.575  79.894   1440
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.12 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.25), residues: 1250
  helix:  3.16 (0.20), residues: 641
  sheet:  0.10 (0.43), residues: 166
  loop : -0.54 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 192 
 TYR   0.006   0.001   TYR A 266 
 PHE   0.014   0.001   PHE A  50 
 TRP   0.011   0.001   TRP A 335 
 HIS   0.007   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9956)
  covalent geometry    : angle       0.52090 (13526)
  hydrogen bonds       : bond        0.04484 (  565)
  hydrogen bonds       : angle       4.08775 ( 1614)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 67
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.9739 (mt) cc_final: 0.9386 (mt)
REVERT: A   87 MET cc_start: 0.9349 (tpp) cc_final: 0.9047 (tpp)
REVERT: A  175 MET cc_start: 0.9369 (mmt) cc_final: 0.9065 (mmm)
REVERT: A  312 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8995 (tt)
REVERT: A  350 LEU cc_start: 0.9759 (OUTLIER) cc_final: 0.9545 (mm)
REVERT: A  398 MET cc_start: 0.8834 (tpp) cc_final: 0.8558 (tpp)
REVERT: A  402 MET cc_start: 0.8560 (mmt) cc_final: 0.8250 (mmm)
REVERT: A  424 MET cc_start: 0.8709 (tpp) cc_final: 0.8042 (tpp)
REVERT: A  575 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8805 (tmm)
REVERT: A  691 CYS cc_start: 0.8993 (m) cc_final: 0.8721 (t)
REVERT: A  739 SER cc_start: 0.9388 (OUTLIER) cc_final: 0.9038 (p)
  outliers start: 37
  outliers final: 21
  residues processed: 101
  average time/residue: 0.0786
  time to fit residues: 12.1073
Evaluate side-chains
  85 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 60
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  616 ARG
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  204 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:   30.0000
   chunk 19 optimal weight:   20.0000
   chunk 11 optimal weight:    9.9990
   chunk 94 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.3215 r_free = 0.3215 target = 0.055573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.039388 restraints weight = 46444.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.040818 restraints weight = 21411.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.041782 restraints weight = 13030.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.042396 restraints weight = 9375.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.042748 restraints weight = 7535.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8826
moved from start:          0.0923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9956  Z= 0.181
  Angle     :  0.553   6.778  13526  Z= 0.275
  Chirality :  0.038   0.163   1565
  Planarity :  0.003   0.045   1728
  Dihedral  :  7.336  80.545   1435
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 21.22 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.25), residues: 1250
  helix:  3.13 (0.20), residues: 643
  sheet: -0.00 (0.43), residues: 165
  loop : -0.53 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 192 
 TYR   0.006   0.001   TYR A 197 
 PHE   0.013   0.001   PHE A  50 
 TRP   0.013   0.001   TRP A 641 
 HIS   0.007   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9956)
  covalent geometry    : angle       0.55325 (13526)
  hydrogen bonds       : bond        0.04510 (  565)
  hydrogen bonds       : angle       4.09326 ( 1614)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 61
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.9740 (mt) cc_final: 0.9375 (mt)
REVERT: A   87 MET cc_start: 0.9322 (tpp) cc_final: 0.9024 (tpp)
REVERT: A  170 MET cc_start: 0.8323 (tpp) cc_final: 0.7987 (tpp)
REVERT: A  175 MET cc_start: 0.9359 (mmt) cc_final: 0.9044 (mmm)
REVERT: A  312 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8986 (tt)
REVERT: A  398 MET cc_start: 0.8854 (tpp) cc_final: 0.8581 (tpp)
REVERT: A  402 MET cc_start: 0.8565 (mmt) cc_final: 0.8258 (mmm)
REVERT: A  424 MET cc_start: 0.8713 (tpp) cc_final: 0.8050 (tpp)
REVERT: A  575 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8714 (tmm)
REVERT: A  739 SER cc_start: 0.9397 (OUTLIER) cc_final: 0.9036 (p)
REVERT: C  201 ILE cc_start: 0.9466 (mm) cc_final: 0.9065 (mm)
  outliers start: 43
  outliers final: 25
  residues processed: 99
  average time/residue: 0.0769
  time to fit residues: 12.0018
Evaluate side-chains
  87 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 59
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  204 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 109 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 113 optimal weight:    0.8980
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 512 HIS
B 176 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.055557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.038701 restraints weight = 45645.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.040156 restraints weight = 22108.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.041144 restraints weight = 13823.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.041757 restraints weight = 10065.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.042195 restraints weight = 8168.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.1015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9956  Z= 0.155
