Starting phenix.real_space_refine
on Mon May 12 03:52:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ext_28662/05_2025/8ext_28662.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ext_28662/05_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_28662/05_2025/8ext_28662.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ext_28662/05_2025/8ext_28662.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ext_28662/05_2025/8ext_28662.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ext_28662/05_2025/8ext_28662.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'ASP: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: 7.89, per 1000 atoms: 0.89
  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: 2.62
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  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: 0.96
  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: 2.38

  Time building geometry restraints manager: 2.94 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: 0.04
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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     26.790
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.460
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (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
 TRP   0.055   0.011   TRP B 540 
 HIS   0.014   0.003   HIS B 213 
 PHE   0.045   0.006   PHE B 151 
 TYR   0.056   0.010   TYR B 203 
 ARG   0.004   0.001   ARG B 384 

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

*********************** 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  : 0.495 
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: 0.1900
  time to fit residues: 38.6774
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  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 61 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   overall best weight:    1.6786
-------------------------------------------------------------------------------
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 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4477 r_free = 0.4477 target = 0.154134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.110559 restraints weight = 13181.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.114481 restraints weight = 8650.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.117186 restraints weight = 6247.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6456
moved from start:          0.4506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9050  Z= 0.188
  Angle     :  0.749   7.072  12172  Z= 0.408
  Chirality :  0.047   0.220   1336
  Planarity :  0.005   0.050   1488
  Dihedral  :  5.382  20.345   1156
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.64 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.25), residues: 1050
  helix:  0.70 (0.19), residues: 584
  sheet: -0.49 (0.48), residues: 120
  loop : -0.55 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  39 
 HIS   0.015   0.002   HIS A 213 
 PHE   0.023   0.003   PHE B 248 
 TYR   0.038   0.002   TYR B 203 
 ARG   0.005   0.001   ARG A  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06594 (  495)
  hydrogen bonds       : angle       6.05146 ( 1461)
  metal coordination   : bond        0.00244 (    4)
  covalent geometry    : bond        0.00365 ( 9046)
  covalent geometry    : angle       0.74890 (12172)

*********************** 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
  135 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ILE cc_start: 0.9351 (mt) cc_final: 0.9066 (mt)
REVERT: B   18 LEU cc_start: 0.9455 (mt) cc_final: 0.9193 (mt)
REVERT: B   36 TYR cc_start: 0.7583 (p90) cc_final: 0.7216 (p90)
REVERT: B   37 LYS cc_start: 0.8600 (mttt) cc_final: 0.7735 (mmtp)
REVERT: B  136 LEU cc_start: 0.8821 (mm) cc_final: 0.8561 (tp)
REVERT: B  202 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8467 (mm-30)
REVERT: B  209 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7648 (mtt180)
REVERT: B  214 LEU cc_start: 0.9662 (tp) cc_final: 0.9415 (tp)
REVERT: B  218 ASN cc_start: 0.9281 (m110) cc_final: 0.8966 (m110)
REVERT: B  221 SER cc_start: 0.8962 (m) cc_final: 0.8660 (p)
REVERT: B  240 ASP cc_start: 0.8518 (p0) cc_final: 0.7999 (p0)
REVERT: B  241 ASN cc_start: 0.9236 (m-40) cc_final: 0.8899 (m110)
REVERT: B  244 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8688 (mt-10)
REVERT: B  266 MET cc_start: 0.8019 (tmm) cc_final: 0.7691 (tmm)
REVERT: B  296 ILE cc_start: 0.9430 (mm) cc_final: 0.9213 (mm)
REVERT: B  330 MET cc_start: 0.2929 (ppp) cc_final: 0.2721 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1563
  time to fit residues: 26.7122
Evaluate side-chains
  104 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 101 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0070
   chunk 29 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 103 optimal weight:    0.0670
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.5536
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 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 = 0.4536 r_free = 0.4536 target = 0.149437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.107766 restraints weight = 12849.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.112573 restraints weight = 7813.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.115900 restraints weight = 5322.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6434
moved from start:          0.5579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9050  Z= 0.134
  Angle     :  0.606   6.916  12172  Z= 0.333
  Chirality :  0.042   0.146   1336
  Planarity :  0.004   0.037   1488
  Dihedral  :  5.050  22.467   1156
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.43 %
    Favored  : 97.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.25), residues: 1050
  helix:  0.34 (0.20), residues: 592
  sheet: -0.73 (0.50), residues: 120
  loop : -0.73 (0.36), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  39 
 HIS   0.025   0.002   HIS B 239 
 PHE   0.028   0.002   PHE A 442 
 TYR   0.036   0.002   TYR B 203 
 ARG   0.004   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04958 (  495)
  hydrogen bonds       : angle       5.63245 ( 1461)
  metal coordination   : bond        0.00082 (    4)
  covalent geometry    : bond        0.00270 ( 9046)
  covalent geometry    : angle       0.60631 (12172)

