Starting phenix.real_space_refine
on Thu Mar 13 06:43:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ext_28662/03_2025/8ext_28662.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ext_28662/03_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_28662/03_2025/8ext_28662.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ext_28662/03_2025/8ext_28662.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ext_28662/03_2025/8ext_28662.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ext_28662/03_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-5624/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: 7.62, per 1000 atoms: 0.86
  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: 2.24
  Conformation dependent library (CDL) restraints added in 937.2 milliseconds
  
  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: 0.83
  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: 2.53

  Time building geometry restraints manager: 2.64 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:             0.480
  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:             0.020
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     26.550
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.580
-------------------------------------------------------------------------------
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   9046  Z= 1.677
  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 

*********************** 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  : 0.518 
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: 0.1925
  time to fit residues: 39.3001
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  : 0.533 
-------------------------------------------------------------------------------
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 = 58)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.110560 restraints weight = 13181.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.114473 restraints weight = 8652.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.117199 restraints weight = 6251.133|
|-----------------------------------------------------------------------------|
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   9046  Z= 0.236
  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 B  39 
 HIS   0.015   0.002   HIS A 213 
 PHE   0.023   0.003   PHE A 248 
 TYR   0.038   0.002   TYR A 203 
 ARG   0.005   0.001   ARG A  28 

*********************** 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  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ILE cc_start: 0.9352 (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: 0.7585 (p90) cc_final: 0.7217 (p90)
REVERT: B   37 LYS cc_start: 0.8600 (mttt) cc_final: 0.7736 (mmtp)
REVERT: B  136 LEU cc_start: 0.8820 (mm) cc_final: 0.8561 (tp)
REVERT: B  202 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8466 (mm-30)
REVERT: B  209 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7647 (mtt180)
REVERT: B  214 LEU cc_start: 0.9662 (tp) cc_final: 0.9416 (tp)
REVERT: B  218 ASN cc_start: 0.9280 (m110) cc_final: 0.8965 (m110)
REVERT: B  221 SER cc_start: 0.8961 (m) cc_final: 0.8659 (p)
REVERT: B  240 ASP cc_start: 0.8518 (p0) cc_final: 0.8000 (p0)
REVERT: B  241 ASN cc_start: 0.9237 (m-40) cc_final: 0.8900 (m110)
REVERT: B  244 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8687 (mt-10)
REVERT: B  266 MET cc_start: 0.8020 (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: 0.1619
  time to fit residues: 27.6248
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  : 0.497 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 66 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 101 optimal weight:    8.9990
   chunk 36 optimal weight:    0.0050
   chunk 29 optimal weight:    8.9990
   chunk 14 optimal weight:    0.0870
   chunk 103 optimal weight:    3.9990
   chunk 60 optimal weight:    0.3980
   overall best weight:    1.0774
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4401 r_free = 0.4401 target = 0.144500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.103604 restraints weight = 12810.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.107175 restraints weight = 8771.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.109961 restraints weight = 6511.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6454
moved from start:          0.5452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9046  Z= 0.183
  Angle     :  0.619   7.046  12172  Z= 0.339
  Chirality :  0.042   0.148   1336
  Planarity :  0.004   0.039   1488
  Dihedral  :  5.098  21.747   1156
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.84 %
    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: -0.35 (0.25), residues: 1050
  helix:  0.32 (0.20), residues: 592
  sheet: -0.84 (0.50), residues: 120
  loop : -0.77 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 475 
 HIS   0.028   0.003   HIS B 239 
 PHE   0.032   0.002   PHE A 442 
 TYR   0.037   0.002   TYR A 203 
 ARG   0.005   0.001   ARG A 293 

