Starting phenix.real_space_refine
on Thu Mar 13 21:28:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exq_28659/03_2025/8exq_28659.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exq_28659/03_2025/8exq_28659.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exq_28659/03_2025/8exq_28659.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exq_28659/03_2025/8exq_28659.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exq_28659/03_2025/8exq_28659.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exq_28659/03_2025/8exq_28659.cif"
  }
  resolution = 4.9
  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=   0.003 sd=   0.045
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    6112      2.51       5
     N    1534      2.21       5
     O    1618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 61 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9304
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 554, 4651
          Classifications: {'peptide': 554}
          Link IDs: {'PTRANS': 11, 'TRANS': 542}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 554, 4651
          Classifications: {'peptide': 554}
          Link IDs: {'PTRANS': 11, 'TRANS': 542}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.77, per 1000 atoms: 0.62
  Number of scatterers: 9304
  At special positions: 0
  Unit cell: (73.9927, 108.282, 135.353, 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    1618      8.00
     N    1534      7.00
     C    6112      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: 2.34
  Conformation dependent library (CDL) restraints added in 999.3 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 "


  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      57.5% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 31
    Processing helix  chain 'B' and resid 35 through 38
    Processing helix  chain 'B' and resid 39 through 46
    Processing helix  chain 'B' and resid 99 through 133
      removed outlier: 3.571A  pdb=" N   ASP B 103 " --> pdb=" O   TRP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
    Processing helix  chain 'B' and resid 184 through 189
    Processing helix  chain 'B' and resid 190 through 193
    Processing helix  chain 'B' and resid 194 through 208
    Processing helix  chain 'B' and resid 209 through 224
    Processing helix  chain 'B' and resid 229 through 251
      removed outlier: 3.969A  pdb=" N   ARG B 235 " --> pdb=" O   HIS B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 253
      No H-bonds generated for 'chain 'B' and resid 252 through 253'
    Processing helix  chain 'B' and resid 254 through 256
      No H-bonds generated for 'chain 'B' and resid 254 through 256'
    Processing helix  chain 'B' and resid 257 through 268
      removed outlier: 3.647A  pdb=" N   SER B 268 " --> pdb=" O   SER B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 308 through 327
    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 389
      No H-bonds generated for 'chain 'B' and resid 387 through 389'
    Processing helix  chain 'B' and resid 390 through 402
      removed outlier: 4.270A  pdb=" N   TYR B 394 " --> pdb=" O   THR B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 425
    Processing helix  chain 'B' and resid 429 through 436
    Processing helix  chain 'B' and resid 438 through 448
    Processing helix  chain 'B' and resid 450 through 462
    Processing helix  chain 'B' and resid 483 through 497
    Processing helix  chain 'B' and resid 502 through 513
    Processing helix  chain 'B' and resid 564 through 579
    Processing helix  chain 'A' and resid 2 through 31
    Processing helix  chain 'A' and resid 35 through 38
    Processing helix  chain 'A' and resid 39 through 46
      removed outlier: 3.563A  pdb=" N   LEU A  43 " --> pdb=" O   TRP A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 99 through 132
    Processing helix  chain 'A' and resid 139 through 152
      removed outlier: 4.659A  pdb=" N   ASN A 152 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 187
      No H-bonds generated for 'chain 'A' and resid 185 through 187'
    Processing helix  chain 'A' and resid 194 through 208
    Processing helix  chain 'A' and resid 209 through 224
    Processing helix  chain 'A' and resid 228 through 233
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.620A  pdb=" N   ASN A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 256
      removed outlier: 5.426A  pdb=" N   ASN A 256 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 253 through 256'
    Processing helix  chain 'A' and resid 257 through 272
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 308 through 327
    Processing helix  chain 'A' and resid 333 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 389
      No H-bonds generated for 'chain 'A' and resid 387 through 389'
    Processing helix  chain 'A' and resid 390 through 402
      removed outlier: 4.455A  pdb=" N   TYR A 394 " --> pdb=" O   THR A 390 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   MET A 397 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 425
    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
    Processing helix  chain 'A' and resid 483 through 497
    Processing helix  chain 'A' and resid 502 through 513
    Processing helix  chain 'A' and resid 564 through 579
    Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 94
      removed outlier: 6.686A  pdb=" N   PHE B  90 " --> pdb=" O   THR A 529 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ILE A 531 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   THR B  92 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL A 532 " --> pdb=" O   TYR A 536 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   TYR A 536 " --> pdb=" O   VAL A 532 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ASP A 346 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ILE A 375 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   GLN A 348 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94
      removed outlier: 6.686A  pdb=" N   PHE B  90 " --> pdb=" O   THR A 529 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ILE A 531 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   THR B  92 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   GLY A 525 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   LEU A 514 " --> pdb=" O   GLY A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164
      removed outlier: 6.457A  pdb=" N   VAL B 160 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   ILE B 182 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.752A  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: 6.693A  pdb=" N   ASP B 346 " --> pdb=" O   TYR B 373 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   ILE B 375 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLN B 348 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   TYR B 536 " --> pdb=" O   VAL B 532 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL B 532 " --> pdb=" O   TYR B 536 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   GLY B 525 " --> pdb=" O   LEU B 514 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   LEU B 514 " --> pdb=" O   GLY B 525 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 350
      removed outlier: 6.693A  pdb=" N   ASP B 346 " --> pdb=" O   TYR B 373 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   ILE B 375 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLN B 348 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   TYR B 536 " --> pdb=" O   VAL B 532 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL B 532 " --> pdb=" O   TYR B 536 " (cutoff:3.500A)
      removed outlier: 8.784A  pdb=" N   THR A  92 " --> pdb=" O   THR B 527 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   THR B 529 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   ILE A  94 " --> pdb=" O   THR B 529 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ILE B 531 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 136 through 137

    538 hydrogen bonds defined for protein.