*********************** 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
  128 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5117 (ttt) cc_final: 0.3269 (mmt)
REVERT: B   18 LEU cc_start: 0.9573 (mt) cc_final: 0.9113 (mt)
REVERT: B   22 PHE cc_start: 0.9286 (m-80) cc_final: 0.8878 (m-80)
REVERT: B  105 ILE cc_start: 0.8868 (mt) cc_final: 0.8614 (mm)
REVERT: B  181 LEU cc_start: 0.8188 (mp) cc_final: 0.7984 (mp)
REVERT: B  202 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8391 (mm-30)
REVERT: B  209 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7712 (mtt180)
REVERT: B  214 LEU cc_start: 0.9689 (tp) cc_final: 0.9456 (tp)
REVERT: B  218 ASN cc_start: 0.9260 (m110) cc_final: 0.8977 (m110)
REVERT: B  244 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8504 (mt-10)
REVERT: B  292 LYS cc_start: 0.8725 (mttt) cc_final: 0.8424 (mttm)
REVERT: B  319 PHE cc_start: 0.9051 (t80) cc_final: 0.8622 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1433
  time to fit residues: 23.4490
Evaluate side-chains
  105 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 69 optimal weight:    0.1980
   chunk 99 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 89 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0060
   chunk 42 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.5796
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.149104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.106660 restraints weight = 12529.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.110516 restraints weight = 8516.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.113363 restraints weight = 6275.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          0.6199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9050  Z= 0.127
  Angle     :  0.594   6.767  12172  Z= 0.326
  Chirality :  0.042   0.174   1336
  Planarity :  0.004   0.038   1488
  Dihedral  :  4.796  17.445   1156
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.25), residues: 1050
  helix:  0.23 (0.19), residues: 600
  sheet: -0.89 (0.49), residues: 120
  loop : -0.85 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  39 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.020   0.002   PHE A 442 
 TYR   0.032   0.001   TYR B 203 
 ARG   0.003   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04669 (  495)
  hydrogen bonds       : angle       5.54121 ( 1461)
  metal coordination   : bond        0.00054 (    4)
  covalent geometry    : bond        0.00251 ( 9046)
  covalent geometry    : angle       0.59409 (12172)

*********************** 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
  118 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5071 (ttt) cc_final: 0.3193 (mmt)
REVERT: A   12 PHE cc_start: 0.9196 (t80) cc_final: 0.8511 (t80)
REVERT: A   14 PHE cc_start: 0.8551 (t80) cc_final: 0.8134 (t80)
REVERT: A   16 PHE cc_start: 0.8900 (t80) cc_final: 0.8693 (t80)
REVERT: A   18 LEU cc_start: 0.9591 (mt) cc_final: 0.9158 (mt)
REVERT: A   22 PHE cc_start: 0.9309 (m-80) cc_final: 0.8954 (m-80)
REVERT: A   37 LYS cc_start: 0.8365 (mttt) cc_final: 0.7479 (mmtm)
REVERT: A   39 TRP cc_start: 0.8779 (m100) cc_final: 0.8546 (m100)
REVERT: A  105 ILE cc_start: 0.8725 (mt) cc_final: 0.8525 (mm)
REVERT: A  202 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8486 (mm-30)
REVERT: A  209 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7402 (mtt180)
REVERT: A  216 ILE cc_start: 0.9605 (mt) cc_final: 0.9352 (mt)
REVERT: A  224 MET cc_start: 0.8305 (mmm) cc_final: 0.7795 (tpt)
REVERT: A  229 LEU cc_start: 0.9509 (mt) cc_final: 0.9231 (pp)
REVERT: A  230 VAL cc_start: 0.8539 (m) cc_final: 0.8269 (m)
REVERT: A  244 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8415 (mt-10)
REVERT: A  292 LYS cc_start: 0.8392 (mttp) cc_final: 0.8148 (mtmm)
REVERT: A  494 MET cc_start: 0.7958 (ttp) cc_final: 0.7736 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1425
  time to fit residues: 21.8737
Evaluate side-chains
  101 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 42 optimal weight:    0.0270
   chunk 92 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 61 optimal weight:    0.1980
   chunk 87 optimal weight:    0.0270
   chunk 11 optimal weight:    8.9990
   chunk 55 optimal weight:    0.0470
   chunk 56 optimal weight:    0.4980
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.0994
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 239 HIS
** 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 = 0.4479 r_free = 0.4479 target = 0.151930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.108407 restraints weight = 12874.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.112361 restraints weight = 8636.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.115212 restraints weight = 6309.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6387
moved from start:          0.6666