  Angle     :  0.537   7.335  13526  Z= 0.270
  Chirality :  0.039   0.330   1565
  Planarity :  0.003   0.056   1728
  Dihedral  :  6.945  80.430   1429
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.12 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.25), residues: 1250
  helix:  3.14 (0.20), residues: 643
  sheet:  0.00 (0.43), residues: 164
  loop : -0.51 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 192 
 TYR   0.006   0.001   TYR A 197 
 PHE   0.013   0.001   PHE A  50 
 TRP   0.013   0.001   TRP A 641 
 HIS   0.007   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9956)
  covalent geometry    : angle       0.53703 (13526)
  hydrogen bonds       : bond        0.04447 (  565)
  hydrogen bonds       : angle       4.04071 ( 1614)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 61
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.9746 (mt) cc_final: 0.9382 (mt)
REVERT: A   87 MET cc_start: 0.9342 (tpp) cc_final: 0.9043 (tpp)
REVERT: A  170 MET cc_start: 0.8317 (tpp) cc_final: 0.7981 (tpp)
REVERT: A  175 MET cc_start: 0.9357 (mmt) cc_final: 0.9033 (mmm)
REVERT: A  312 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8981 (tt)
REVERT: A  398 MET cc_start: 0.8848 (tpp) cc_final: 0.8560 (tpp)
REVERT: A  402 MET cc_start: 0.8556 (mmt) cc_final: 0.8252 (mmm)
REVERT: A  424 MET cc_start: 0.8704 (tpp) cc_final: 0.8034 (tpp)
REVERT: A  511 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7852 (tm-30)
REVERT: A  575 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8750 (tmm)
REVERT: A  594 MET cc_start: 0.7981 (tpt) cc_final: 0.7657 (ppp)
REVERT: A  739 SER cc_start: 0.9402 (OUTLIER) cc_final: 0.9042 (p)
REVERT: C  202 MET cc_start: 0.8309 (mpp) cc_final: 0.8098 (mpp)
  outliers start: 40
  outliers final: 29
  residues processed: 98
  average time/residue: 0.0765
  time to fit residues: 11.5802
Evaluate side-chains
  93 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 60
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  511 GLU
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  204 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 109 optimal weight:    8.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 105 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 93 optimal weight:    9.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.3241 r_free = 0.3241 target = 0.056650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.039900 restraints weight = 45702.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.041398 restraints weight = 21584.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.042429 restraints weight = 13322.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.043063 restraints weight = 9602.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.043546 restraints weight = 7739.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9956  Z= 0.119
  Angle     :  0.515   7.654  13526  Z= 0.259
  Chirality :  0.037   0.194   1565
  Planarity :  0.003   0.046   1728
  Dihedral  :  6.799  78.572   1429
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.41 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.25), residues: 1250
  helix:  3.18 (0.20), residues: 643
  sheet: -0.03 (0.43), residues: 165
  loop : -0.47 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 192 
 TYR   0.005   0.001   TYR A 266 
 PHE   0.014   0.001   PHE A  50 
 TRP   0.011   0.001   TRP A 335 
 HIS   0.007   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9956)
  covalent geometry    : angle       0.51514 (13526)
  hydrogen bonds       : bond        0.04212 (  565)
  hydrogen bonds       : angle       3.89225 ( 1614)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 66
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.9742 (mt) cc_final: 0.9386 (mt)
REVERT: A  170 MET cc_start: 0.8338 (tpp) cc_final: 0.8004 (tpp)
REVERT: A  175 MET cc_start: 0.9348 (mmt) cc_final: 0.9037 (mmm)
REVERT: A  312 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8978 (tt)
REVERT: A  350 LEU cc_start: 0.9748 (OUTLIER) cc_final: 0.9534 (mm)
REVERT: A  398 MET cc_start: 0.8828 (tpp) cc_final: 0.8550 (tpp)
REVERT: A  402 MET cc_start: 0.8531 (mmt) cc_final: 0.8228 (mmm)
REVERT: A  424 MET cc_start: 0.8717 (tpp) cc_final: 0.8077 (tpp)
REVERT: A  432 MET cc_start: 0.8113 (tpp) cc_final: 0.7833 (tpp)
REVERT: A  575 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8765 (tmm)
REVERT: A  594 MET cc_start: 0.7952 (tpt) cc_final: 0.7607 (ppp)
REVERT: A  616 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8449 (mtp180)
REVERT: A  691 CYS cc_start: 0.8637 (t) cc_final: 0.8368 (t)
REVERT: A  739 SER cc_start: 0.9392 (OUTLIER) cc_final: 0.9044 (p)
REVERT: B  202 MET cc_start: 0.8640 (mpp) cc_final: 0.8298 (mpp)