    1542 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: 3.93

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2085
        1.32 -     1.46: 3022
        1.46 -     1.59: 4346
        1.59 -     1.73: 11
        1.73 -     1.86: 68
  Bond restraints: 9532
  Sorted by residual:
  bond pdb=" CB  HIS B 201 "
       pdb=" CG  HIS B 201 "
    ideal  model  delta    sigma   weight residual
    1.497  1.397  0.100 1.40e-02 5.10e+03 5.14e+01
  bond pdb=" CB  HIS B 153 "
       pdb=" CG  HIS B 153 "
    ideal  model  delta    sigma   weight residual
    1.497  1.418  0.079 1.40e-02 5.10e+03 3.22e+01
  bond pdb=" CB  TYR B 552 "
       pdb=" CG  TYR B 552 "
    ideal  model  delta    sigma   weight residual
    1.512  1.397  0.115 2.20e-02 2.07e+03 2.75e+01
  bond pdb=" CB  PHE A  90 "
       pdb=" CG  PHE A  90 "
    ideal  model  delta    sigma   weight residual
    1.502  1.385  0.117 2.30e-02 1.89e+03 2.58e+01
  bond pdb=" CG  MET B 494 "
       pdb=" SD  MET B 494 "
    ideal  model  delta    sigma   weight residual
    1.803  1.678  0.125 2.50e-02 1.60e+03 2.52e+01
  ... (remaining 9527 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 10461
        2.06 -     4.11: 1944
        4.11 -     6.17: 331
        6.17 -     8.22: 79
        8.22 -    10.28: 21
  Bond angle restraints: 12836
  Sorted by residual:
  angle pdb=" CA  PHE A 313 "
        pdb=" CB  PHE A 313 "
        pdb=" CG  PHE A 313 "
      ideal   model   delta    sigma   weight residual
     113.80  105.83    7.97 1.00e+00 1.00e+00 6.36e+01
  angle pdb=" CA  ASP A 550 "
        pdb=" CB  ASP A 550 "
        pdb=" CG  ASP A 550 "
      ideal   model   delta    sigma   weight residual
     112.60  120.57   -7.97 1.00e+00 1.00e+00 6.36e+01
  angle pdb=" C   SER B 386 "
        pdb=" N   PRO B 387 "
        pdb=" CA  PRO B 387 "
      ideal   model   delta    sigma   weight residual
     119.56  127.47   -7.91 1.01e+00 9.80e-01 6.13e+01
  angle pdb=" C   TYR B 419 "
        pdb=" N   PRO B 420 "
        pdb=" CA  PRO B 420 "
      ideal   model   delta    sigma   weight residual
     119.56  127.53   -7.97 1.02e+00 9.61e-01 6.11e+01
  angle pdb=" C   TYR A 419 "
        pdb=" N   PRO A 420 "
        pdb=" CA  PRO A 420 "
      ideal   model   delta    sigma   weight residual
     119.56  127.44   -7.88 1.02e+00 9.61e-01 5.96e+01
  ... (remaining 12831 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 5476
       17.91 -    35.81: 176
       35.81 -    53.72: 26
       53.72 -    71.62: 9
       71.62 -    89.53: 7
  Dihedral angle restraints: 5694
    sinusoidal: 2374
      harmonic: 3320
  Sorted by residual:
  dihedral pdb=" C   ILE B  48 "
           pdb=" N   ILE B  48 "
           pdb=" CA  ILE B  48 "
           pdb=" CB  ILE B  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.80    9.80     0      2.50e+00 1.60e-01 1.54e+01
  dihedral pdb=" C   PHE B 501 "
           pdb=" N   PHE B 501 "
           pdb=" CA  PHE B 501 "
           pdb=" CB  PHE B 501 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.60   -9.00     0      2.50e+00 1.60e-01 1.30e+01
  dihedral pdb=" C   TYR B 385 "
           pdb=" N   TYR B 385 "
           pdb=" CA  TYR B 385 "
           pdb=" CB  TYR B 385 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.89   -8.71     0      2.50e+00 1.60e-01 1.21e+01
  ... (remaining 5691 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 923
       0.095 -    0.189: 364
       0.189 -    0.284: 87
       0.284 -    0.379: 13
       0.379 -    0.473: 1
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CB  ILE B 531 "
            pdb=" CA  ILE B 531 "
            pdb=" CG1 ILE B 531 "
            pdb=" CG2 ILE B 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.47 2.00e-01 2.50e+01 5.60e+00
  chirality pdb=" CA  PHE A 313 "
            pdb=" N   PHE A 313 "
            pdb=" C   PHE A 313 "
            pdb=" CB  PHE A 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.54e+00
  chirality pdb=" CA  ASN B 436 "
            pdb=" N   ASN B 436 "
            pdb=" C   ASN B 436 "
            pdb=" CB  ASN B 436 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.25e+00
  ... (remaining 1385 not shown)

  Planarity restraints: 1574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  36 "   -0.077 2.00e-02 2.50e+03   4.24e-02 3.60e+01
        pdb=" CG  TYR A  36 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  36 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  36 "    0.033 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  36 "    0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  36 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  36 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A  36 "   -0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 540 "   -0.075 2.00e-02 2.50e+03   3.64e-02 3.32e+01
        pdb=" CG  TRP A 540 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 540 "    0.035 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 540 "    0.030 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 540 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 540 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 540 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 540 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 540 "    0.023 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 540 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 373 "    0.064 2.00e-02 2.50e+03   3.95e-02 3.12e+01
        pdb=" CG  TYR B 373 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 373 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 373 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 373 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 373 "   -0.040 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 373 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 373 "    0.068 2.00e-02 2.50e+03