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     :  0.624  10.497  12172  Z= 0.329
  Chirality :  0.042   0.153   1336
  Planarity :  0.004   0.040   1488
  Dihedral  :  4.663  16.471   1156
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.22 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.25), residues: 1050
  helix:  0.31 (0.19), residues: 600
  sheet: -0.97 (0.49), residues: 120
  loop : -0.95 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 475 
 HIS   0.009   0.001   HIS A 213 
 PHE   0.020   0.001   PHE B 442 
 TYR   0.029   0.001   TYR A 203 
 ARG   0.002   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04338 (  495)
  hydrogen bonds       : angle       5.35796 ( 1461)
  metal coordination   : bond        0.00012 (    4)
  covalent geometry    : bond        0.00232 ( 9046)
  covalent geometry    : angle       0.62393 (12172)

*********************** 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
  122 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4981 (ttt) cc_final: 0.3242 (mmt)
REVERT: B   14 PHE cc_start: 0.8658 (t80) cc_final: 0.8067 (t80)
REVERT: B   16 PHE cc_start: 0.8943 (t80) cc_final: 0.8688 (t80)
REVERT: B   18 LEU cc_start: 0.9566 (mt) cc_final: 0.9162 (mt)
REVERT: B   20 LEU cc_start: 0.9550 (mt) cc_final: 0.9342 (mt)
REVERT: B   22 PHE cc_start: 0.9286 (m-80) cc_final: 0.8935 (m-80)
REVERT: B   37 LYS cc_start: 0.8331 (mttt) cc_final: 0.7406 (mmtm)
REVERT: B   39 TRP cc_start: 0.8656 (m100) cc_final: 0.8082 (m100)
REVERT: B  202 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8409 (mm-30)
REVERT: B  209 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7408 (mtt180)
REVERT: B  214 LEU cc_start: 0.9671 (tp) cc_final: 0.9446 (tp)
REVERT: B  224 MET cc_start: 0.8438 (mmm) cc_final: 0.8025 (tpt)
REVERT: B  235 ARG cc_start: 0.8185 (mmt180) cc_final: 0.7570 (mmm160)
REVERT: B  244 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8329 (mt-10)
REVERT: B  292 LYS cc_start: 0.8305 (mttp) cc_final: 0.8042 (mtmm)
REVERT: B  330 MET cc_start: 0.2253 (ppp) cc_final: 0.1892 (ppp)
REVERT: B  412 MET cc_start: 0.1384 (ptm) cc_final: 0.1135 (ptm)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1428
  time to fit residues: 22.6586
Evaluate side-chains
  98 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0030
   chunk 101 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 79 optimal weight:    0.1980
   chunk 66 optimal weight:    0.2980
   chunk 98 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 96 optimal weight:    4.9990
   chunk 102 optimal weight:   30.0000
   overall best weight:    1.0994
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 538 ASN
B 557 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.150149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.107772 restraints weight = 12770.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.112570 restraints weight = 7964.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.115884 restraints weight = 5468.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6452
moved from start:          0.6978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9050  Z= 0.124
  Angle     :  0.603  10.394  12172  Z= 0.320
  Chirality :  0.042   0.158   1336
  Planarity :  0.004   0.039   1488
  Dihedral  :  4.479  17.065   1156
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.25), residues: 1050
  helix:  0.45 (0.19), residues: 602
  sheet: -1.15 (0.47), residues: 120
  loop : -1.14 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 475 
 HIS   0.008   0.001   HIS B 213 
 PHE   0.013   0.001   PHE A 442 
 TYR   0.020   0.002   TYR B 203 
 ARG   0.002   0.000   ARG B 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04185 (  495)
  hydrogen bonds       : angle       5.38929 ( 1461)
  metal coordination   : bond        0.00119 (    4)
  covalent geometry    : bond        0.00261 ( 9046)
  covalent geometry    : angle       0.60284 (12172)

