Starting phenix.real_space_refine
on Sat Aug 23 00:06:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ext_28662/08_2025/8ext_28662.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ext_28662/08_2025/8ext_28662.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ext_28662/08_2025/8ext_28662.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ext_28662/08_2025/8ext_28662.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ext_28662/08_2025/8ext_28662.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ext_28662/08_2025/8ext_28662.cif"
  }
  resolution = 4.6
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      38      5.16       5
     C    5806      2.51       5
     N    1460      2.21       5
     O    1540      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8846
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 531, 4422
          Classifications: {'peptide': 531}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 520}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.90, per 1000 atoms: 0.33
  Number of scatterers: 8846
  At special positions: 0
  Unit cell: (88.395, 92.655, 116.085, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      38     16.00
     O    1540      8.00
     N    1460      7.00
     C    5806      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: 0.86
  Conformation dependent library (CDL) restraints added in 314.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 201 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 205 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 201 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 205 "


  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2048

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      60.0% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 31
    Processing helix  chain 'A' and resid 36 through 48
      removed outlier: 4.044A  pdb=" N   TYR A  40 " --> pdb=" O   TYR A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 99 through 134
      removed outlier: 3.846A  pdb=" N   ASP A 103 " --> pdb=" O   TRP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 152
      removed outlier: 5.172A  pdb=" N   LYS A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 189
    Processing helix  chain 'A' and resid 193 through 208
    Processing helix  chain 'A' and resid 209 through 225
    Processing helix  chain 'A' and resid 228 through 252
    Processing helix  chain 'A' and resid 257 through 271
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 307 through 328
      removed outlier: 3.808A  pdb=" N   LEU A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 352 through 357
    Processing helix  chain 'A' and resid 377 through 382
    Processing helix  chain 'A' and resid 387 through 390
    Processing helix  chain 'A' and resid 391 through 402
    Processing helix  chain 'A' and resid 429 through 436
    Processing helix  chain 'A' and resid 438 through 449
    Processing helix  chain 'A' and resid 450 through 461
      removed outlier: 3.530A  pdb=" N   THR A 454 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 497
    Processing helix  chain 'A' and resid 502 through 513
      removed outlier: 3.617A  pdb=" N   SER A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 579
    Processing helix  chain 'B' and resid 2 through 31
    Processing helix  chain 'B' and resid 36 through 48
      removed outlier: 4.044A  pdb=" N   TYR B  40 " --> pdb=" O   TYR B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 99 through 134
      removed outlier: 3.846A  pdb=" N   ASP B 103 " --> pdb=" O   TRP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 152
      removed outlier: 5.173A  pdb=" N   LYS B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 189
    Processing helix  chain 'B' and resid 193 through 208
    Processing helix  chain 'B' and resid 209 through 225
    Processing helix  chain 'B' and resid 228 through 252
    Processing helix  chain 'B' and resid 257 through 271
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 307 through 328
      removed outlier: 3.808A  pdb=" N   LEU B 311 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 337
    Processing helix  chain 'B' and resid 352 through 357
    Processing helix  chain 'B' and resid 377 through 382
    Processing helix  chain 'B' and resid 387 through 390
    Processing helix  chain 'B' and resid 391 through 402
    Processing helix  chain 'B' and resid 429 through 436
    Processing helix  chain 'B' and resid 438 through 449
    Processing helix  chain 'B' and resid 450 through 461
      removed outlier: 3.530A  pdb=" N   THR B 454 " --> pdb=" O   PRO B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 497
    Processing helix  chain 'B' and resid 502 through 513
      removed outlier: 3.616A  pdb=" N   SER B 512 " --> pdb=" O   GLN B 508 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU B 513 " --> pdb=" O   LEU B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164
      removed outlier: 6.645A  pdb=" N   VAL A 160 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   ARG A 162 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.615A  pdb=" N   ASP A 346 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   ILE A 375 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   GLN A 348 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   GLY A 530 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 4.959A  pdb=" N   GLY A 539 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   GLY A 528 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE A 541 " --> pdb=" O   LYS A 526 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LYS A 526 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   GLY A 543 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   TYR A 524 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   VAL A 545 " --> pdb=" O   GLU A 522 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   GLU A 522 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LYS A 517 " --> pdb=" O   TYR A 521 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU A 523 " --> pdb=" O   ILE A 515 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164
      removed outlier: 6.645A  pdb=" N   VAL B 160 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   ILE B 182 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   ARG B 162 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350
      removed outlier: 6.615A  pdb=" N   ASP B 346 " --> pdb=" O   TYR B 373 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   ILE B 375 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   GLN B 348 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   GLY B 530 " --> pdb=" O   ASN B 537 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   GLY B 539 " --> pdb=" O   GLY B 528 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   GLY B 528 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE B 541 " --> pdb=" O   LYS B 526 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LYS B 526 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   GLY B 543 " --> pdb=" O   TYR B 524 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   TYR B 524 " --> pdb=" O   GLY B 543 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   VAL B 545 " --> pdb=" O   GLU B 522 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   GLU B 522 " --> pdb=" O   VAL B 545 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR B 521 " --> pdb=" O   LYS B 517 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LYS B 517 " --> pdb=" O   TYR B 521 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU B 523 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)

    495 hydrogen bonds defined for protein.