*********************** 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
  124 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4898 (ttt) cc_final: 0.3168 (mmt)
REVERT: B   18 LEU cc_start: 0.9579 (mt) cc_final: 0.9165 (mt)
REVERT: B   22 PHE cc_start: 0.9350 (m-80) cc_final: 0.9005 (m-80)
REVERT: B  105 ILE cc_start: 0.8890 (mt) cc_final: 0.8647 (mm)
REVERT: B  132 LYS cc_start: 0.8198 (tmtt) cc_final: 0.7716 (tttm)
REVERT: B  136 LEU cc_start: 0.8911 (mm) cc_final: 0.8675 (tp)
REVERT: B  179 ILE cc_start: 0.8953 (mt) cc_final: 0.8715 (mt)
REVERT: B  202 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8474 (mm-30)
REVERT: B  209 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7625 (mtt180)
REVERT: B  214 LEU cc_start: 0.9718 (tp) cc_final: 0.9496 (tp)
REVERT: B  218 ASN cc_start: 0.9278 (m110) cc_final: 0.9010 (m110)
REVERT: B  240 ASP cc_start: 0.8346 (p0) cc_final: 0.7711 (p0)
REVERT: B  241 ASN cc_start: 0.9072 (m-40) cc_final: 0.8706 (m-40)
REVERT: B  244 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8583 (mt-10)
REVERT: B  246 ASP cc_start: 0.9255 (m-30) cc_final: 0.9052 (m-30)
REVERT: B  292 LYS cc_start: 0.8730 (mttt) cc_final: 0.8418 (mttm)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1472
  time to fit residues: 23.6021
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  : 0.456 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 69 optimal weight:    0.4980
   chunk 99 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 89 optimal weight:    9.9990
   chunk 96 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0270
   chunk 42 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.6038
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.147398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.106304 restraints weight = 12658.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.110021 restraints weight = 8639.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.112744 restraints weight = 6365.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6428
moved from start:          0.6109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9046  Z= 0.153
  Angle     :  0.585   6.703  12172  Z= 0.319
  Chirality :  0.042   0.183   1336
  Planarity :  0.004   0.039   1488
  Dihedral  :  4.747  17.514   1156
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.04 %
    Favored  : 96.75 %
  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: -0.48 (0.25), residues: 1050
  helix:  0.24 (0.20), residues: 596
  sheet: -0.94 (0.49), residues: 120
  loop : -0.86 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  39 
 HIS   0.009   0.001   HIS A 213 
 PHE   0.021   0.002   PHE A 442 
 TYR   0.033   0.001   TYR A 203 
 ARG   0.003   0.001   ARG B 411 

*********************** 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
  121 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5096 (ttt) cc_final: 0.3225 (mmt)
REVERT: B   14 PHE cc_start: 0.8571 (t80) cc_final: 0.8078 (t80)
REVERT: B   16 PHE cc_start: 0.8962 (t80) cc_final: 0.8730 (t80)
REVERT: B   18 LEU cc_start: 0.9585 (mt) cc_final: 0.9216 (mt)
REVERT: B   22 PHE cc_start: 0.9291 (m-80) cc_final: 0.8927 (m-80)
REVERT: B   37 LYS cc_start: 0.8388 (mttt) cc_final: 0.7495 (mmtm)
REVERT: B  202 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8435 (mm-30)
REVERT: B  209 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7659 (mtt180)
REVERT: B  216 ILE cc_start: 0.9619 (mt) cc_final: 0.9317 (mt)
REVERT: B  240 ASP cc_start: 0.8495 (p0) cc_final: 0.8183 (p0)
REVERT: B  244 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8521 (mt-10)
REVERT: B  292 LYS cc_start: 0.8423 (mttp) cc_final: 0.8172 (mtmm)
REVERT: B  368 MET cc_start: 0.5185 (mmm) cc_final: 0.4891 (mmt)
REVERT: B  412 MET cc_start: 0.1917 (ptt) cc_final: 0.1376 (ptt)
REVERT: B  428 GLN cc_start: 0.3698 (OUTLIER) cc_final: 0.3078 (mp10)
REVERT: B  494 MET cc_start: 0.7908 (ttp) cc_final: 0.7635 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1442
  time to fit residues: 22.8859
Evaluate side-chains
  98 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 92 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0020
   chunk 11 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0010
   chunk 8 optimal weight:    0.8980
   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 239 HIS
B 428 GLN
** B 498 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 = 0.4549 r_free = 0.4549 target = 0.149788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.107606 restraints weight = 13088.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.112253 restraints weight = 8118.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.115449 restraints weight = 5559.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6438
moved from start:          0.6566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9046  Z= 0.141
  Angle     :  0.603   9.783  12172  Z= 0.321
  Chirality :  0.043   0.162   1336
  Planarity :  0.004   0.040   1488
  Dihedral  :  4.499  17.244   1156
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.81 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.38 (0.25), residues: 1050
  helix:  0.35 (0.20), residues: 600
  sheet: -0.92 (0.48), residues: 122
  loop : -0.90 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 540 
 HIS   0.010   0.001   HIS B 213 
 PHE   0.017   0.001   PHE A 442 
 TYR   0.030   0.001   TYR B 203 
 ARG   0.002   0.000   ARG B  23 