  ... (remaining 1571 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 67
        2.58 -     3.16: 8618
        3.16 -     3.74: 15153
        3.74 -     4.32: 22622
        4.32 -     4.90: 34188
  Nonbonded interactions: 80648
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.002 2.230
  nonbonded pdb=" OE2 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.033 2.230
  nonbonded pdb=" OE2 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.044 2.230
  nonbonded pdb=" OE1 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.061 2.230
  nonbonded pdb=" CD  GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.345 2.460
  ... (remaining 80643 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: 0.08
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:             1.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     28.350
  Find NCS groups from input model:        0.800
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:4.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4707
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      :  0.020   0.130   9532  Z= 1.264
  Angle     :  1.739  10.276  12836  Z= 1.191
  Chirality :  0.104   0.473   1388
  Planarity :  0.009   0.044   1574
  Dihedral  : 10.285  89.529   3554
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.55 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  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:  0.34 (0.24), residues: 1100
  helix:  0.79 (0.20), residues: 534
  sheet: -0.15 (0.46), residues: 117
  loop : -0.21 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.075   0.013   TRP A 540 
 HIS   0.009   0.002   HIS A 153 
 PHE   0.037   0.007   PHE A 274 
 TYR   0.077   0.012   TYR A  36 
 ARG   0.007   0.001   ARG A 162 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.8886 (t80) cc_final: 0.7920 (t80)
REVERT: A  131 LEU cc_start: 0.9043 (mt) cc_final: 0.8838 (mp)
REVERT: A  143 LYS cc_start: 0.8863 (tttm) cc_final: 0.8445 (tmtt)
REVERT: A  147 ASP cc_start: 0.8624 (m-30) cc_final: 0.8340 (m-30)
REVERT: A  149 ILE cc_start: 0.9315 (mt) cc_final: 0.8812 (mm)
REVERT: A  180 ILE cc_start: 0.8271 (mt) cc_final: 0.7615 (mt)
REVERT: A  181 LEU cc_start: 0.9043 (mp) cc_final: 0.8751 (mp)
REVERT: A  208 ASN cc_start: 0.9097 (m-40) cc_final: 0.7563 (m110)
REVERT: A  215 ILE cc_start: 0.8958 (mt) cc_final: 0.8726 (mt)
REVERT: A  216 ILE cc_start: 0.9672 (mt) cc_final: 0.9248 (mt)
REVERT: A  220 PHE cc_start: 0.7931 (m-10) cc_final: 0.7512 (m-80)
REVERT: A  227 ASN cc_start: 0.8976 (t0) cc_final: 0.8402 (t0)
REVERT: A  248 PHE cc_start: 0.6596 (m-80) cc_final: 0.6072 (m-80)
REVERT: A  292 LYS cc_start: 0.8466 (tptt) cc_final: 0.7860 (tttm)
REVERT: A  296 ILE cc_start: 0.9503 (mt) cc_final: 0.9228 (mm)
REVERT: A  297 ASN cc_start: 0.8594 (m-40) cc_final: 0.8230 (m110)
REVERT: A  311 LEU cc_start: 0.9239 (pp) cc_final: 0.8840 (mp)
REVERT: A  368 MET cc_start: -0.2061 (tpt) cc_final: -0.2607 (ttm)
REVERT: A  462 ASN cc_start: 0.5872 (t0) cc_final: 0.5219 (m-40)
REVERT: A  553 TYR cc_start: 0.3296 (m-80) cc_final: 0.1548 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1909
  time to fit residues: 46.0846
Evaluate side-chains
  114 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:   20.0000
   chunk 83 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0040
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:   30.0000
   chunk 86 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.4980
   chunk 99 optimal weight:    0.9990
   overall best weight:    1.2396
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 241 ASN
** A 567 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 = 0.4535 r_free = 0.4535 target = 0.186387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.144289 restraints weight = 12811.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.148869 restraints weight = 8641.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.152366 restraints weight = 6216.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6047
moved from start:          1.0546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9532  Z= 0.261
  Angle     :  0.774   9.122  12836  Z= 0.431
  Chirality :  0.048   0.156   1388
  Planarity :  0.005   0.042   1574
  Dihedral  :  5.727  29.939   1208
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  3.47 %
    Favored  : 95.75 %
  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:  0.57 (0.25), residues: 1100
  helix:  1.28 (0.21), residues: 562
  sheet:  0.24 (0.46), residues: 126
  loop : -0.78 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP B 414 
 HIS   0.009   0.002   HIS B 213 
 PHE   0.035   0.003   PHE B  14 
 TYR   0.030   0.002   TYR B 524 
 ARG   0.003   0.001   ARG B 293 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.8942 (tpt) cc_final: 0.8732 (tmm)
REVERT: A   27 LYS cc_start: 0.8647 (pttp) cc_final: 0.8085 (pttt)
REVERT: A   31 ASN cc_start: 0.9353 (m-40) cc_final: 0.8908 (p0)
REVERT: A   54 LYS cc_start: 0.9200 (mmmt) cc_final: 0.8963 (mmmt)
REVERT: A   92 THR cc_start: 0.6913 (p) cc_final: 0.6685 (t)
REVERT: A  110 TRP cc_start: 0.8527 (t60) cc_final: 0.7789 (t60)
REVERT: A  121 PHE cc_start: 0.9456 (t80) cc_final: 0.9083 (t80)
REVERT: A  126 LEU cc_start: 0.9403 (mt) cc_final: 0.9029 (mt)
REVERT: A  127 TYR cc_start: 0.9027 (t80) cc_final: 0.8705 (t80)
REVERT: A  147 ASP cc_start: 0.8614 (m-30) cc_final: 0.8386 (m-30)
REVERT: A  163 LYS cc_start: 0.6655 (pttt) cc_final: 0.6358 (tmmt)
REVERT: A  208 ASN cc_start: 0.8527 (m-40) cc_final: 0.7895 (m110)
REVERT: A  227 ASN cc_start: 0.8522 (t0) cc_final: 0.8053 (t0)
REVERT: A  233 VAL cc_start: 0.8815 (m) cc_final: 0.8474 (m)