    1461 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: 1.38

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1815
        1.31 -     1.44: 2726
        1.44 -     1.58: 4399
        1.58 -     1.71: 38
        1.71 -     1.84: 68
  Bond restraints: 9046
  Sorted by residual:
  bond pdb=" CB  HIS A 282 "
       pdb=" CG  HIS A 282 "
    ideal  model  delta    sigma   weight residual
    1.497  1.335  0.162 1.40e-02 5.10e+03 1.34e+02
  bond pdb=" CB  HIS B 282 "
       pdb=" CG  HIS B 282 "
    ideal  model  delta    sigma   weight residual
    1.497  1.335  0.162 1.40e-02 5.10e+03 1.34e+02
  bond pdb=" CB  HIS B 153 "
       pdb=" CG  HIS B 153 "
    ideal  model  delta    sigma   weight residual
    1.497  1.349  0.148 1.40e-02 5.10e+03 1.11e+02
  bond pdb=" CB  HIS A 153 "
       pdb=" CG  HIS A 153 "
    ideal  model  delta    sigma   weight residual
    1.497  1.349  0.148 1.40e-02 5.10e+03 1.11e+02
  bond pdb=" CB  PHE A 220 "
       pdb=" CG  PHE A 220 "
    ideal  model  delta    sigma   weight residual
    1.502  1.312  0.190 2.30e-02 1.89e+03 6.83e+01
  ... (remaining 9041 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.92: 12014
        5.92 -    11.84: 144
       11.84 -    17.77: 6
       17.77 -    23.69: 2
       23.69 -    29.61: 6
  Bond angle restraints: 12172
  Sorted by residual:
  angle pdb=" O   ASP B 346 "
        pdb=" C   ASP B 346 "
        pdb=" N   TYR B 347 "
      ideal   model   delta    sigma   weight residual
     122.79  148.72  -25.93 1.14e+00 7.69e-01 5.17e+02
  angle pdb=" O   ASP A 346 "
        pdb=" C   ASP A 346 "
        pdb=" N   TYR A 347 "
      ideal   model   delta    sigma   weight residual
     122.79  148.72  -25.93 1.14e+00 7.69e-01 5.17e+02
  angle pdb=" CA  ASP A 346 "
        pdb=" C   ASP A 346 "
        pdb=" N   TYR A 347 "
      ideal   model   delta    sigma   weight residual
     115.27   85.66   29.61 1.34e+00 5.57e-01 4.88e+02
  angle pdb=" CA  ASP B 346 "
        pdb=" C   ASP B 346 "
        pdb=" N   TYR B 347 "
      ideal   model   delta    sigma   weight residual
     115.27   85.66   29.61 1.34e+00 5.57e-01 4.88e+02
  angle pdb=" O   ILE A  51 "
        pdb=" C   ILE A  51 "
        pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     121.10  136.04  -14.94 1.14e+00 7.69e-01 1.72e+02
  ... (remaining 12167 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.03: 5016
       14.03 -    28.05: 308
       28.05 -    42.08: 70
       42.08 -    56.10: 28
       56.10 -    70.13: 10
  Dihedral angle restraints: 5432
    sinusoidal: 2256
      harmonic: 3176
  Sorted by residual:
  dihedral pdb=" C   LEU B  18 "
           pdb=" N   LEU B  18 "
           pdb=" CA  LEU B  18 "
           pdb=" CB  LEU B  18 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.59  -10.01     0      2.50e+00 1.60e-01 1.60e+01
  dihedral pdb=" C   LEU A  18 "
           pdb=" N   LEU A  18 "
           pdb=" CA  LEU A  18 "
           pdb=" CB  LEU A  18 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.59  -10.01     0      2.50e+00 1.60e-01 1.60e+01
  dihedral pdb=" C   ASN B 406 "
           pdb=" N   ASN B 406 "
           pdb=" CA  ASN B 406 "
           pdb=" CB  ASN B 406 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.21    9.61     0      2.50e+00 1.60e-01 1.48e+01
  ... (remaining 5429 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 716
       0.085 -    0.171: 414
       0.171 -    0.256: 156
       0.256 -    0.341: 36
       0.341 -    0.426: 14
  Chirality restraints: 1336
  Sorted by residual:
  chirality pdb=" CA  TYR A 178 "
            pdb=" N   TYR A 178 "
            pdb=" C   TYR A 178 "
            pdb=" CB  TYR A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.54e+00
  chirality pdb=" CA  TYR B 178 "
            pdb=" N   TYR B 178 "
            pdb=" C   TYR B 178 "
            pdb=" CB  TYR B 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.43 2.00e-01 2.50e+01 4.52e+00
  chirality pdb=" CA  PHE B 151 "
            pdb=" N   PHE B 151 "
            pdb=" C   PHE B 151 "
            pdb=" CB  PHE B 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.56e+00
  ... (remaining 1333 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 346 "    0.022 2.00e-02 2.50e+03   7.33e-02 5.37e+01
        pdb=" C   ASP A 346 "   -0.125 2.00e-02 2.50e+03
        pdb=" O   ASP A 346 "    0.058 2.00e-02 2.50e+03
        pdb=" N   TYR A 347 "    0.045 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 346 "   -0.022 2.00e-02 2.50e+03   7.33e-02 5.37e+01
        pdb=" C   ASP B 346 "    0.125 2.00e-02 2.50e+03
        pdb=" O   ASP B 346 "   -0.058 2.00e-02 2.50e+03
        pdb=" N   TYR B 347 "   -0.045 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  51 "    0.024 2.00e-02 2.50e+03   6.08e-02 3.70e+01
        pdb=" C   ILE A  51 "   -0.105 2.00e-02 2.50e+03
        pdb=" O   ILE A  51 "    0.044 2.00e-02 2.50e+03
        pdb=" N   PRO A  52 "    0.036 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 174
        2.59 -     3.17: 9050
        3.17 -     3.75: 15210
        3.75 -     4.32: 22367
        4.32 -     4.90: 32315
  Nonbonded interactions: 79116
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.014 2.230
  nonbonded pdb=" OE2 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.014 2.230
  nonbonded pdb=" OE1 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.021 2.230
  nonbonded pdb=" OE1 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.022 2.230
  nonbonded pdb=" O   MET A  33 "
            pdb=" CD1 LEU B 311 "
     model   vdw
     2.281 3.460