*********************** 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  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5221 (ttt) cc_final: 0.3114 (mmt)
REVERT: B   14 PHE cc_start: 0.8616 (t80) cc_final: 0.8003 (t80)
REVERT: B   16 PHE cc_start: 0.8894 (t80) cc_final: 0.8631 (t80)
REVERT: B   18 LEU cc_start: 0.9569 (mt) cc_final: 0.9163 (mt)
REVERT: B   20 LEU cc_start: 0.9534 (mt) cc_final: 0.9332 (mt)
REVERT: B   22 PHE cc_start: 0.9272 (m-80) cc_final: 0.8901 (m-80)
REVERT: B   37 LYS cc_start: 0.8363 (mttt) cc_final: 0.7448 (mmtm)
REVERT: B   39 TRP cc_start: 0.8411 (m100) cc_final: 0.8184 (m100)
REVERT: B  171 ILE cc_start: 0.8745 (mt) cc_final: 0.8542 (tp)
REVERT: B  202 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8376 (mm-30)
REVERT: B  214 LEU cc_start: 0.9672 (tp) cc_final: 0.9398 (tp)
REVERT: B  218 ASN cc_start: 0.8984 (m110) cc_final: 0.8702 (m110)
REVERT: B  244 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8470 (mt-10)
REVERT: B  292 LYS cc_start: 0.8498 (mttp) cc_final: 0.8152 (mtmm)
REVERT: B  330 MET cc_start: 0.2166 (ppp) cc_final: 0.1817 (ppp)
REVERT: B  412 MET cc_start: 0.1663 (ptt) cc_final: 0.1167 (ptt)
REVERT: B  428 GLN cc_start: 0.4089 (OUTLIER) cc_final: 0.3242 (mp-120)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1415
  time to fit residues: 22.7947
Evaluate side-chains
  102 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 77 optimal weight:    0.0020
   chunk 101 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0370
   chunk 66 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 96 optimal weight:    6.9990
   chunk 102 optimal weight:   30.0000
   overall best weight:    0.6086
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.150309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.107966 restraints weight = 12745.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.112770 restraints weight = 7893.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.115961 restraints weight = 5408.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6444
moved from start:          0.6989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9046  Z= 0.143
  Angle     :  0.594  10.037  12172  Z= 0.319
  Chirality :  0.043   0.181   1336
  Planarity :  0.004   0.041   1488
  Dihedral  :  4.427  18.699   1156
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.62 %
    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: -0.40 (0.25), residues: 1050
  helix:  0.41 (0.20), residues: 598
  sheet: -0.67 (0.51), residues: 112
  loop : -1.16 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 540 
 HIS   0.009   0.001   HIS B 213 
 PHE   0.017   0.001   PHE B  12 
 TYR   0.018   0.001   TYR A 203 
 ARG   0.002   0.000   ARG A  23 

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

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5308 (ttt) cc_final: 0.3011 (mmt)
REVERT: B   14 PHE cc_start: 0.8544 (t80) cc_final: 0.8103 (t80)
REVERT: B   16 PHE cc_start: 0.8859 (t80) cc_final: 0.8647 (t80)
REVERT: B   18 LEU cc_start: 0.9598 (mt) cc_final: 0.9268 (mt)
REVERT: B   22 PHE cc_start: 0.9405 (m-80) cc_final: 0.9130 (m-80)
REVERT: B   37 LYS cc_start: 0.8257 (mttt) cc_final: 0.7355 (mmtm)
REVERT: B   39 TRP cc_start: 0.8563 (m100) cc_final: 0.7951 (m100)
REVERT: B  202 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8353 (mm-30)
REVERT: B  214 LEU cc_start: 0.9750 (tp) cc_final: 0.9521 (tp)
REVERT: B  216 ILE cc_start: 0.9594 (mt) cc_final: 0.9259 (mt)
REVERT: B  218 ASN cc_start: 0.9102 (m110) cc_final: 0.8885 (m110)
REVERT: B  244 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8424 (mt-10)
REVERT: B  292 LYS cc_start: 0.8605 (mttp) cc_final: 0.8257 (mtmm)
REVERT: B  412 MET cc_start: 0.1750 (ptt) cc_final: 0.1307 (ptt)
REVERT: B  428 GLN cc_start: 0.4243 (OUTLIER) cc_final: 0.3317 (mp-120)
  outliers start: 1
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1388
  time to fit residues: 21.7143
Evaluate side-chains
  101 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   overall best weight:    2.1786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 403 HIS
A 428 GLN
A 538 ASN
A 557 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.143253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.100489 restraints weight = 13077.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.104199 restraints weight = 8808.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.106738 restraints weight = 6471.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6560
moved from start:          0.7088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9046  Z= 0.209
  Angle     :  0.657   9.880  12172  Z= 0.351
  Chirality :  0.044   0.177   1336
  Planarity :  0.004   0.037   1488
  Dihedral  :  4.556  18.819   1156
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  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: -0.84 (0.25), residues: 1050
  helix:  0.01 (0.20), residues: 594
  sheet: -0.84 (0.50), residues: 112
  loop : -1.26 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 540 
 HIS   0.020   0.002   HIS B 213 
 PHE   0.030   0.002   PHE A  12 
 TYR   0.019   0.002   TYR A 203 
 ARG   0.004   0.001   ARG B 235 