REVERT: A  244 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8032 (mm-30)
REVERT: A  248 PHE cc_start: 0.8010 (m-80) cc_final: 0.7357 (m-80)
REVERT: A  275 PHE cc_start: 0.8047 (t80) cc_final: 0.7824 (t80)
REVERT: A  295 LEU cc_start: 0.9502 (mt) cc_final: 0.9218 (mt)
REVERT: A  297 ASN cc_start: 0.9093 (m-40) cc_final: 0.8589 (m-40)
  outliers start: 4
  outliers final: 1
  residues processed: 159
  average time/residue: 0.1847
  time to fit residues: 36.6920
Evaluate side-chains
  126 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 3 optimal weight:    0.2980
   chunk 25 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 12 optimal weight:    0.1980
   chunk 80 optimal weight:    7.9990
   chunk 103 optimal weight:    9.9990
   chunk 106 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0470
   chunk 28 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.4278
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 500 HIS
A 557 HIS
A 567 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 = 0.4555 r_free = 0.4555 target = 0.186444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.145884 restraints weight = 13423.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.150158 restraints weight = 9274.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.153328 restraints weight = 6811.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          1.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9532  Z= 0.190
  Angle     :  0.661   8.451  12836  Z= 0.366
  Chirality :  0.043   0.145   1388
  Planarity :  0.004   0.041   1574
  Dihedral  :  5.191  20.990   1208
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.28 %
    Favored  : 96.53 %
  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: -0.03 (0.25), residues: 1100
  helix:  0.66 (0.21), residues: 566
  sheet:  0.27 (0.46), residues: 126
  loop : -0.98 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 414 
 HIS   0.004   0.001   HIS B 201 
 PHE   0.041   0.002   PHE B  14 
 TYR   0.019   0.002   TYR A 524 
 ARG   0.002   0.000   ARG B 247 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LEU cc_start: 0.8877 (tp) cc_final: 0.8620 (pp)
REVERT: A  110 TRP cc_start: 0.8428 (t60) cc_final: 0.7711 (t60)
REVERT: A  121 PHE cc_start: 0.9245 (t80) cc_final: 0.8994 (t80)
REVERT: A  126 LEU cc_start: 0.9244 (mt) cc_final: 0.8915 (mt)
REVERT: A  141 ASN cc_start: 0.9440 (m-40) cc_final: 0.9026 (m-40)
REVERT: A  198 ILE cc_start: 0.9220 (pt) cc_final: 0.8929 (pt)
REVERT: A  199 ILE cc_start: 0.9748 (mm) cc_final: 0.9493 (mm)
REVERT: A  208 ASN cc_start: 0.8471 (m-40) cc_final: 0.8142 (m110)
REVERT: A  212 LEU cc_start: 0.9578 (tt) cc_final: 0.9185 (tp)
REVERT: A  213 HIS cc_start: 0.8920 (m90) cc_final: 0.8525 (m90)
REVERT: A  215 ILE cc_start: 0.9135 (tp) cc_final: 0.8819 (pt)
REVERT: A  218 ASN cc_start: 0.9234 (t0) cc_final: 0.8341 (t0)
REVERT: A  227 ASN cc_start: 0.8470 (t0) cc_final: 0.7840 (t0)
REVERT: A  233 VAL cc_start: 0.8809 (m) cc_final: 0.8390 (m)
REVERT: A  237 ILE cc_start: 0.9553 (mt) cc_final: 0.9328 (mt)
REVERT: A  244 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8429 (mm-30)
REVERT: A  248 PHE cc_start: 0.7799 (m-80) cc_final: 0.7190 (m-10)
REVERT: A  295 LEU cc_start: 0.9399 (mt) cc_final: 0.9090 (mt)
REVERT: A  297 ASN cc_start: 0.8874 (m-40) cc_final: 0.8476 (m110)
REVERT: A  302 ASN cc_start: 0.8872 (t0) cc_final: 0.8586 (t0)
REVERT: A  495 MET cc_start: 0.6227 (mmt) cc_final: 0.5841 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 144
  average time/residue: 0.1742
  time to fit residues: 31.4597
Evaluate side-chains
  120 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0970
   chunk 43 optimal weight:    0.5980
   chunk 24 optimal weight:   20.0000
   chunk 37 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.5578
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.186919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.145379 restraints weight = 13882.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.149703 restraints weight = 9851.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.152709 restraints weight = 7315.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6242
moved from start:          1.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9532  Z= 0.183
  Angle     :  0.646   6.666  12836  Z= 0.356
  Chirality :  0.042   0.139   1388
  Planarity :  0.004   0.039   1574
  Dihedral  :  4.890  19.043   1208
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  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: -0.32 (0.24), residues: 1100
  helix:  0.51 (0.21), residues: 566
  sheet:  0.09 (0.41), residues: 136
  loop : -1.29 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 414 
 HIS   0.007   0.001   HIS B 201 
 PHE   0.033   0.002   PHE A  14 
 TYR   0.024   0.002   TYR A 544 
 ARG   0.006   0.001   ARG B 247 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5992 (mtt) cc_final: 0.5791 (mtt)
REVERT: A    7 MET cc_start: 0.9278 (mtm) cc_final: 0.8989 (tpt)
REVERT: A   22 PHE cc_start: 0.8978 (m-80) cc_final: 0.8759 (m-80)
REVERT: A   28 ARG cc_start: 0.8165 (tpt90) cc_final: 0.7481 (tpt90)
REVERT: A   34 LEU cc_start: 0.8974 (tp) cc_final: 0.8614 (pp)
REVERT: A  110 TRP cc_start: 0.8426 (t60) cc_final: 0.7776 (t60)
REVERT: A  116 ILE cc_start: 0.9488 (mm) cc_final: 0.9171 (pt)
REVERT: A  120 LYS cc_start: 0.9380 (mttt) cc_final: 0.9173 (tttt)
REVERT: A  121 PHE cc_start: 0.9432 (t80) cc_final: 0.9054 (t80)
REVERT: A  126 LEU cc_start: 0.9281 (mt) cc_final: 0.8922 (mt)
REVERT: A  127 TYR cc_start: 0.8943 (t80) cc_final: 0.8629 (p90)
REVERT: A  141 ASN cc_start: 0.9340 (m-40) cc_final: 0.9030 (m-40)
REVERT: A  147 ASP cc_start: 0.8662 (m-30) cc_final: 0.8433 (m-30)
REVERT: A  174 TRP cc_start: 0.8735 (t60) cc_final: 0.8525 (t60)