*********************** 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
  117 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5362 (ttt) cc_final: 0.3163 (mmt)
REVERT: B   16 PHE cc_start: 0.8898 (t80) cc_final: 0.8648 (t80)
REVERT: B   18 LEU cc_start: 0.9564 (mt) cc_final: 0.9341 (mt)
REVERT: B   22 PHE cc_start: 0.9438 (m-80) cc_final: 0.9155 (m-80)
REVERT: B   37 LYS cc_start: 0.8312 (mttt) cc_final: 0.7409 (mmtm)
REVERT: B   39 TRP cc_start: 0.8702 (m100) cc_final: 0.8152 (m100)
REVERT: B  214 LEU cc_start: 0.9710 (tp) cc_final: 0.9510 (tp)
REVERT: B  218 ASN cc_start: 0.9071 (m110) cc_final: 0.8834 (m110)
REVERT: B  224 MET cc_start: 0.8415 (mmm) cc_final: 0.8134 (tpt)
REVERT: B  235 ARG cc_start: 0.8428 (mmt180) cc_final: 0.7781 (mmm160)
REVERT: B  244 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8298 (mt-10)
REVERT: B  292 LYS cc_start: 0.8478 (mttp) cc_final: 0.8147 (mtmm)
REVERT: B  412 MET cc_start: 0.1646 (ptm) cc_final: 0.1352 (ptm)
REVERT: B  434 MET cc_start: 0.4155 (tmm) cc_final: 0.2872 (ptm)
REVERT: B  435 GLN cc_start: 0.5388 (tm-30) cc_final: 0.4702 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1417
  time to fit residues: 21.5798
Evaluate side-chains
  99 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0060
   chunk 76 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 79 optimal weight:    0.0970
   chunk 48 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 93 optimal weight:    3.9990
   overall best weight:    0.5194
-------------------------------------------------------------------------------
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 239 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.149779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.107426 restraints weight = 13009.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.111176 restraints weight = 8730.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.113991 restraints weight = 6388.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6435
moved from start:          0.7299

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= 0.122
  Angle     :  0.607   8.500  12172  Z= 0.326
  Chirality :  0.044   0.199   1336
  Planarity :  0.004   0.039   1488
  Dihedral  :  4.395  16.371   1156
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.25), residues: 1050
  helix:  0.44 (0.20), residues: 600
  sheet: -1.26 (0.48), residues: 122
  loop : -1.09 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 475 
 HIS   0.007   0.001   HIS A 239 
 PHE   0.032   0.001   PHE A  12 
 TYR   0.017   0.001   TYR B 203 
 ARG   0.003   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04302 (  495)
  hydrogen bonds       : angle       5.35457 ( 1461)
  metal coordination   : bond        0.00114 (    4)
  covalent geometry    : bond        0.00248 ( 9046)
  covalent geometry    : angle       0.60688 (12172)