  ... (remaining 79111 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
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:             0.740
  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:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     10.860
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4877
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      :  0.026   0.190   9050  Z= 1.544
  Angle     :  2.042  29.611  12172  Z= 1.432
  Chirality :  0.123   0.426   1336
  Planarity :  0.010   0.073   1488
  Dihedral  : 10.968  70.129   3384
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  5.33 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  1.01 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.24), residues: 1050
  helix: -0.09 (0.19), residues: 550
  sheet: -0.87 (0.47), residues: 118
  loop : -0.57 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 384 
 TYR   0.056   0.010   TYR B 203 
 PHE   0.045   0.006   PHE B 151 
 TRP   0.055   0.011   TRP B 540 
 HIS   0.014   0.003   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.02633 ( 9046)
  covalent geometry    : angle       2.04192 (12172)
  hydrogen bonds       : bond        0.20237 (  495)
  hydrogen bonds       : angle       8.18963 ( 1461)
  metal coordination   : bond        0.12888 (    4)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ILE cc_start: 0.8475 (mt) cc_final: 0.8015 (mm)
REVERT: A   20 LEU cc_start: 0.8877 (mt) cc_final: 0.8629 (mt)
REVERT: A   37 LYS cc_start: 0.8324 (mttt) cc_final: 0.8005 (mttt)
REVERT: A  119 PHE cc_start: 0.7232 (m-10) cc_final: 0.6999 (m-80)
REVERT: A  260 THR cc_start: 0.7838 (t) cc_final: 0.7605 (t)
REVERT: A  314 ILE cc_start: 0.8847 (mt) cc_final: 0.8631 (mt)
REVERT: A  341 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5324 (tppt)
  outliers start: 10
  outliers final: 4
  residues processed: 167
  average time/residue: 0.0745
  time to fit residues: 15.3307
Evaluate side-chains
  101 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0010
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0270
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    0.0980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.2044
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 153 HIS
** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 ASN
B 487 GLN
B 538 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.159768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.115060 restraints weight = 12669.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.119244 restraints weight = 8420.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.122284 restraints weight = 6191.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.124442 restraints weight = 4836.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.126074 restraints weight = 3961.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6327
moved from start:          0.4603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9050  Z= 0.172
  Angle     :  0.741   7.973  12172  Z= 0.402
  Chirality :  0.047   0.269   1336
  Planarity :  0.005   0.046   1488
  Dihedral  :  5.379  21.049   1156
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.03 %
    Favored  : 97.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.25), residues: 1050
  helix:  0.86 (0.20), residues: 584
  sheet: -0.42 (0.48), residues: 120
  loop : -0.42 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  28 
 TYR   0.037   0.002   TYR A 203 
 PHE   0.025   0.003   PHE A 248 
 TRP   0.018   0.002   TRP B  39 
 HIS   0.014   0.002   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 9046)
  covalent geometry    : angle       0.74111 (12172)
  hydrogen bonds       : bond        0.06497 (  495)
  hydrogen bonds       : angle       6.00977 ( 1461)
  metal coordination   : bond        0.00769 (    4)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ILE cc_start: 0.9264 (mt) cc_final: 0.8922 (mt)
REVERT: B   18 LEU cc_start: 0.9452 (mt) cc_final: 0.9050 (mt)
REVERT: B   20 LEU cc_start: 0.9506 (mt) cc_final: 0.9300 (mt)
REVERT: B   37 LYS cc_start: 0.8576 (mttt) cc_final: 0.7759 (mmtm)
REVERT: B  181 LEU cc_start: 0.8199 (mp) cc_final: 0.7880 (mp)
REVERT: B  202 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8369 (mm-30)
REVERT: B  209 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7657 (mtt180)
REVERT: B  214 LEU cc_start: 0.9625 (tp) cc_final: 0.9369 (tp)
REVERT: B  218 ASN cc_start: 0.9180 (m110) cc_final: 0.8833 (m110)
REVERT: B  221 SER cc_start: 0.8884 (m) cc_final: 0.8586 (p)
REVERT: B  235 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7875 (mmm160)
REVERT: B  240 ASP cc_start: 0.8462 (p0) cc_final: 0.7807 (p0)
REVERT: B  241 ASN cc_start: 0.9117 (m-40) cc_final: 0.8866 (m110)
REVERT: B  244 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8655 (mt-10)
REVERT: B  266 MET cc_start: 0.7975 (tmm) cc_final: 0.7682 (tmm)
REVERT: B  292 LYS cc_start: 0.8694 (mptt) cc_final: 0.8385 (mttt)
REVERT: B  294 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7381 (mtp180)
REVERT: B  330 MET cc_start: 0.2966 (ppp) cc_final: 0.2709 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0699
  time to fit residues: 12.1525
Evaluate side-chains
  107 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0050
   chunk 66 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0980
   chunk 53 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 93 optimal weight:    7.9990
   chunk 54 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.9398
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 208 ASN
B 428 GLN
B 497 GLN
** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.156231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.113102 restraints weight = 12754.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.117554 restraints weight = 8270.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.120562 restraints weight = 5911.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.122766 restraints weight = 4518.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.124301 restraints weight = 3628.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6393
moved from start:          0.5453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9050  Z= 0.139
  Angle     :  0.623   9.428  12172  Z= 0.337
  Chirality :  0.042   0.146   1336
  Planarity :  0.004   0.039   1488
  Dihedral  :  5.004  18.200   1156
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.04 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.26), residues: 1050
  helix:  0.47 (0.20), residues: 590
  sheet: -0.44 (0.50), residues: 120
  loop : -0.73 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 235 
 TYR   0.060   0.002   TYR A 203 
 PHE   0.013   0.002   PHE A  16 
 TRP   0.009   0.001   TRP A 475 
 HIS   0.009   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9046)
  covalent geometry    : angle       0.62297 (12172)
  hydrogen bonds       : bond        0.05044 (  495)
  hydrogen bonds       : angle       5.66670 ( 1461)
  metal coordination   : bond        0.00088 (    4)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4895 (ttt) cc_final: 0.2929 (mmt)
REVERT: B    9 ILE cc_start: 0.9122 (mt) cc_final: 0.8901 (mt)
REVERT: B   18 LEU cc_start: 0.9469 (mt) cc_final: 0.8955 (mt)
REVERT: B   22 PHE cc_start: 0.9237 (m-80) cc_final: 0.8815 (m-80)
REVERT: B   37 LYS cc_start: 0.8534 (mttt) cc_final: 0.7667 (mmtm)
REVERT: B  105 ILE cc_start: 0.8866 (mt) cc_final: 0.8626 (mm)
REVERT: B  202 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8406 (mm-30)
REVERT: B  209 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7732 (mtt180)
REVERT: B  212 LEU cc_start: 0.9400 (tp) cc_final: 0.9149 (tp)
REVERT: B  214 LEU cc_start: 0.9679 (tp) cc_final: 0.9436 (tp)
REVERT: B  215 ILE cc_start: 0.9109 (pt) cc_final: 0.8891 (pt)
REVERT: B  218 ASN cc_start: 0.9239 (m110) cc_final: 0.8907 (m110)
REVERT: B  235 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7791 (mmm160)
REVERT: B  244 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8617 (mt-10)
REVERT: B  266 MET cc_start: 0.7710 (tmm) cc_final: 0.7350 (tmm)
REVERT: B  292 LYS cc_start: 0.8732 (mptt) cc_final: 0.8466 (mttt)
  outliers start: 2
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0643
  time to fit residues: 10.5131
Evaluate side-chains
  107 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 13 optimal weight:    0.0060
   chunk 79 optimal weight:    0.0010
   chunk 64 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0040
   chunk 81 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.9816
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 208 ASN
B 239 HIS
B 428 GLN
** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.147494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.105289 restraints weight = 12844.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.108975 restraints weight = 8772.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.111724 restraints weight = 6538.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.113646 restraints weight = 5115.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.115097 restraints weight = 4173.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6456
moved from start:          0.5961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9050  Z= 0.128
  Angle     :  0.593   6.786  12172  Z= 0.323
  Chirality :  0.042   0.173   1336
  Planarity :  0.004   0.038   1488
  Dihedral  :  4.788  18.245   1156
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.23 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.25), residues: 1050
  helix:  0.41 (0.20), residues: 596
  sheet: -0.78 (0.50), residues: 120
  loop : -0.79 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 384 
 TYR   0.046   0.001   TYR A 203 
 PHE   0.014   0.002   PHE B 319 
 TRP   0.010   0.001   TRP B  39 
 HIS   0.009   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9046)
  covalent geometry    : angle       0.59295 (12172)
  hydrogen bonds       : bond        0.04466 (  495)
  hydrogen bonds       : angle       5.53005 ( 1461)
  metal coordination   : bond        0.00112 (    4)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5004 (ttt) cc_final: 0.2997 (mmt)
REVERT: B   18 LEU cc_start: 0.9506 (mt) cc_final: 0.9172 (mt)
REVERT: B   20 LEU cc_start: 0.9538 (mt) cc_final: 0.9313 (mt)
REVERT: B   22 PHE cc_start: 0.9237 (m-80) cc_final: 0.8858 (m-80)
REVERT: B   37 LYS cc_start: 0.8590 (mttt) cc_final: 0.7707 (mmtm)
REVERT: B  202 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8406 (mm-30)
REVERT: B  209 ARG cc_start: 0.8182 (mtt180) cc_final: 0.7726 (mtt180)
REVERT: B  212 LEU cc_start: 0.9367 (tp) cc_final: 0.9137 (tp)
REVERT: B  214 LEU cc_start: 0.9670 (tp) cc_final: 0.9434 (tp)
REVERT: B  215 ILE cc_start: 0.9124 (pt) cc_final: 0.8914 (pt)
REVERT: B  216 ILE cc_start: 0.9559 (mt) cc_final: 0.9250 (mt)
REVERT: B  235 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7767 (mmm160)
REVERT: B  244 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8545 (mt-10)
REVERT: B  287 LYS cc_start: 0.2846 (tppp) cc_final: 0.2336 (tptm)
REVERT: B  412 MET cc_start: 0.0389 (ptm) cc_final: -0.0503 (mtm)
REVERT: B  428 GLN cc_start: 0.4059 (OUTLIER) cc_final: 0.3625 (pm20)