REVERT: C   90 VAL cc_start: 0.9591 (t) cc_final: 0.9327 (p)
REVERT: C  202 MET cc_start: 0.8417 (mpp) cc_final: 0.8164 (mpp)
  outliers start: 36
  outliers final: 24
  residues processed: 99
  average time/residue: 0.0819
  time to fit residues: 12.4103
Evaluate side-chains
  93 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 64
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  616 ARG
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  204 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   chunk 123 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
B 176 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.056148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.039238 restraints weight = 45296.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.040709 restraints weight = 21969.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.041717 restraints weight = 13746.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.042342 restraints weight = 10012.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.042792 restraints weight = 8126.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9956  Z= 0.132
  Angle     :  0.518   6.599  13526  Z= 0.259
  Chirality :  0.037   0.170   1565
  Planarity :  0.003   0.060   1728
  Dihedral  :  6.732  77.546   1429
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.71 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.25), residues: 1250
  helix:  3.21 (0.20), residues: 642
  sheet: -0.01 (0.43), residues: 165
  loop : -0.44 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 192 
 TYR   0.005   0.001   TYR A 197 
 PHE   0.013   0.001   PHE A  50 
 TRP   0.010   0.001   TRP A 641 
 HIS   0.006   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9956)
  covalent geometry    : angle       0.51765 (13526)
  hydrogen bonds       : bond        0.04167 (  565)
  hydrogen bonds       : angle       3.89807 ( 1614)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 64
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.9746 (mt) cc_final: 0.9377 (mt)
REVERT: A   87 MET cc_start: 0.9226 (tpp) cc_final: 0.9010 (tpp)
REVERT: A  170 MET cc_start: 0.8343 (tpp) cc_final: 0.8006 (tpp)
REVERT: A  175 MET cc_start: 0.9350 (mmt) cc_final: 0.9039 (mmm)
REVERT: A  312 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8978 (tt)
REVERT: A  398 MET cc_start: 0.8847 (tpp) cc_final: 0.8553 (tpp)
REVERT: A  402 MET cc_start: 0.8539 (mmt) cc_final: 0.8234 (mmm)
REVERT: A  424 MET cc_start: 0.8722 (tpp) cc_final: 0.8078 (tpp)
REVERT: A  575 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8760 (tmm)
REVERT: A  594 MET cc_start: 0.7951 (tpt) cc_final: 0.7564 (ppp)
REVERT: A  616 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8514 (mtp180)
REVERT: A  691 CYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8416 (t)
REVERT: A  739 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.9048 (p)
REVERT: B   63 SER cc_start: 0.9628 (OUTLIER) cc_final: 0.9396 (p)
REVERT: B  202 MET cc_start: 0.8650 (mpp) cc_final: 0.8334 (mpp)
REVERT: C   90 VAL cc_start: 0.9591 (t) cc_final: 0.9320 (p)
  outliers start: 39
  outliers final: 24
  residues processed: 99
  average time/residue: 0.0771
  time to fit residues: 11.9482
Evaluate side-chains
  94 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 64
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  616 ARG
Chi-restraints excluded: chain A residue  691 CYS
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  204 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 54 optimal weight:   20.0000
   chunk 45 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 6 optimal weight:    0.5980
   chunk 18 optimal weight:   20.0000
   chunk 121 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 9 optimal weight:   20.0000
   overall best weight:    3.0984

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

Flipped N/Q/H residues before XYZ refinement:
B 176 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.055764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.038883 restraints weight = 46126.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.040334 restraints weight = 22423.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.041323 restraints weight = 14057.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.041971 restraints weight = 10194.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.042455 restraints weight = 8257.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8818
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9956  Z= 0.167
  Angle     :  0.563   9.153  13526  Z= 0.279
  Chirality :  0.039   0.404   1565
  Planarity :  0.004   0.062   1728
  Dihedral  :  6.769  77.495   1429
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.61 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.25), residues: 1250
  helix:  3.17 (0.20), residues: 642
  sheet: -0.01 (0.43), residues: 165
  loop : -0.44 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 192 
 TYR   0.007   0.001   TYR A 520 