REVERT: A  198 ILE cc_start: 0.9265 (pt) cc_final: 0.8947 (pt)
REVERT: A  199 ILE cc_start: 0.9749 (mm) cc_final: 0.9494 (mm)
REVERT: A  202 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8997 (mt-10)
REVERT: A  208 ASN cc_start: 0.8776 (m-40) cc_final: 0.8157 (m110)
REVERT: A  212 LEU cc_start: 0.9591 (tt) cc_final: 0.9193 (mt)
REVERT: A  213 HIS cc_start: 0.8862 (m90) cc_final: 0.8522 (m90)
REVERT: A  215 ILE cc_start: 0.9134 (tp) cc_final: 0.8873 (pt)
REVERT: A  218 ASN cc_start: 0.9312 (t0) cc_final: 0.8412 (t0)
REVERT: A  227 ASN cc_start: 0.8457 (t0) cc_final: 0.7793 (t0)
REVERT: A  233 VAL cc_start: 0.8789 (m) cc_final: 0.8335 (m)
REVERT: A  240 ASP cc_start: 0.9449 (m-30) cc_final: 0.9142 (m-30)
REVERT: A  241 ASN cc_start: 0.9347 (t0) cc_final: 0.8921 (t0)
REVERT: A  248 PHE cc_start: 0.7846 (m-80) cc_final: 0.7479 (m-10)
REVERT: A  275 PHE cc_start: 0.8225 (t80) cc_final: 0.7975 (t80)
REVERT: A  295 LEU cc_start: 0.9453 (mt) cc_final: 0.9232 (mt)
REVERT: A  297 ASN cc_start: 0.8982 (m-40) cc_final: 0.8625 (m110)
REVERT: A  320 LEU cc_start: 0.9366 (mm) cc_final: 0.9123 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1712
  time to fit residues: 33.1335
Evaluate side-chains
  116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 96 optimal weight:    0.0870
   chunk 92 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 30 optimal weight:    0.0370
   chunk 53 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0170
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0470
   overall best weight:    0.2372
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 231 HIS
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 285 ASN
A 567 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.187575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.146428 restraints weight = 13221.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.150828 restraints weight = 9018.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.154153 restraints weight = 6560.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6236
moved from start:          1.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9532  Z= 0.179
  Angle     :  0.651   9.523  12836  Z= 0.353
  Chirality :  0.041   0.135   1388
  Planarity :  0.004   0.034   1574
  Dihedral  :  4.782  17.931   1208
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  2.90 %
    Favored  : 96.72 %
  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 (0.24), residues: 1100
  helix:  0.42 (0.20), residues: 568
  sheet:  0.14 (0.42), residues: 136
  loop : -1.48 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 424 
 HIS   0.006   0.001   HIS A 231 
 PHE   0.035   0.002   PHE A  14 
 TYR   0.021   0.001   TYR A 544 
 ARG   0.005   0.000   ARG B 194 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 141
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.9291 (mtm) cc_final: 0.9029 (tpt)
REVERT: A   22 PHE cc_start: 0.9008 (m-80) cc_final: 0.8808 (m-80)
REVERT: A   28 ARG cc_start: 0.8232 (tpt90) cc_final: 0.7767 (tpt90)
REVERT: A   34 LEU cc_start: 0.8988 (tp) cc_final: 0.8602 (pp)
REVERT: A  110 TRP cc_start: 0.8406 (t60) cc_final: 0.7784 (t60)
REVERT: A  117 LEU cc_start: 0.9090 (mt) cc_final: 0.8852 (mt)
REVERT: A  121 PHE cc_start: 0.9569 (t80) cc_final: 0.8999 (t80)
REVERT: A  122 LEU cc_start: 0.9492 (tp) cc_final: 0.9268 (tp)
REVERT: A  126 LEU cc_start: 0.9195 (mt) cc_final: 0.8869 (mt)
REVERT: A  141 ASN cc_start: 0.9215 (m-40) cc_final: 0.8511 (p0)
REVERT: A  153 HIS cc_start: 0.8830 (m90) cc_final: 0.8586 (m90)
REVERT: A  172 THR cc_start: 0.8539 (m) cc_final: 0.8090 (m)
REVERT: A  178 TYR cc_start: 0.6894 (m-80) cc_final: 0.5881 (m-80)
REVERT: A  198 ILE cc_start: 0.9226 (pt) cc_final: 0.8930 (pt)
REVERT: A  199 ILE cc_start: 0.9728 (mm) cc_final: 0.9459 (mm)
REVERT: A  202 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8910 (mt-10)
REVERT: A  208 ASN cc_start: 0.8749 (m-40) cc_final: 0.8233 (m110)
REVERT: A  212 LEU cc_start: 0.9369 (tt) cc_final: 0.9153 (tp)
REVERT: A  213 HIS cc_start: 0.8795 (m90) cc_final: 0.8452 (m90)
REVERT: A  218 ASN cc_start: 0.9241 (t0) cc_final: 0.8521 (t0)
REVERT: A  227 ASN cc_start: 0.8485 (t0) cc_final: 0.7776 (t0)
REVERT: A  233 VAL cc_start: 0.8760 (m) cc_final: 0.8357 (m)
REVERT: A  239 HIS cc_start: 0.9134 (m-70) cc_final: 0.8680 (m90)
REVERT: A  248 PHE cc_start: 0.7598 (m-80) cc_final: 0.7269 (m-10)
REVERT: A  263 GLU cc_start: 0.9468 (pt0) cc_final: 0.9251 (pt0)
REVERT: A  267 ASP cc_start: 0.9245 (m-30) cc_final: 0.8761 (m-30)
REVERT: A  275 PHE cc_start: 0.8192 (t80) cc_final: 0.7659 (t80)
REVERT: A  295 LEU cc_start: 0.9370 (mt) cc_final: 0.9052 (mt)
REVERT: A  297 ASN cc_start: 0.8912 (m-40) cc_final: 0.8578 (m110)
REVERT: A  495 MET cc_start: 0.6141 (mmt) cc_final: 0.5888 (mmt)
  outliers start: 2
  outliers final: 1
  residues processed: 141
  average time/residue: 0.1620
  time to fit residues: 29.2847
Evaluate side-chains
  116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 96 optimal weight:    0.4980
   chunk 3 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0060
   chunk 97 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.5002
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.184887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.144378 restraints weight = 13976.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.148926 restraints weight = 9323.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.152069 restraints weight = 6649.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6340
moved from start:          1.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9532  Z= 0.180
  Angle     :  0.636   9.116  12836  Z= 0.353
  Chirality :  0.041   0.159   1388
  Planarity :  0.004   0.035   1574