*********************** 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
  116 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5109 (ttt) cc_final: 0.3167 (mmt)
REVERT: A   14 PHE cc_start: 0.8566 (t80) cc_final: 0.8141 (t80)
REVERT: A   16 PHE cc_start: 0.9004 (t80) cc_final: 0.8741 (t80)
REVERT: A   18 LEU cc_start: 0.9609 (mt) cc_final: 0.9282 (mt)
REVERT: A   20 LEU cc_start: 0.9610 (mt) cc_final: 0.9401 (mt)
REVERT: A   22 PHE cc_start: 0.9452 (m-80) cc_final: 0.9176 (m-80)
REVERT: A   37 LYS cc_start: 0.8284 (mttt) cc_final: 0.7366 (mmtm)
REVERT: A  214 LEU cc_start: 0.9701 (tp) cc_final: 0.9438 (tp)
REVERT: A  218 ASN cc_start: 0.9158 (m110) cc_final: 0.8829 (m110)
REVERT: A  235 ARG cc_start: 0.8431 (mmt180) cc_final: 0.7971 (mmm160)
REVERT: A  244 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8567 (mt-10)
REVERT: A  282 HIS cc_start: 0.7302 (m90) cc_final: 0.6867 (m170)
REVERT: A  291 LEU cc_start: 0.8713 (tp) cc_final: 0.8491 (tp)
REVERT: A  292 LYS cc_start: 0.8674 (mttp) cc_final: 0.8340 (mtmm)
REVERT: A  294 ARG cc_start: 0.7431 (mtp180) cc_final: 0.6451 (mtp180)
REVERT: A  314 ILE cc_start: 0.9553 (mm) cc_final: 0.9298 (pt)
REVERT: A  412 MET cc_start: 0.2072 (ptt) cc_final: 0.1804 (ptt)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.2315
  time to fit residues: 34.4850
Evaluate side-chains
  93 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0000
   chunk 81 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 60 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.146942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.104567 restraints weight = 12999.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.108327 restraints weight = 8751.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.110939 restraints weight = 6335.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6505
moved from start:          0.7339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9046  Z= 0.144
  Angle     :  0.590   7.963  12172  Z= 0.317
  Chirality :  0.043   0.172   1336
  Planarity :  0.003   0.038   1488
  Dihedral  :  4.339  17.341   1156
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 12.60
  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: -0.64 (0.25), residues: 1050
  helix:  0.28 (0.20), residues: 600
  sheet: -1.01 (0.50), residues: 114
  loop : -1.33 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 540 
 HIS   0.005   0.001   HIS B 213 
 PHE   0.030   0.001   PHE B 119 
 TYR   0.016   0.001   TYR B 203 
 ARG   0.002   0.000   ARG B 162 