 PHE   0.012   0.001   PHE A  50 
 TRP   0.012   0.001   TRP A 195 
 HIS   0.007   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9956)
  covalent geometry    : angle       0.56271 (13526)
  hydrogen bonds       : bond        0.04239 (  565)
  hydrogen bonds       : angle       3.98909 ( 1614)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 65
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.9752 (mt) cc_final: 0.9379 (mt)
REVERT: A   87 MET cc_start: 0.9225 (tpp) cc_final: 0.8984 (tpp)
REVERT: A  170 MET cc_start: 0.8356 (tpp) cc_final: 0.8021 (tpp)
REVERT: A  175 MET cc_start: 0.9353 (mmt) cc_final: 0.9052 (mmm)
REVERT: A  398 MET cc_start: 0.8868 (tpp) cc_final: 0.8581 (tpp)
REVERT: A  402 MET cc_start: 0.8558 (mmt) cc_final: 0.8256 (mmm)
REVERT: A  424 MET cc_start: 0.8734 (tpp) cc_final: 0.8093 (tpp)
REVERT: A  432 MET cc_start: 0.8149 (tpp) cc_final: 0.7918 (tpp)
REVERT: A  575 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8764 (tmm)
REVERT: A  594 MET cc_start: 0.7927 (tpt) cc_final: 0.7516 (ppp)
REVERT: A  691 CYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8467 (t)
REVERT: A  739 SER cc_start: 0.9406 (OUTLIER) cc_final: 0.9049 (p)
REVERT: B   63 SER cc_start: 0.9632 (OUTLIER) cc_final: 0.9404 (p)
REVERT: B  202 MET cc_start: 0.8647 (mpp) cc_final: 0.8290 (mpp)
REVERT: C   90 VAL cc_start: 0.9616 (t) cc_final: 0.9351 (p)
REVERT: C  200 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9261 (mp)
  outliers start: 37
  outliers final: 27
  residues processed: 99
  average time/residue: 0.0811
  time to fit residues: 12.3562
Evaluate side-chains
  95 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 63
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  616 ARG
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  691 CYS
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  204 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    0.3980
   chunk 43 optimal weight:    0.0470
   chunk 46 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.7880

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

Flipped N/Q/H residues before XYZ refinement:
B 176 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.057660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.040936 restraints weight = 45060.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.042462 restraints weight = 21299.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.043501 restraints weight = 13083.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.044146 restraints weight = 9376.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.044582 restraints weight = 7524.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8770
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9956  Z= 0.102
  Angle     :  0.521   7.833  13526  Z= 0.260
  Chirality :  0.037   0.168   1565
  Planarity :  0.003   0.062   1728
  Dihedral  :  6.486  74.581   1427
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.38 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.36 (0.25), residues: 1250
  helix:  3.21 (0.20), residues: 643
  sheet:  0.10 (0.46), residues: 143
  loop : -0.37 (0.32), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 707 
 TYR   0.005   0.001   TYR A 520 
 PHE   0.014   0.001   PHE A  50 
 TRP   0.019   0.001   TRP A 195 
 HIS   0.006   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 9956)
  covalent geometry    : angle       0.52091 (13526)
  hydrogen bonds       : bond        0.03906 (  565)
  hydrogen bonds       : angle       3.82841 ( 1614)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8932 (mm-30)
REVERT: A   57 LEU cc_start: 0.9744 (mt) cc_final: 0.9386 (mt)
REVERT: A   87 MET cc_start: 0.9212 (tpp) cc_final: 0.8963 (tpp)
REVERT: A  170 MET cc_start: 0.8341 (tpp) cc_final: 0.8012 (tpp)
REVERT: A  175 MET cc_start: 0.9340 (mmt) cc_final: 0.9005 (mmm)
REVERT: A  344 MET cc_start: 0.8793 (tmm) cc_final: 0.8494 (tmm)
REVERT: A  348 SER cc_start: 0.9435 (t) cc_final: 0.9009 (p)
REVERT: A  398 MET cc_start: 0.8815 (tpp) cc_final: 0.8549 (tpp)
REVERT: A  402 MET cc_start: 0.8499 (mmt) cc_final: 0.8192 (mmm)
REVERT: A  424 MET cc_start: 0.8720 (tpp) cc_final: 0.8058 (tpp)
REVERT: A  432 MET cc_start: 0.8127 (tpp) cc_final: 0.7901 (tpp)
REVERT: A  575 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8786 (tmm)
REVERT: A  594 MET cc_start: 0.7902 (tpt) cc_final: 0.7492 (ppp)
REVERT: A  616 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8370 (mtp180)
REVERT: A  691 CYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8332 (t)
REVERT: A  739 SER cc_start: 0.9397 (OUTLIER) cc_final: 0.9056 (p)
REVERT: B   63 SER cc_start: 0.9624 (OUTLIER) cc_final: 0.9416 (p)
REVERT: B  202 MET cc_start: 0.8640 (mpp) cc_final: 0.8360 (mpp)
REVERT: C   90 VAL cc_start: 0.9553 (t) cc_final: 0.9263 (p)
  outliers start: 29
  outliers final: 19
  residues processed: 99
  average time/residue: 0.0766
  time to fit residues: 11.6824
Evaluate side-chains
  93 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  616 ARG