  Dihedral  :  4.629  17.248   1208
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  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: -0.39 (0.24), residues: 1100
  helix:  0.45 (0.20), residues: 570
  sheet:  0.22 (0.42), residues: 136
  loop : -1.40 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A 414 
 HIS   0.004   0.001   HIS B 201 
 PHE   0.063   0.002   PHE A  14 
 TYR   0.020   0.002   TYR B 553 
 ARG   0.002   0.000   ARG A 162 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.9574 (t80) cc_final: 0.9145 (t80)
REVERT: A   28 ARG cc_start: 0.8319 (tpt90) cc_final: 0.7717 (tpt90)
REVERT: A   34 LEU cc_start: 0.8958 (tp) cc_final: 0.8757 (tp)
REVERT: A  110 TRP cc_start: 0.8460 (t60) cc_final: 0.7677 (t60)
REVERT: A  116 ILE cc_start: 0.9297 (mm) cc_final: 0.9078 (pt)
REVERT: A  121 PHE cc_start: 0.9519 (t80) cc_final: 0.9104 (t80)
REVERT: A  126 LEU cc_start: 0.9207 (mt) cc_final: 0.8893 (mt)
REVERT: A  138 LEU cc_start: 0.7783 (mt) cc_final: 0.7401 (mt)
REVERT: A  141 ASN cc_start: 0.9307 (m-40) cc_final: 0.8751 (p0)
REVERT: A  153 HIS cc_start: 0.9032 (m90) cc_final: 0.8777 (m90)
REVERT: A  178 TYR cc_start: 0.7236 (m-80) cc_final: 0.6129 (m-80)
REVERT: A  180 ILE cc_start: 0.9077 (mp) cc_final: 0.8415 (mp)
REVERT: A  208 ASN cc_start: 0.8632 (m-40) cc_final: 0.8101 (m110)
REVERT: A  212 LEU cc_start: 0.9415 (tt) cc_final: 0.9041 (mt)
REVERT: A  215 ILE cc_start: 0.9209 (tp) cc_final: 0.8903 (pt)
REVERT: A  218 ASN cc_start: 0.9249 (t0) cc_final: 0.8418 (t0)
REVERT: A  233 VAL cc_start: 0.8841 (m) cc_final: 0.8496 (m)
REVERT: A  239 HIS cc_start: 0.9137 (m-70) cc_final: 0.8675 (m90)
REVERT: A  248 PHE cc_start: 0.7645 (m-10) cc_final: 0.7035 (m-10)
REVERT: A  275 PHE cc_start: 0.8452 (t80) cc_final: 0.7903 (t80)
REVERT: A  295 LEU cc_start: 0.9448 (mt) cc_final: 0.9205 (mt)
REVERT: A  297 ASN cc_start: 0.8951 (m-40) cc_final: 0.8638 (m110)
REVERT: A  320 LEU cc_start: 0.9551 (mm) cc_final: 0.9172 (mm)
REVERT: A  330 MET cc_start: 0.1017 (tpp) cc_final: 0.0797 (tpp)
REVERT: A  368 MET cc_start: -0.3643 (mtt) cc_final: -0.4105 (mtt)
REVERT: A  495 MET cc_start: 0.6844 (mmt) cc_final: 0.6378 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1391
  time to fit residues: 24.5822
Evaluate side-chains
  106 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 107 optimal weight:    0.0370
   chunk 46 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0470
   chunk 94 optimal weight:    0.2980
   chunk 58 optimal weight:    0.0980
   chunk 69 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    0.2356
-------------------------------------------------------------------------------
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 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.187568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.145893 restraints weight = 13247.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.150327 restraints weight = 9008.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.153597 restraints weight = 6525.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6262
moved from start:          1.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9532  Z= 0.171
  Angle     :  0.631   8.706  12836  Z= 0.341
  Chirality :  0.041   0.154   1388
  Planarity :  0.004   0.036   1574
  Dihedral  :  4.478  15.787   1208
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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: -0.33 (0.24), residues: 1100
  helix:  0.57 (0.20), residues: 570
  sheet:  0.36 (0.44), residues: 136
  loop : -1.54 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B 174 
 HIS   0.005   0.001   HIS B 201 
 PHE   0.038   0.002   PHE A  14 
 TYR   0.018   0.001   TYR B 544 
 ARG   0.003   0.000   ARG B 194 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.9349 (mtm) cc_final: 0.8649 (tmm)
REVERT: A   12 PHE cc_start: 0.9674 (t80) cc_final: 0.9151 (t80)
REVERT: A   28 ARG cc_start: 0.8193 (tpt90) cc_final: 0.7688 (tpt90)
REVERT: A  110 TRP cc_start: 0.8412 (t60) cc_final: 0.7760 (t60)
REVERT: A  121 PHE cc_start: 0.9514 (t80) cc_final: 0.9142 (t80)
REVERT: A  126 LEU cc_start: 0.9134 (mt) cc_final: 0.8894 (mt)
REVERT: A  137 TYR cc_start: 0.8717 (p90) cc_final: 0.8517 (p90)
REVERT: A  138 LEU cc_start: 0.7403 (mt) cc_final: 0.6865 (mt)
REVERT: A  141 ASN cc_start: 0.9292 (m-40) cc_final: 0.8605 (p0)
REVERT: A  153 HIS cc_start: 0.8679 (m90) cc_final: 0.8356 (m90)
REVERT: A  174 TRP cc_start: 0.8303 (t60) cc_final: 0.8095 (t-100)
REVERT: A  178 TYR cc_start: 0.7127 (m-80) cc_final: 0.6226 (m-80)
REVERT: A  188 LYS cc_start: 0.9165 (tptp) cc_final: 0.8886 (mmtm)
REVERT: A  198 ILE cc_start: 0.9340 (pt) cc_final: 0.9070 (pt)
REVERT: A  199 ILE cc_start: 0.9752 (mm) cc_final: 0.9486 (mm)
REVERT: A  202 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8964 (mt-10)
REVERT: A  208 ASN cc_start: 0.8456 (m-40) cc_final: 0.7795 (m110)
REVERT: A  215 ILE cc_start: 0.9187 (tp) cc_final: 0.8908 (pt)
REVERT: A  218 ASN cc_start: 0.9217 (t0) cc_final: 0.8431 (t0)
REVERT: A  233 VAL cc_start: 0.8754 (m) cc_final: 0.8395 (m)
REVERT: A  239 HIS cc_start: 0.9158 (m-70) cc_final: 0.8736 (m90)
REVERT: A  248 PHE cc_start: 0.7631 (m-10) cc_final: 0.7038 (m-10)
REVERT: A  275 PHE cc_start: 0.8537 (t80) cc_final: 0.7897 (t80)
REVERT: A  291 LEU cc_start: 0.8904 (tp) cc_final: 0.8457 (tp)
REVERT: A  293 ARG cc_start: 0.9288 (ptp-170) cc_final: 0.9033 (ptp-170)
REVERT: A  295 LEU cc_start: 0.9420 (mt) cc_final: 0.9052 (mt)
REVERT: A  297 ASN cc_start: 0.9026 (m-40) cc_final: 0.8699 (m110)
REVERT: A  317 PHE cc_start: 0.9334 (m-80) cc_final: 0.8822 (m-80)
REVERT: A  320 LEU cc_start: 0.9528 (mm) cc_final: 0.9117 (mm)
REVERT: A  330 MET cc_start: 0.0636 (tpp) cc_final: 0.0319 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1702