*********************** 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: 0
    poor density    : 118
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5426 (ttt) cc_final: 0.3413 (mmt)
REVERT: B   20 LEU cc_start: 0.9566 (mt) cc_final: 0.9332 (mt)
REVERT: B   22 PHE cc_start: 0.9383 (m-80) cc_final: 0.9133 (m-80)
REVERT: B   37 LYS cc_start: 0.8065 (mttt) cc_final: 0.7103 (mmtm)
REVERT: B   39 TRP cc_start: 0.8558 (m100) cc_final: 0.8134 (m100)
REVERT: B  214 LEU cc_start: 0.9673 (tp) cc_final: 0.9425 (tp)
REVERT: B  218 ASN cc_start: 0.9087 (m110) cc_final: 0.8748 (m110)
REVERT: B  224 MET cc_start: 0.8504 (mmm) cc_final: 0.8225 (tpt)
REVERT: B  235 ARG cc_start: 0.8460 (mmt180) cc_final: 0.8199 (mmm160)
REVERT: B  244 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8349 (mt-10)
REVERT: B  266 MET cc_start: 0.7408 (ttt) cc_final: 0.6868 (mtp)
REVERT: B  289 SER cc_start: 0.7849 (t) cc_final: 0.7260 (p)
REVERT: B  292 LYS cc_start: 0.8523 (mttp) cc_final: 0.8218 (mtmm)
REVERT: B  314 ILE cc_start: 0.9521 (mm) cc_final: 0.9238 (pt)
REVERT: B  394 TYR cc_start: 0.6584 (m-10) cc_final: 0.6306 (m-10)
REVERT: B  412 MET cc_start: 0.1621 (ptm) cc_final: 0.1366 (ptm)
REVERT: B  434 MET cc_start: 0.3962 (tmm) cc_final: 0.2706 (ptm)
REVERT: B  435 GLN cc_start: 0.5256 (tm-30) cc_final: 0.4667 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1465
  time to fit residues: 22.2991
Evaluate side-chains
  97 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 4 optimal weight:    0.5980
   chunk 33 optimal weight:    0.3980
   chunk 81 optimal weight:    2.9990
   chunk 37 optimal weight:   10.0000
   chunk 60 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 38 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.6982
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 282 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.149283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.105579 restraints weight = 13114.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.109448 restraints weight = 8690.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.112213 restraints weight = 6324.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.7515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9050  Z= 0.114
  Angle     :  0.584   8.469  12172  Z= 0.315
  Chirality :  0.042   0.169   1336
  Planarity :  0.003   0.038   1488
  Dihedral  :  4.218  16.596   1156
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.25), residues: 1050
  helix:  0.34 (0.19), residues: 596
  sheet: -1.17 (0.50), residues: 114
  loop : -1.24 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 174 
 HIS   0.003   0.001   HIS B 239 
 PHE   0.029   0.002   PHE B 119 
 TYR   0.017   0.001   TYR B 203 
 ARG   0.002   0.000   ARG B 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04073 (  495)
  hydrogen bonds       : angle       5.35373 ( 1461)
  metal coordination   : bond        0.00089 (    4)
  covalent geometry    : bond        0.00234 ( 9046)
  covalent geometry    : angle       0.58400 (12172)

*********************** 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
  114 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5362 (ttt) cc_final: 0.3140 (mmt)
REVERT: A   13 CYS cc_start: 0.9400 (p) cc_final: 0.9149 (m)
REVERT: A   16 PHE cc_start: 0.8827 (t80) cc_final: 0.8573 (t80)
REVERT: A   20 LEU cc_start: 0.9518 (mt) cc_final: 0.9303 (mt)
REVERT: A   22 PHE cc_start: 0.9306 (m-80) cc_final: 0.9090 (m-80)
REVERT: A   28 ARG cc_start: 0.6313 (tpm170) cc_final: 0.4869 (ttt-90)
REVERT: A   39 TRP cc_start: 0.8587 (m100) cc_final: 0.8101 (m100)
REVERT: A  214 LEU cc_start: 0.9655 (tp) cc_final: 0.9384 (tp)
REVERT: A  218 ASN cc_start: 0.9104 (m110) cc_final: 0.8782 (m110)
REVERT: A  235 ARG cc_start: 0.8331 (mmt180) cc_final: 0.7695 (mmm160)
REVERT: A  240 ASP cc_start: 0.8828 (p0) cc_final: 0.8597 (p0)
REVERT: A  244 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8333 (mt-10)
REVERT: A  266 MET cc_start: 0.7325 (ttt) cc_final: 0.6785 (mtp)
REVERT: A  289 SER cc_start: 0.7828 (t) cc_final: 0.7229 (p)
REVERT: A  292 LYS cc_start: 0.8672 (mttp) cc_final: 0.8348 (mtmm)
REVERT: A  294 ARG cc_start: 0.7533 (mtp180) cc_final: 0.6564 (mtp180)
REVERT: A  314 ILE cc_start: 0.9495 (mm) cc_final: 0.9208 (pt)
REVERT: A  321 LEU cc_start: 0.9509 (mm) cc_final: 0.9296 (mm)
REVERT: A  412 MET cc_start: 0.1882 (ptm) cc_final: 0.1668 (ptm)
REVERT: A  434 MET cc_start: 0.3969 (tmm) cc_final: 0.2710 (ptm)
REVERT: A  435 GLN cc_start: 0.5391 (tm-30) cc_final: 0.4795 (mp10)
REVERT: A  494 MET cc_start: 0.7529 (ptt) cc_final: 0.7057 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1461
  time to fit residues: 21.4614
Evaluate side-chains
  99 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 64 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0470
   chunk 43 optimal weight:    5.9990
   chunk 102 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0370
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.7560
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.148965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.105955 restraints weight = 13213.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.109964 restraints weight = 8723.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.112587 restraints weight = 6314.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.7718