Chi-restraints excluded: chain A residue  691 CYS
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  204 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0030
   chunk 38 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    2.5996

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

Flipped N/Q/H residues before XYZ refinement:
B 176 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.056414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.039341 restraints weight = 45413.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.040840 restraints weight = 21898.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.041839 restraints weight = 13667.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.042543 restraints weight = 9898.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.043000 restraints weight = 7969.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9956  Z= 0.147
  Angle     :  0.563   8.851  13526  Z= 0.274
  Chirality :  0.038   0.176   1565
  Planarity :  0.004   0.065   1728
  Dihedral  :  6.377  74.691   1424
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 22.58 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.25), residues: 1250
  helix:  3.18 (0.20), residues: 643
  sheet:  0.18 (0.44), residues: 163
  loop : -0.44 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  82 
 TYR   0.006   0.001   TYR A 197 
 PHE   0.013   0.001   PHE A  50 
 TRP   0.016   0.001   TRP A 195 
 HIS   0.007   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9956)
  covalent geometry    : angle       0.56253 (13526)
  hydrogen bonds       : bond        0.04050 (  565)
  hydrogen bonds       : angle       3.92236 ( 1614)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 65
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8950 (mm-30)
REVERT: A   57 LEU cc_start: 0.9753 (mt) cc_final: 0.9381 (mt)
REVERT: A  170 MET cc_start: 0.8367 (tpp) cc_final: 0.8043 (tpp)
REVERT: A  175 MET cc_start: 0.9356 (mmt) cc_final: 0.9024 (mmm)
REVERT: A  398 MET cc_start: 0.8855 (tpp) cc_final: 0.8570 (tpp)
REVERT: A  402 MET cc_start: 0.8537 (mmt) cc_final: 0.8236 (mmm)
REVERT: A  424 MET cc_start: 0.8721 (tpp) cc_final: 0.8057 (tpp)
REVERT: A  432 MET cc_start: 0.8141 (tpp) cc_final: 0.7902 (tpp)
REVERT: A  575 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8766 (tmm)
REVERT: A  594 MET cc_start: 0.7907 (tpt) cc_final: 0.7483 (ppp)
REVERT: A  691 CYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8424 (t)
REVERT: A  739 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.9048 (p)
REVERT: B   63 SER cc_start: 0.9625 (OUTLIER) cc_final: 0.9402 (p)
REVERT: B  202 MET cc_start: 0.8652 (mpp) cc_final: 0.8338 (mpp)
REVERT: C   90 VAL cc_start: 0.9588 (t) cc_final: 0.9312 (p)
  outliers start: 28
  outliers final: 24
  residues processed: 90
  average time/residue: 0.0769
  time to fit residues: 10.7848
Evaluate side-chains
  92 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 64
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  616 ARG
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  691 CYS
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  193 ASN
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  204 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 52 optimal weight:   20.0000
   chunk 117 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 64 optimal weight:    9.9990
   chunk 105 optimal weight:    0.0970
   chunk 94 optimal weight:    0.6980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B 176 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.057083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.040055 restraints weight = 45298.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.041575 restraints weight = 21708.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.042594 restraints weight = 13485.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.043201 restraints weight = 9775.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.043699 restraints weight = 7950.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9956  Z= 0.117
  Angle     :  0.568  10.692  13526  Z= 0.276
  Chirality :  0.038   0.170   1565
  Planarity :  0.003   0.064   1728
  Dihedral  :  6.321  73.433   1424
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.48 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.25), residues: 1250
  helix:  3.12 (0.20), residues: 642
  sheet:  0.18 (0.46), residues: 143
  loop : -0.37 (0.32), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 707 
 TYR   0.005   0.001   TYR A 197 
 PHE   0.013   0.001   PHE A  50 
 TRP   0.014   0.001   TRP A 195 
 HIS   0.006   0.001   HIS A 558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9956)
  covalent geometry    : angle       0.56817 (13526)
  hydrogen bonds       : bond        0.04034 (  565)
  hydrogen bonds       : angle       3.86808 ( 1614)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1593.65 seconds
wall clock time: 28 minutes 14.09 seconds (1694.09 seconds total)