  time to fit residues: 29.4093
Evaluate side-chains
  106 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 2 optimal weight:    0.8980
   chunk 107 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 0 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 39 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    2.0784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 487 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 = 0.4531 r_free = 0.4531 target = 0.182176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.142741 restraints weight = 13624.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.147066 restraints weight = 9299.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.150178 restraints weight = 6747.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          1.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9532  Z= 0.199
  Angle     :  0.646   9.337  12836  Z= 0.355
  Chirality :  0.042   0.186   1388
  Planarity :  0.004   0.038   1574
  Dihedral  :  4.461  16.222   1208
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  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: -0.50 (0.24), residues: 1100
  helix:  0.33 (0.20), residues: 578
  sheet:  0.37 (0.48), residues: 122
  loop : -1.45 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 414 
 HIS   0.005   0.001   HIS A 201 
 PHE   0.040   0.002   PHE B  14 
 TYR   0.016   0.002   TYR B 544 
 ARG   0.005   0.001   ARG A 294 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.9300 (mtm) cc_final: 0.8978 (tmm)
REVERT: A   12 PHE cc_start: 0.9421 (t80) cc_final: 0.8851 (t80)
REVERT: A   28 ARG cc_start: 0.8313 (tpt90) cc_final: 0.7715 (tpt90)
REVERT: A  110 TRP cc_start: 0.8392 (t60) cc_final: 0.7695 (t60)
REVERT: A  116 ILE cc_start: 0.9242 (mm) cc_final: 0.8997 (pt)
REVERT: A  121 PHE cc_start: 0.9411 (t80) cc_final: 0.9023 (t80)
REVERT: A  126 LEU cc_start: 0.9159 (mt) cc_final: 0.8860 (mt)
REVERT: A  138 LEU cc_start: 0.7094 (mt) cc_final: 0.6886 (mt)
REVERT: A  141 ASN cc_start: 0.9187 (m-40) cc_final: 0.8495 (p0)
REVERT: A  143 LYS cc_start: 0.8986 (tttm) cc_final: 0.8684 (tttm)
REVERT: A  147 ASP cc_start: 0.8596 (m-30) cc_final: 0.8376 (m-30)
REVERT: A  153 HIS cc_start: 0.8877 (m90) cc_final: 0.8612 (m-70)
REVERT: A  178 TYR cc_start: 0.7317 (m-80) cc_final: 0.6367 (m-80)
REVERT: A  198 ILE cc_start: 0.9344 (pt) cc_final: 0.9023 (pt)
REVERT: A  199 ILE cc_start: 0.9771 (mm) cc_final: 0.9496 (mm)
REVERT: A  202 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8902 (mt-10)
REVERT: A  208 ASN cc_start: 0.8484 (m-40) cc_final: 0.7829 (m110)
REVERT: A  212 LEU cc_start: 0.9551 (tt) cc_final: 0.9284 (mp)
REVERT: A  213 HIS cc_start: 0.8909 (m90) cc_final: 0.8639 (m90)
REVERT: A  215 ILE cc_start: 0.9245 (tp) cc_final: 0.8917 (pt)
REVERT: A  218 ASN cc_start: 0.9261 (t0) cc_final: 0.8325 (t0)
REVERT: A  233 VAL cc_start: 0.8878 (m) cc_final: 0.8556 (m)
REVERT: A  239 HIS cc_start: 0.9075 (m-70) cc_final: 0.8702 (m90)
REVERT: A  248 PHE cc_start: 0.7453 (m-10) cc_final: 0.6847 (m-10)
REVERT: A  275 PHE cc_start: 0.8787 (t80) cc_final: 0.8214 (t80)
REVERT: A  291 LEU cc_start: 0.8886 (tp) cc_final: 0.8394 (tp)
REVERT: A  295 LEU cc_start: 0.9500 (mt) cc_final: 0.9137 (mt)
REVERT: A  317 PHE cc_start: 0.9342 (m-80) cc_final: 0.8728 (m-80)
REVERT: A  330 MET cc_start: 0.1488 (tpp) cc_final: 0.1030 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1914
  time to fit residues: 32.5693
Evaluate side-chains
  109 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0670
   chunk 51 optimal weight:    0.3980
   chunk 70 optimal weight:    0.0040
   chunk 105 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0670
   chunk 16 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.2668
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.186347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.145382 restraints weight = 13507.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.149859 restraints weight = 9154.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.153034 restraints weight = 6644.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6309
moved from start:          1.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9532  Z= 0.194
  Angle     :  0.663   8.375  12836  Z= 0.357
  Chirality :  0.043   0.189   1388
  Planarity :  0.006   0.114   1574
  Dihedral  :  4.508  20.574   1208
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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 (0.24), residues: 1100
  helix:  0.53 (0.20), residues: 576
  sheet:  0.61 (0.47), residues: 126
  loop : -1.67 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 440 
 HIS   0.004   0.001   HIS A 416 
 PHE   0.042   0.002   PHE A  14 
 TYR   0.018   0.001   TYR B 544 
 ARG   0.015   0.001   ARG B 444 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.9331 (mtm) cc_final: 0.9052 (tmm)
REVERT: A   12 PHE cc_start: 0.9546 (t80) cc_final: 0.9005 (t80)
REVERT: A   22 PHE cc_start: 0.9415 (m-80) cc_final: 0.9200 (m-80)
REVERT: A   31 ASN cc_start: 0.9491 (m-40) cc_final: 0.8734 (p0)
REVERT: A   34 LEU cc_start: 0.8715 (tp) cc_final: 0.8408 (tp)
REVERT: A   36 TYR cc_start: 0.8787 (p90) cc_final: 0.8213 (p90)
REVERT: A   39 TRP cc_start: 0.8626 (m100) cc_final: 0.6994 (m-90)
REVERT: A  110 TRP cc_start: 0.8597 (t60) cc_final: 0.7906 (t60)
REVERT: A  117 LEU cc_start: 0.9285 (mt) cc_final: 0.9056 (mt)
REVERT: A  121 PHE cc_start: 0.9509 (t80) cc_final: 0.9224 (t80)
REVERT: A  126 LEU cc_start: 0.9047 (mt) cc_final: 0.8720 (mt)
REVERT: A  137 TYR cc_start: 0.8720 (p90) cc_final: 0.8440 (p90)
REVERT: A  138 LEU cc_start: 0.6837 (mt) cc_final: 0.6253 (mt)
REVERT: A  141 ASN cc_start: 0.9229 (m-40) cc_final: 0.8615 (p0)