*********************** 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
  110 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5353 (ttt) cc_final: 0.3309 (mmt)
REVERT: B   14 PHE cc_start: 0.8557 (t80) cc_final: 0.8236 (t80)
REVERT: B   16 PHE cc_start: 0.8929 (t80) cc_final: 0.8707 (t80)
REVERT: B   18 LEU cc_start: 0.9599 (mt) cc_final: 0.9315 (mt)
REVERT: B   20 LEU cc_start: 0.9514 (mt) cc_final: 0.9302 (mt)
REVERT: B   22 PHE cc_start: 0.9371 (m-80) cc_final: 0.9148 (m-80)
REVERT: B  214 LEU cc_start: 0.9733 (tp) cc_final: 0.9448 (tp)
REVERT: B  218 ASN cc_start: 0.9194 (m110) cc_final: 0.8902 (m110)
REVERT: B  240 ASP cc_start: 0.8930 (p0) cc_final: 0.8689 (p0)
REVERT: B  244 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8495 (mt-10)
REVERT: B  291 LEU cc_start: 0.8720 (tp) cc_final: 0.8476 (tp)
REVERT: B  292 LYS cc_start: 0.8693 (mttp) cc_final: 0.8334 (mtmm)
REVERT: B  294 ARG cc_start: 0.7513 (mtp180) cc_final: 0.6542 (mtp180)
REVERT: B  314 ILE cc_start: 0.9558 (mm) cc_final: 0.9276 (pt)
REVERT: B  412 MET cc_start: 0.1857 (ptt) cc_final: 0.1351 (ptt)
REVERT: B  428 GLN cc_start: 0.4306 (OUTLIER) cc_final: 0.3161 (mp-120)
  outliers start: 1
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1605
  time to fit residues: 23.2995
Evaluate side-chains
  93 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 98 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0670
   chunk 43 optimal weight:    7.9990
   chunk 102 optimal weight:    6.9990
   chunk 82 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.9320
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 HIS
B 428 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.146406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.104486 restraints weight = 13261.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.108214 restraints weight = 8856.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.110938 restraints weight = 6455.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6530
moved from start:          0.7597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   9046  Z= 0.150
  Angle     :  0.608   9.206  12172  Z= 0.325
  Chirality :  0.043   0.182   1336
  Planarity :  0.003   0.036   1488
  Dihedral  :  4.287  18.220   1156
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.41 %
    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: -0.75 (0.25), residues: 1050
  helix:  0.21 (0.20), residues: 592
  sheet: -0.95 (0.51), residues: 114
  loop : -1.42 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 475 
 HIS   0.011   0.001   HIS A 239 
 PHE   0.014   0.001   PHE A  12 
 TYR   0.016   0.002   TYR A 130 
 ARG   0.003   0.000   ARG A 247 

*********************** 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
  116 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5418 (ttt) cc_final: 0.3232 (mmt)
REVERT: B   13 CYS cc_start: 0.9461 (p) cc_final: 0.9108 (m)
REVERT: B   14 PHE cc_start: 0.8769 (t80) cc_final: 0.8229 (t80)
REVERT: B   16 PHE cc_start: 0.8969 (t80) cc_final: 0.8679 (t80)
REVERT: B   18 LEU cc_start: 0.9579 (mt) cc_final: 0.9246 (mt)
REVERT: B   20 LEU cc_start: 0.9559 (mt) cc_final: 0.9331 (mt)
REVERT: B   22 PHE cc_start: 0.9347 (m-80) cc_final: 0.9031 (m-80)
REVERT: B   28 ARG cc_start: 0.6499 (tpm170) cc_final: 0.5028 (ttt-90)
REVERT: B   37 LYS cc_start: 0.8282 (mttt) cc_final: 0.7400 (mmtp)
REVERT: B  126 LEU cc_start: 0.9376 (mp) cc_final: 0.9144 (mp)
REVERT: B  182 ILE cc_start: 0.8553 (mp) cc_final: 0.8338 (mp)
REVERT: B  214 LEU cc_start: 0.9741 (tp) cc_final: 0.9518 (tp)
REVERT: B  216 ILE cc_start: 0.9380 (mt) cc_final: 0.9034 (mt)
REVERT: B  218 ASN cc_start: 0.9217 (m110) cc_final: 0.8943 (m110)
REVERT: B  220 PHE cc_start: 0.8773 (m-80) cc_final: 0.8568 (m-80)
REVERT: B  240 ASP cc_start: 0.8921 (p0) cc_final: 0.8686 (p0)
REVERT: B  244 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8502 (mt-10)
REVERT: B  266 MET cc_start: 0.7368 (ttt) cc_final: 0.6828 (mtp)
REVERT: B  289 SER cc_start: 0.7863 (t) cc_final: 0.7267 (p)
REVERT: B  292 LYS cc_start: 0.8762 (mttp) cc_final: 0.8408 (mtmm)
REVERT: B  294 ARG cc_start: 0.7450 (mtp180) cc_final: 0.6452 (mtp180)
REVERT: B  314 ILE cc_start: 0.9527 (mm) cc_final: 0.9255 (pt)
REVERT: B  412 MET cc_start: 0.2065 (ptt) cc_final: 0.1589 (ptt)
REVERT: B  428 GLN cc_start: 0.4319 (OUTLIER) cc_final: 0.3206 (mp-120)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1902
  time to fit residues: 29.0468
Evaluate side-chains
  95 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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:    0.0020
   chunk 16 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 60 optimal weight:    0.6980
   chunk 79 optimal weight:    0.1980
   chunk 41 optimal weight:    3.9990
   chunk 36 optimal weight:    0.2980
   chunk 10 optimal weight:    4.9990
   chunk 100 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 102 optimal weight:   20.0000
   overall best weight:    0.3588
-------------------------------------------------------------------------------
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 241 ASN
B 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.148835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.105583 restraints weight = 12779.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.109572 restraints weight = 8541.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.112326 restraints weight = 6179.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6505
moved from start:          0.7873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   9046  Z= 0.145
  Angle     :  0.640  10.581  12172  Z= 0.328
  Chirality :  0.044   0.188   1336
  Planarity :  0.003   0.037   1488
  Dihedral  :  4.206  17.831   1156
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.41 %
    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: -0.71 (0.25), residues: 1050
  helix:  0.25 (0.20), residues: 592
  sheet: -0.97 (0.51), residues: 114
  loop : -1.39 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.029   0.002   PHE B 119 
 TYR   0.022   0.001   TYR B 394 
 ARG   0.003   0.000   ARG A  23 