REVERT: B  494 MET cc_start: 0.7883 (ttp) cc_final: 0.7663 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0584
  time to fit residues: 9.2051
Evaluate side-chains
  101 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0270
   chunk 59 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    0.6240
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 428 GLN
** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.149579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.106624 restraints weight = 12768.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.110406 restraints weight = 8692.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.113068 restraints weight = 6425.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.114972 restraints weight = 5042.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.116401 restraints weight = 4146.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6436
moved from start:          0.6457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9050  Z= 0.118
  Angle     :  0.583   7.509  12172  Z= 0.317
  Chirality :  0.042   0.158   1336
  Planarity :  0.004   0.039   1488
  Dihedral  :  4.557  17.270   1156
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  1.83 %
    Favored  : 97.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.25), residues: 1050
  helix:  0.32 (0.19), residues: 596
  sheet: -0.67 (0.51), residues: 114
  loop : -0.99 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 384 
 TYR   0.041   0.001   TYR B 203 
 PHE   0.025   0.001   PHE B 442 
 TRP   0.015   0.001   TRP B  39 
 HIS   0.008   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9046)
  covalent geometry    : angle       0.58330 (12172)
  hydrogen bonds       : bond        0.04273 (  495)
  hydrogen bonds       : angle       5.38265 ( 1461)
  metal coordination   : bond        0.00032 (    4)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5277 (ttt) cc_final: 0.2986 (mmt)
REVERT: B   16 PHE cc_start: 0.8759 (t80) cc_final: 0.8502 (t80)
REVERT: B   18 LEU cc_start: 0.9524 (mt) cc_final: 0.9268 (mt)
REVERT: B   20 LEU cc_start: 0.9559 (mt) cc_final: 0.9331 (mt)
REVERT: B   22 PHE cc_start: 0.9255 (m-80) cc_final: 0.8965 (m-80)
REVERT: B   37 LYS cc_start: 0.8572 (mttt) cc_final: 0.7694 (mmtm)
REVERT: B  202 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8402 (mm-30)
REVERT: B  209 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7533 (mtt180)
REVERT: B  216 ILE cc_start: 0.9565 (mt) cc_final: 0.9279 (mt)
REVERT: B  235 ARG cc_start: 0.8253 (mmt90) cc_final: 0.8048 (mmm160)
REVERT: B  240 ASP cc_start: 0.8792 (p0) cc_final: 0.8569 (p0)
REVERT: B  244 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8481 (mt-10)
REVERT: B  292 LYS cc_start: 0.8731 (mptt) cc_final: 0.8485 (mttt)
REVERT: B  319 PHE cc_start: 0.8941 (t80) cc_final: 0.8637 (t80)
REVERT: B  330 MET cc_start: 0.2229 (ppp) cc_final: 0.1920 (ppp)
REVERT: B  412 MET cc_start: 0.0863 (ptm) cc_final: 0.0625 (ptm)
  outliers start: 2
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0591
  time to fit residues: 9.7175
Evaluate side-chains
  103 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0040
   chunk 58 optimal weight:    8.9990
   chunk 95 optimal weight:    0.7980
   chunk 91 optimal weight:    7.9990
   chunk 88 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 21 optimal weight:    0.1980
   chunk 57 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.7194
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 297 ASN
B 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.148678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.105944 restraints weight = 12871.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.109826 restraints weight = 8821.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.112571 restraints weight = 6554.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.114632 restraints weight = 5146.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.115988 restraints weight = 4220.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6429
moved from start:          0.6921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9050  Z= 0.123
  Angle     :  0.638  10.437  12172  Z= 0.335
  Chirality :  0.043   0.157   1336
  Planarity :  0.004   0.040   1488
  Dihedral  :  4.470  17.438   1156
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.61 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.25), residues: 1050
  helix:  0.43 (0.20), residues: 598
  sheet: -0.70 (0.50), residues: 114
  loop : -1.15 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  23 
 TYR   0.035   0.001   TYR A 203 
 PHE   0.017   0.001   PHE A 442 
 TRP   0.011   0.001   TRP A  39 
 HIS   0.002   0.001   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9046)
  covalent geometry    : angle       0.63764 (12172)
  hydrogen bonds       : bond        0.04119 (  495)
  hydrogen bonds       : angle       5.40589 ( 1461)
  metal coordination   : bond        0.00093 (    4)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 117
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5241 (ttt) cc_final: 0.2865 (mmt)
REVERT: B   14 PHE cc_start: 0.8415 (t80) cc_final: 0.7975 (t80)
REVERT: B   16 PHE cc_start: 0.8868 (t80) cc_final: 0.8594 (t80)
REVERT: B   18 LEU cc_start: 0.9538 (mt) cc_final: 0.9176 (mt)
REVERT: B   20 LEU cc_start: 0.9561 (mt) cc_final: 0.9339 (mt)
REVERT: B   22 PHE cc_start: 0.9309 (m-80) cc_final: 0.8983 (m-80)
REVERT: B   37 LYS cc_start: 0.8522 (mttt) cc_final: 0.7650 (mmtm)
REVERT: B   39 TRP cc_start: 0.8588 (m100) cc_final: 0.7975 (m100)