REVERT: A  172 THR cc_start: 0.9087 (m) cc_final: 0.8810 (m)
REVERT: A  178 TYR cc_start: 0.7135 (m-80) cc_final: 0.6447 (m-80)
REVERT: A  198 ILE cc_start: 0.9352 (pt) cc_final: 0.9091 (pt)
REVERT: A  199 ILE cc_start: 0.9781 (mm) cc_final: 0.9535 (mm)
REVERT: A  202 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8948 (mt-10)
REVERT: A  208 ASN cc_start: 0.8404 (m-40) cc_final: 0.7782 (m110)
REVERT: A  213 HIS cc_start: 0.8862 (m90) cc_final: 0.8640 (m90)
REVERT: A  218 ASN cc_start: 0.9290 (t0) cc_final: 0.8460 (t0)
REVERT: A  233 VAL cc_start: 0.8765 (m) cc_final: 0.8311 (m)
REVERT: A  240 ASP cc_start: 0.9472 (m-30) cc_final: 0.9152 (m-30)
REVERT: A  248 PHE cc_start: 0.7520 (m-10) cc_final: 0.6926 (m-10)
REVERT: A  275 PHE cc_start: 0.8899 (t80) cc_final: 0.8667 (t80)
REVERT: A  295 LEU cc_start: 0.9385 (mt) cc_final: 0.9161 (mt)
REVERT: A  297 ASN cc_start: 0.9077 (m-40) cc_final: 0.8808 (m110)
REVERT: A  317 PHE cc_start: 0.9322 (m-80) cc_final: 0.8727 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1448
  time to fit residues: 25.1874
Evaluate side-chains
  108 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 102 optimal weight:    0.7980
   chunk 105 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.9182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
A 302 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 = 0.4560 r_free = 0.4560 target = 0.185315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.144524 restraints weight = 13728.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.148982 restraints weight = 9319.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.152156 restraints weight = 6761.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6356
moved from start:          1.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9532  Z= 0.183
  Angle     :  0.667  10.684  12836  Z= 0.358
  Chirality :  0.042   0.186   1388
  Planarity :  0.004   0.038   1574
  Dihedral  :  4.436  20.288   1208
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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 (0.24), residues: 1100
  helix:  0.52 (0.20), residues: 576
  sheet:  0.52 (0.45), residues: 126
  loop : -1.75 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A 414 
 HIS   0.005   0.001   HIS A 201 
 PHE   0.042   0.002   PHE B  14 
 TYR   0.018   0.001   TYR A 441 
 ARG   0.007   0.001   ARG A 444 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.9358 (mtm) cc_final: 0.8906 (tmm)
REVERT: A   12 PHE cc_start: 0.9520 (t80) cc_final: 0.8995 (t80)
REVERT: A   31 ASN cc_start: 0.9481 (m-40) cc_final: 0.8790 (p0)
REVERT: A   36 TYR cc_start: 0.8748 (p90) cc_final: 0.8243 (p90)
REVERT: A   39 TRP cc_start: 0.8723 (m100) cc_final: 0.7164 (m-90)
REVERT: A  110 TRP cc_start: 0.8561 (t60) cc_final: 0.7868 (t60)
REVERT: A  126 LEU cc_start: 0.9045 (mt) cc_final: 0.8723 (mt)
REVERT: A  137 TYR cc_start: 0.8649 (p90) cc_final: 0.8425 (p90)
REVERT: A  138 LEU cc_start: 0.7082 (mt) cc_final: 0.6431 (mt)
REVERT: A  141 ASN cc_start: 0.9126 (m-40) cc_final: 0.8680 (m110)
REVERT: A  172 THR cc_start: 0.9085 (m) cc_final: 0.8851 (m)
REVERT: A  178 TYR cc_start: 0.7164 (m-80) cc_final: 0.6441 (m-80)
REVERT: A  198 ILE cc_start: 0.9369 (pt) cc_final: 0.9098 (pt)
REVERT: A  199 ILE cc_start: 0.9775 (mm) cc_final: 0.9528 (mm)
REVERT: A  202 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8925 (mt-10)
REVERT: A  208 ASN cc_start: 0.8307 (m-40) cc_final: 0.7717 (m110)
REVERT: A  213 HIS cc_start: 0.8931 (m90) cc_final: 0.8635 (m90)
REVERT: A  222 ILE cc_start: 0.9380 (pt) cc_final: 0.9144 (pt)
REVERT: A  233 VAL cc_start: 0.8607 (m) cc_final: 0.8156 (m)
REVERT: A  240 ASP cc_start: 0.9396 (m-30) cc_final: 0.9162 (m-30)
REVERT: A  248 PHE cc_start: 0.7538 (m-10) cc_final: 0.6917 (m-10)
REVERT: A  275 PHE cc_start: 0.8863 (t80) cc_final: 0.8630 (t80)
REVERT: A  295 LEU cc_start: 0.9423 (mt) cc_final: 0.9176 (mt)
REVERT: A  317 PHE cc_start: 0.9316 (m-80) cc_final: 0.8888 (m-80)
REVERT: A  322 MET cc_start: 0.9282 (mpp) cc_final: 0.8990 (mpp)
REVERT: A  330 MET cc_start: 0.1456 (tpp) cc_final: 0.1096 (tpp)
REVERT: A  495 MET cc_start: 0.6310 (mmt) cc_final: 0.5881 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1381
  time to fit residues: 24.4975
Evaluate side-chains
  109 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0010
   chunk 29 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 102 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0010
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.5996
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
A 218 ASN
A 567 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.186824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.146330 restraints weight = 13105.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.150513 restraints weight = 9130.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.153704 restraints weight = 6791.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6335
moved from start:          1.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9532  Z= 0.181
  Angle     :  0.661   9.937  12836  Z= 0.356
  Chirality :  0.042   0.163   1388
  Planarity :  0.004   0.038   1574
  Dihedral  :  4.486  21.533   1208
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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 (0.24), residues: 1100
  helix:  0.53 (0.20), residues: 578
  sheet:  0.50 (0.49), residues: 110
  loop : -1.70 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP B 414 
 HIS   0.006   0.001   HIS A 418 
 PHE   0.042   0.002   PHE B  14 
 TYR   0.018   0.001   TYR B 441 
 ARG   0.005   0.001   ARG A 444 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2398.85 seconds
wall clock time: 43 minutes 55.01 seconds (2635.01 seconds total)