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     :  0.628  10.295  12172  Z= 0.329
  Chirality :  0.043   0.225   1336
  Planarity :  0.003   0.037   1488
  Dihedral  :  4.172  17.001   1156
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.25), residues: 1050
  helix:  0.29 (0.20), residues: 598
  sheet: -1.46 (0.48), residues: 114
  loop : -1.22 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 174 
 HIS   0.005   0.001   HIS B 282 
 PHE   0.016   0.001   PHE A  12 
 TYR   0.017   0.001   TYR A 203 
 ARG   0.002   0.000   ARG B 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04106 (  495)
  hydrogen bonds       : angle       5.37673 ( 1461)
  metal coordination   : bond        0.00462 (    4)
  covalent geometry    : bond        0.00249 ( 9046)
  covalent geometry    : angle       0.62846 (12172)

*********************** 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
  111 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5230 (ttt) cc_final: 0.3077 (mmt)
REVERT: B   13 CYS cc_start: 0.9482 (p) cc_final: 0.9159 (m)
REVERT: B   16 PHE cc_start: 0.8895 (t80) cc_final: 0.8635 (t80)
REVERT: B   20 LEU cc_start: 0.9540 (mt) cc_final: 0.9332 (mt)
REVERT: B   22 PHE cc_start: 0.9362 (m-80) cc_final: 0.9144 (m-80)
REVERT: B   28 ARG cc_start: 0.6545 (tpm170) cc_final: 0.5199 (ttt-90)
REVERT: B   39 TRP cc_start: 0.8615 (m100) cc_final: 0.8106 (m100)
REVERT: B  214 LEU cc_start: 0.9661 (tp) cc_final: 0.9425 (tp)
REVERT: B  218 ASN cc_start: 0.9190 (m110) cc_final: 0.8908 (m110)
REVERT: B  235 ARG cc_start: 0.8550 (mmt180) cc_final: 0.7960 (mmm160)
REVERT: B  240 ASP cc_start: 0.8836 (p0) cc_final: 0.8126 (p0)
REVERT: B  241 ASN cc_start: 0.8987 (m110) cc_final: 0.8774 (m-40)
REVERT: B  244 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8206 (mp0)
REVERT: B  266 MET cc_start: 0.7355 (ttt) cc_final: 0.6819 (mtp)
REVERT: B  289 SER cc_start: 0.7812 (t) cc_final: 0.7225 (p)
REVERT: B  292 LYS cc_start: 0.8740 (mttp) cc_final: 0.8379 (mtmm)
REVERT: B  294 ARG cc_start: 0.7525 (mtp180) cc_final: 0.6566 (mtp180)
REVERT: B  314 ILE cc_start: 0.9499 (mm) cc_final: 0.9220 (pt)
REVERT: B  434 MET cc_start: 0.4042 (tmm) cc_final: 0.2784 (ptm)
REVERT: B  435 GLN cc_start: 0.5158 (tm-30) cc_final: 0.4624 (mp10)
REVERT: B  494 MET cc_start: 0.7666 (ptt) cc_final: 0.7146 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1552
  time to fit residues: 22.0451
Evaluate side-chains
  96 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 54 optimal weight:    0.0000
   chunk 16 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 102 optimal weight:    4.9990
   overall best weight:    0.6784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.149438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.106418 restraints weight = 13006.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.110371 restraints weight = 8628.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.113126 restraints weight = 6272.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6482
moved from start:          0.7882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9050  Z= 0.117
  Angle     :  0.613   8.462  12172  Z= 0.325
  Chirality :  0.044   0.229   1336
  Planarity :  0.003   0.039   1488
  Dihedral  :  4.257  25.949   1156
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.25), residues: 1050
  helix:  0.32 (0.20), residues: 600
  sheet: -1.49 (0.48), residues: 112
  loop : -1.23 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 475 
 HIS   0.004   0.001   HIS B 282 
 PHE   0.030   0.002   PHE A 119 
 TYR   0.016   0.001   TYR B 203 
 ARG   0.002   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03972 (  495)
  hydrogen bonds       : angle       5.39028 ( 1461)
  metal coordination   : bond        0.00074 (    4)
  covalent geometry    : bond        0.00244 ( 9046)
  covalent geometry    : angle       0.61282 (12172)