REVERT: B  202 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8404 (mm-30)
REVERT: B  209 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7420 (mtt180)
REVERT: B  214 LEU cc_start: 0.9690 (tp) cc_final: 0.9483 (tp)
REVERT: B  215 ILE cc_start: 0.9220 (pt) cc_final: 0.8989 (pt)
REVERT: B  216 ILE cc_start: 0.9599 (mt) cc_final: 0.9172 (mt)
REVERT: B  218 ASN cc_start: 0.9034 (m110) cc_final: 0.8775 (m110)
REVERT: B  240 ASP cc_start: 0.8628 (p0) cc_final: 0.8410 (p0)
REVERT: B  244 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8498 (mt-10)
REVERT: B  319 PHE cc_start: 0.8989 (t80) cc_final: 0.8731 (t80)
REVERT: B  412 MET cc_start: 0.0531 (ptm) cc_final: 0.0261 (ptm)
REVERT: B  434 MET cc_start: 0.3963 (tmm) cc_final: 0.2638 (ptm)
REVERT: B  435 GLN cc_start: 0.5300 (tm-30) cc_final: 0.4637 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0441
  time to fit residues: 6.9334
Evaluate side-chains
  103 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 32 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0070
   chunk 87 optimal weight:    0.0970
   chunk 44 optimal weight:    4.9990
   chunk 36 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 103 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.4196
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 428 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.152384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.108763 restraints weight = 12782.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.113559 restraints weight = 7790.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.116979 restraints weight = 5325.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.119221 restraints weight = 3945.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.120946 restraints weight = 3112.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6395
moved from start:          0.7152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9050  Z= 0.118
  Angle     :  0.607  10.247  12172  Z= 0.325
  Chirality :  0.043   0.176   1336
  Planarity :  0.004   0.041   1488
  Dihedral  :  4.341  19.656   1156
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.01 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.25), residues: 1050
  helix:  0.27 (0.20), residues: 592
  sheet: -0.62 (0.51), residues: 112
  loop : -1.22 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  23 
 TYR   0.033   0.001   TYR A 203 
 PHE   0.031   0.002   PHE B  12 
 TRP   0.010   0.001   TRP B  39 
 HIS   0.003   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9046)
  covalent geometry    : angle       0.60730 (12172)
  hydrogen bonds       : bond        0.04078 (  495)
  hydrogen bonds       : angle       5.40942 ( 1461)
  metal coordination   : bond        0.00194 (    4)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5461 (ttt) cc_final: 0.3109 (mmt)
REVERT: B   14 PHE cc_start: 0.8411 (t80) cc_final: 0.7978 (t80)
REVERT: B   16 PHE cc_start: 0.8873 (t80) cc_final: 0.8608 (t80)
REVERT: B   18 LEU cc_start: 0.9579 (mt) cc_final: 0.9216 (mt)
REVERT: B   20 LEU cc_start: 0.9565 (mt) cc_final: 0.9333 (mt)
REVERT: B   22 PHE cc_start: 0.9381 (m-80) cc_final: 0.9117 (m-80)
REVERT: B   37 LYS cc_start: 0.8381 (mttt) cc_final: 0.7498 (mmtm)
REVERT: B   39 TRP cc_start: 0.8491 (m100) cc_final: 0.7856 (m100)
REVERT: B   41 LEU cc_start: 0.8653 (tp) cc_final: 0.8440 (tp)
REVERT: B  202 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8376 (mm-30)
REVERT: B  214 LEU cc_start: 0.9620 (tp) cc_final: 0.9358 (tp)
REVERT: B  215 ILE cc_start: 0.9203 (pt) cc_final: 0.8927 (pt)
REVERT: B  218 ASN cc_start: 0.9062 (m110) cc_final: 0.8703 (m110)
REVERT: B  229 LEU cc_start: 0.9423 (tp) cc_final: 0.9092 (tt)
REVERT: B  240 ASP cc_start: 0.8728 (p0) cc_final: 0.8489 (p0)
REVERT: B  244 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8548 (mt-10)
REVERT: B  319 PHE cc_start: 0.8960 (t80) cc_final: 0.8732 (t80)
REVERT: B  412 MET cc_start: 0.0726 (ptm) cc_final: 0.0109 (ptm)
REVERT: B  428 GLN cc_start: 0.4406 (OUTLIER) cc_final: 0.3257 (mp10)
REVERT: B  434 MET cc_start: 0.3816 (tmm) cc_final: 0.2579 (ptm)
REVERT: B  435 GLN cc_start: 0.5489 (tm-30) cc_final: 0.4883 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0470
  time to fit residues: 7.3846
Evaluate side-chains
  106 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0270
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 18 optimal weight:    0.3980
   chunk 95 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.4438
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 428 GLN
B 484 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.150321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.107743 restraints weight = 12648.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.111519 restraints weight = 8702.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.114378 restraints weight = 6460.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.116367 restraints weight = 5045.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.117922 restraints weight = 4137.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.7363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9050  Z= 0.116
  Angle     :  0.597   8.491  12172  Z= 0.325
  Chirality :  0.043   0.167   1336
  Planarity :  0.004   0.040   1488
  Dihedral  :  4.179  16.149   1156
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.81 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.24), residues: 1050
  helix:  0.22 (0.19), residues: 598
  sheet: -0.79 (0.50), residues: 112
  loop : -1.21 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  23 