********************** 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
  111 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.5409 (ttt) cc_final: 0.3381 (mmt)
REVERT: B   14 PHE cc_start: 0.8854 (t80) cc_final: 0.8444 (t80)
REVERT: B   16 PHE cc_start: 0.8943 (t80) cc_final: 0.8668 (t80)
REVERT: B   18 LEU cc_start: 0.9561 (mt) cc_final: 0.9217 (mt)
REVERT: B   20 LEU cc_start: 0.9483 (mt) cc_final: 0.9248 (mt)
REVERT: B   22 PHE cc_start: 0.9304 (m-80) cc_final: 0.8987 (m-80)
REVERT: B   28 ARG cc_start: 0.6595 (tpm170) cc_final: 0.5272 (ttt-90)
REVERT: B  214 LEU cc_start: 0.9745 (tp) cc_final: 0.9504 (tp)
REVERT: B  216 ILE cc_start: 0.9418 (mt) cc_final: 0.9068 (mt)
REVERT: B  218 ASN cc_start: 0.9238 (m110) cc_final: 0.9003 (m110)
REVERT: B  220 PHE cc_start: 0.8708 (m-80) cc_final: 0.8491 (m-80)
REVERT: B  236 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8640 (mmmt)
REVERT: B  240 ASP cc_start: 0.8878 (p0) cc_final: 0.8651 (p0)
REVERT: B  244 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8479 (mt-10)
REVERT: B  266 MET cc_start: 0.6992 (ttt) cc_final: 0.6775 (mtp)
REVERT: B  289 SER cc_start: 0.7900 (t) cc_final: 0.7315 (p)
REVERT: B  292 LYS cc_start: 0.8786 (mttp) cc_final: 0.8406 (mtmm)
REVERT: B  294 ARG cc_start: 0.7430 (mtp180) cc_final: 0.6454 (mtp180)
REVERT: B  314 ILE cc_start: 0.9516 (mm) cc_final: 0.9233 (pt)
REVERT: B  412 MET cc_start: 0.2125 (ptt) cc_final: 0.1672 (ptt)
REVERT: B  428 GLN cc_start: 0.4367 (OUTLIER) cc_final: 0.3271 (mp-120)
REVERT: B  462 ASN cc_start: 0.8230 (m-40) cc_final: 0.7837 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1560
  time to fit residues: 22.2553
Evaluate side-chains
  96 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0070
   chunk 71 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 85 optimal weight:    0.1980
   chunk 52 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.4198
-------------------------------------------------------------------------------
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 282 HIS
B 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.148791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.105814 restraints weight = 12963.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.109874 restraints weight = 8545.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.112736 restraints weight = 6156.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6504
moved from start:          0.8054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   9046  Z= 0.148
  Angle     :  0.628  10.366  12172  Z= 0.328
  Chirality :  0.044   0.186   1336
  Planarity :  0.003   0.037   1488
  Dihedral  :  4.116  17.906   1156
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.20 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.73 (0.25), residues: 1050
  helix:  0.18 (0.20), residues: 592
  sheet: -1.06 (0.51), residues: 114
  loop : -1.25 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 540 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.019   0.001   PHE B 187 
 TYR   0.013   0.001   TYR B 203 
 ARG   0.003   0.000   ARG B  23 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2414.46 seconds
wall clock time: 44 minutes 22.22 seconds (2662.22 seconds total)