********************** 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
  113 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5234 (ttt) cc_final: 0.3158 (mmt)
REVERT: B   13 CYS cc_start: 0.9499 (p) cc_final: 0.9148 (m)
REVERT: B   16 PHE cc_start: 0.8922 (t80) cc_final: 0.8653 (t80)
REVERT: B   20 LEU cc_start: 0.9501 (mt) cc_final: 0.9297 (mt)
REVERT: B   22 PHE cc_start: 0.9371 (m-80) cc_final: 0.9108 (m-80)
REVERT: B   28 ARG cc_start: 0.6458 (tpm170) cc_final: 0.5104 (ttt-90)
REVERT: B   39 TRP cc_start: 0.8621 (m100) cc_final: 0.8098 (m100)
REVERT: B  214 LEU cc_start: 0.9689 (tp) cc_final: 0.9449 (tp)
REVERT: B  218 ASN cc_start: 0.9167 (m110) cc_final: 0.8898 (m110)
REVERT: B  235 ARG cc_start: 0.8560 (mmt180) cc_final: 0.8161 (mmm160)
REVERT: B  240 ASP cc_start: 0.8792 (p0) cc_final: 0.8154 (p0)
REVERT: B  244 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8242 (mp0)
REVERT: B  266 MET cc_start: 0.7426 (ttt) cc_final: 0.6796 (mtp)
REVERT: B  289 SER cc_start: 0.7925 (t) cc_final: 0.7491 (p)
REVERT: B  292 LYS cc_start: 0.8794 (mttp) cc_final: 0.8490 (mtmm)
REVERT: B  294 ARG cc_start: 0.7429 (mtp180) cc_final: 0.6488 (mtp180)
REVERT: B  314 ILE cc_start: 0.9504 (mm) cc_final: 0.9226 (pt)
REVERT: B  434 MET cc_start: 0.3987 (tmm) cc_final: 0.2823 (ptm)
REVERT: B  494 MET cc_start: 0.7514 (ptt) cc_final: 0.7026 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1472
  time to fit residues: 21.4628
Evaluate side-chains
  94 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 24 optimal weight:    0.0470
   chunk 20 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.6878
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 239 HIS
B 241 ASN
** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.149342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.107043 restraints weight = 13075.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.110949 restraints weight = 8657.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.113744 restraints weight = 6292.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6471
moved from start:          0.8130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   9050  Z= 0.117
  Angle     :  0.641  11.019  12172  Z= 0.335
  Chirality :  0.044   0.213   1336
  Planarity :  0.003   0.039   1488
  Dihedral  :  4.158  17.112   1156
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.25), residues: 1050
  helix:  0.24 (0.20), residues: 600
  sheet: -1.52 (0.48), residues: 114
  loop : -1.30 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 475 
 HIS   0.012   0.001   HIS A 239 
 PHE   0.023   0.001   PHE B 317 
 TYR   0.015   0.001   TYR B 203 
 ARG   0.002   0.000   ARG A 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  495)
  hydrogen bonds       : angle       5.39894 ( 1461)
  metal coordination   : bond        0.00050 (    4)
  covalent geometry    : bond        0.00245 ( 9046)
  covalent geometry    : angle       0.64109 (12172)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2385.43 seconds
wall clock time: 42 minutes 58.46 seconds (2578.46 seconds total)