 TYR   0.030   0.001   TYR B 203 
 PHE   0.028   0.002   PHE B 119 
 TRP   0.010   0.001   TRP B 174 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9046)
  covalent geometry    : angle       0.59694 (12172)
  hydrogen bonds       : bond        0.03993 (  495)
  hydrogen bonds       : angle       5.43847 ( 1461)
  metal coordination   : bond        0.00062 (    4)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5461 (ttt) cc_final: 0.3123 (mmt)
REVERT: B   14 PHE cc_start: 0.8425 (t80) cc_final: 0.8089 (t80)
REVERT: B   16 PHE cc_start: 0.8817 (t80) cc_final: 0.8592 (t80)
REVERT: B   18 LEU cc_start: 0.9575 (mt) cc_final: 0.9226 (mt)
REVERT: B   20 LEU cc_start: 0.9551 (mt) cc_final: 0.9308 (mt)
REVERT: B   37 LYS cc_start: 0.8446 (mttt) cc_final: 0.7524 (mmtm)
REVERT: B   39 TRP cc_start: 0.8500 (m100) cc_final: 0.7894 (m100)
REVERT: B  214 LEU cc_start: 0.9685 (tp) cc_final: 0.9482 (tp)
REVERT: B  215 ILE cc_start: 0.9239 (pt) cc_final: 0.8989 (pt)
REVERT: B  218 ASN cc_start: 0.9127 (m110) cc_final: 0.8897 (m110)
REVERT: B  229 LEU cc_start: 0.9356 (tp) cc_final: 0.8903 (tt)
REVERT: B  240 ASP cc_start: 0.8849 (p0) cc_final: 0.8568 (p0)
REVERT: B  244 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8465 (mt-10)
REVERT: B  266 MET cc_start: 0.7511 (ttt) cc_final: 0.6964 (mtp)
REVERT: B  292 LYS cc_start: 0.8758 (mttp) cc_final: 0.8216 (mtmt)
REVERT: B  314 ILE cc_start: 0.9540 (mm) cc_final: 0.9270 (pt)
REVERT: B  319 PHE cc_start: 0.8948 (t80) cc_final: 0.8666 (t80)
REVERT: B  412 MET cc_start: 0.0603 (ptm) cc_final: -0.0031 (ptm)
REVERT: B  428 GLN cc_start: 0.4594 (OUTLIER) cc_final: 0.3508 (mp10)
REVERT: B  434 MET cc_start: 0.3963 (tmm) cc_final: 0.2750 (ptm)
REVERT: B  435 GLN cc_start: 0.5501 (tm-30) cc_final: 0.4916 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0517
  time to fit residues: 8.0112
Evaluate side-chains
  99 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0870
   chunk 99 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 18 optimal weight:    0.2980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.5558
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 428 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.150051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.107265 restraints weight = 12899.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.111378 restraints weight = 8712.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.114121 restraints weight = 6383.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.116210 restraints weight = 4980.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.117547 restraints weight = 4067.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6433
moved from start:          0.7669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9050  Z= 0.120
  Angle     :  0.621  11.287  12172  Z= 0.331
  Chirality :  0.044   0.161   1336
  Planarity :  0.004   0.040   1488
  Dihedral  :  4.262  24.173   1156
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.20 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.25), residues: 1050
  helix:  0.29 (0.20), residues: 596
  sheet: -0.92 (0.49), residues: 112
  loop : -1.18 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 384 
 TYR   0.022   0.001   TYR A 203 
 PHE   0.021   0.001   PHE B  22 
 TRP   0.010   0.001   TRP A  39 
 HIS   0.004   0.001   HIS B 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9046)
  covalent geometry    : angle       0.62067 (12172)
  hydrogen bonds       : bond        0.04002 (  495)
  hydrogen bonds       : angle       5.51828 ( 1461)
  metal coordination   : bond        0.00139 (    4)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5382 (ttt) cc_final: 0.3244 (mmt)
REVERT: B   13 CYS cc_start: 0.9400 (p) cc_final: 0.9117 (m)
REVERT: B   14 PHE cc_start: 0.8618 (t80) cc_final: 0.8040 (t80)
REVERT: B   16 PHE cc_start: 0.8854 (t80) cc_final: 0.8583 (t80)
REVERT: B   18 LEU cc_start: 0.9606 (mt) cc_final: 0.9353 (mt)
REVERT: B   20 LEU cc_start: 0.9553 (mt) cc_final: 0.9339 (mt)
REVERT: B   28 ARG cc_start: 0.6592 (tpm170) cc_final: 0.5238 (ttt-90)
REVERT: B   37 LYS cc_start: 0.8453 (mttt) cc_final: 0.7536 (mmtm)
REVERT: B  209 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7407 (mtt180)
REVERT: B  214 LEU cc_start: 0.9688 (tp) cc_final: 0.9462 (tp)
REVERT: B  215 ILE cc_start: 0.9197 (pt) cc_final: 0.8965 (pt)
REVERT: B  216 ILE cc_start: 0.9535 (mt) cc_final: 0.9179 (mt)
REVERT: B  218 ASN cc_start: 0.9130 (m110) cc_final: 0.8795 (m110)
REVERT: B  229 LEU cc_start: 0.9333 (tp) cc_final: 0.9058 (tt)
REVERT: B  240 ASP cc_start: 0.8875 (p0) cc_final: 0.8478 (p0)
REVERT: B  244 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8493 (mt-10)
REVERT: B  266 MET cc_start: 0.7228 (ttt) cc_final: 0.7010 (mtt)
REVERT: B  291 LEU cc_start: 0.8713 (tp) cc_final: 0.8449 (tp)
REVERT: B  292 LYS cc_start: 0.8744 (mttp) cc_final: 0.8209 (mtmt)
REVERT: B  294 ARG cc_start: 0.7470 (mtp180) cc_final: 0.6440 (mtp180)
REVERT: B  314 ILE cc_start: 0.9522 (mm) cc_final: 0.9248 (pt)
REVERT: B  319 PHE cc_start: 0.8905 (t80) cc_final: 0.8608 (t80)
REVERT: B  412 MET cc_start: 0.0853 (ptm) cc_final: 0.0185 (ptm)
REVERT: B  428 GLN cc_start: 0.4350 (OUTLIER) cc_final: 0.3346 (mp10)
REVERT: B  434 MET cc_start: 0.3942 (tmm) cc_final: 0.2715 (ptm)
REVERT: B  435 GLN cc_start: 0.5334 (tm-30) cc_final: 0.4811 (mp10)
REVERT: B  462 ASN cc_start: 0.7974 (m-40) cc_final: 0.7432 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0696
  time to fit residues: 10.2387
Evaluate side-chains
  97 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 66 optimal weight:    0.0670
   chunk 79 optimal weight:    0.1980
   chunk 55 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 88 optimal weight:    0.0770
   chunk 11 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 85 optimal weight:    0.0270
   chunk 46 optimal weight:   10.0000
   chunk 103 optimal weight:    8.9990
   overall best weight:    0.1734
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 241 ASN
B 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.151405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.108937 restraints weight = 12699.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.112864 restraints weight = 8594.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.115776 restraints weight = 6362.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.117764 restraints weight = 4977.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.119276 restraints weight = 4078.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6386
moved from start:          0.8009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9050  Z= 0.122
  Angle     :  0.641  11.606  12172  Z= 0.341
  Chirality :  0.044   0.238   1336
  Planarity :  0.004   0.040   1488
  Dihedral  :  4.159  19.052   1156
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.81 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.24), residues: 1050
  helix:  0.15 (0.20), residues: 594
  sheet: -1.02 (0.49), residues: 114
  loop : -1.29 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  23 
 TYR   0.020   0.001   TYR B 203 
 PHE   0.015   0.001   PHE B  12 
 TRP   0.019   0.002   TRP B 475 
 HIS   0.004   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9046)
  covalent geometry    : angle       0.64056 (12172)
  hydrogen bonds       : bond        0.04112 (  495)
  hydrogen bonds       : angle       5.44092 ( 1461)
  metal coordination   : bond        0.00050 (    4)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5409 (ttt) cc_final: 0.3276 (mmt)
REVERT: B   13 CYS cc_start: 0.9489 (p) cc_final: 0.9118 (m)
REVERT: B   14 PHE cc_start: 0.8697 (t80) cc_final: 0.8096 (t80)
REVERT: B   16 PHE cc_start: 0.8869 (t80) cc_final: 0.8519 (t80)
REVERT: B   18 LEU cc_start: 0.9597 (mt) cc_final: 0.9313 (tp)
REVERT: B   20 LEU cc_start: 0.9527 (mt) cc_final: 0.9277 (mt)
REVERT: B   28 ARG cc_start: 0.6521 (tpm170) cc_final: 0.5091 (ttt-90)
REVERT: B   39 TRP cc_start: 0.8373 (m100) cc_final: 0.8104 (m100)
REVERT: B  209 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7429 (mtt180)
REVERT: B  214 LEU cc_start: 0.9674 (tp) cc_final: 0.9429 (tp)
REVERT: B  215 ILE cc_start: 0.9274 (pt) cc_final: 0.9029 (pt)
REVERT: B  218 ASN cc_start: 0.9179 (m110) cc_final: 0.8865 (m110)
REVERT: B  229 LEU cc_start: 0.9303 (tp) cc_final: 0.9030 (tt)
REVERT: B  240 ASP cc_start: 0.8860 (p0) cc_final: 0.8621 (p0)
REVERT: B  266 MET cc_start: 0.7159 (ttt) cc_final: 0.6865 (mtp)
REVERT: B  291 LEU cc_start: 0.8659 (tp) cc_final: 0.8377 (tp)
REVERT: B  292 LYS cc_start: 0.8731 (mttp) cc_final: 0.8195 (mtmt)
REVERT: B  294 ARG cc_start: 0.7404 (mtp180) cc_final: 0.6388 (mtp180)
REVERT: B  314 ILE cc_start: 0.9537 (mm) cc_final: 0.9258 (pt)
REVERT: B  319 PHE cc_start: 0.8907 (t80) cc_final: 0.8596 (t80)
REVERT: B  412 MET cc_start: 0.0658 (ptm) cc_final: -0.0032 (ptm)
REVERT: B  428 GLN cc_start: 0.4364 (OUTLIER) cc_final: 0.3400 (mp10)
REVERT: B  434 MET cc_start: 0.3834 (tmm) cc_final: 0.2688 (ptm)
REVERT: B  462 ASN cc_start: 0.8054 (m-40) cc_final: 0.7622 (p0)
REVERT: B  497 GLN cc_start: 0.5243 (pp30) cc_final: 0.4399 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0675
  time to fit residues: 10.1744
Evaluate side-chains
  95 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 38 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 68 optimal weight:    0.2980
   chunk 61 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 3 optimal weight:    0.5980
   chunk 102 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.4780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 428 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.152899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.106034 restraints weight = 13725.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.110832 restraints weight = 8881.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.114074 restraints weight = 6342.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.116293 restraints weight = 4888.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.117921 restraints weight = 3975.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6468
moved from start:          0.8272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9050  Z= 0.118
  Angle     :  0.634  11.548  12172  Z= 0.330
  Chirality :  0.044   0.215   1336
  Planarity :  0.004   0.040   1488
  Dihedral  :  4.063  17.511   1156
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.00 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.25), residues: 1050
  helix:  0.12 (0.20), residues: 596
  sheet: -1.07 (0.48), residues: 114
  loop : -1.17 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  23 
 TYR   0.026   0.001   TYR A 394 
 PHE   0.015   0.001   PHE B 121 
 TRP   0.028   0.002   TRP B 475 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9046)
  covalent geometry    : angle       0.63361 (12172)
  hydrogen bonds       : bond        0.04065 (  495)
  hydrogen bonds       : angle       5.38836 ( 1461)
  metal coordination   : bond        0.00062 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1251.01 seconds
wall clock time: 22 minutes 34.15 seconds (1354.15 seconds total)