Starting phenix.real_space_refine
on Fri Nov 15 15:43:01 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/11_2024/8exs_28661.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/11_2024/8exs_28661.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/11_2024/8exs_28661.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/11_2024/8exs_28661.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/11_2024/8exs_28661.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exs_28661/11_2024/8exs_28661.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      38      5.16       5
     C    6118      2.51       5
     N    1538      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 9320
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 556, 4659
          Classifications: {'peptide': 556}
          Link IDs: {'PTRANS': 11, 'TRANS': 544}
          Chain breaks: 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}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.45, per 1000 atoms: 0.91
  Number of scatterers: 9320
  At special positions: 0
  Unit cell: (90.015, 90.015, 122.844, 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    1624      8.00
     N    1538      7.00
     C    6118      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.57
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 201 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 205 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 201 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 205 "


  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      58.4% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 31
    Processing helix  chain 'A' and resid 35 through 38
    Processing helix  chain 'A' and resid 39 through 46
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 99 through 134
      removed outlier: 4.522A  pdb=" N   ILE A 105 " --> pdb=" O   SER A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 152
      removed outlier: 5.088A  pdb=" N   LYS A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE A 146 " --> pdb=" O   GLU A 142 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ASN A 152 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 188
    Processing helix  chain 'A' and resid 193 through 208
    Processing helix  chain 'A' and resid 209 through 224
    Processing helix  chain 'A' and resid 228 through 252
    Processing helix  chain 'A' and resid 253 through 256
      removed outlier: 6.117A  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 271
      removed outlier: 3.632A  pdb=" N   VAL A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 307 through 327
      removed outlier: 4.298A  pdb=" N   LEU A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 352 through 357
    Processing helix  chain 'A' and resid 377 through 382
    Processing helix  chain 'A' and resid 387 through 390
    Processing helix  chain 'A' and resid 391 through 402
    Processing helix  chain 'A' and resid 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
      removed outlier: 3.529A  pdb=" N   THR A 454 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 497
    Processing helix  chain 'A' and resid 502 through 513
      removed outlier: 3.616A  pdb=" N   SER A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 579
    Processing helix  chain 'B' and resid 2 through 31
    Processing helix  chain 'B' and resid 35 through 38
    Processing helix  chain 'B' and resid 39 through 46
    Processing helix  chain 'B' and resid 47 through 51
    Processing helix  chain 'B' and resid 99 through 134
      removed outlier: 4.522A  pdb=" N   ILE B 105 " --> pdb=" O   SER B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 152
      removed outlier: 5.088A  pdb=" N   LYS B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE B 146 " --> pdb=" O   GLU B 142 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ASN B 152 " --> pdb=" O   THR B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 188
    Processing helix  chain 'B' and resid 193 through 208
    Processing helix  chain 'B' and resid 209 through 224
    Processing helix  chain 'B' and resid 228 through 252
    Processing helix  chain 'B' and resid 253 through 256
      removed outlier: 6.117A  pdb=" N   ASN B 256 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 253 through 256'
    Processing helix  chain 'B' and resid 257 through 271
      removed outlier: 3.632A  pdb=" N   VAL B 269 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 307 through 327
      removed outlier: 4.296A  pdb=" N   LEU B 311 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 337
    Processing helix  chain 'B' and resid 352 through 357
    Processing helix  chain 'B' and resid 377 through 382
    Processing helix  chain 'B' and resid 387 through 390
    Processing helix  chain 'B' and resid 391 through 402
    Processing helix  chain 'B' and resid 421 through 425
    Processing helix  chain 'B' and resid 429 through 436
    Processing helix  chain 'B' and resid 438 through 449
    Processing helix  chain 'B' and resid 450 through 461
      removed outlier: 3.531A  pdb=" N   THR B 454 " --> pdb=" O   PRO B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 497
    Processing helix  chain 'B' and resid 502 through 513
      removed outlier: 3.617A  pdb=" N   SER B 512 " --> pdb=" O   GLN B 508 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU B 513 " --> pdb=" O   LEU B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164
      removed outlier: 6.597A  pdb=" N   VAL A 160 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ARG A 162 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.898A  pdb=" N   ASP A 346 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   ILE A 375 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   GLN A 348 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   GLY A 530 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   GLY A 539 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   GLY A 528 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE A 541 " --> pdb=" O   LYS A 526 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LYS A 526 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLY A 543 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   TYR A 524 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   VAL A 545 " --> pdb=" O   GLU A 522 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU A 522 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   TYR A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LYS A 517 " --> pdb=" O   TYR A 521 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU A 523 " --> pdb=" O   ILE A 515 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164
      removed outlier: 6.596A  pdb=" N   VAL B 160 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   ILE B 182 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.642A  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: 6.897A  pdb=" N   ASP B 346 " --> pdb=" O   TYR B 373 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE B 375 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   GLN B 348 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   GLY B 530 " --> pdb=" O   ASN B 537 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   GLY B 539 " --> pdb=" O   GLY B 528 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLY B 528 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE B 541 " --> pdb=" O   LYS B 526 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LYS B 526 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLY B 543 " --> pdb=" O   TYR B 524 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   TYR B 524 " --> pdb=" O   GLY B 543 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   VAL B 545 " --> pdb=" O   GLU B 522 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU B 522 " --> pdb=" O   VAL B 545 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR B 521 " --> pdb=" O   LYS B 517 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS B 517 " --> pdb=" O   TYR B 521 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU B 523 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)

    489 hydrogen bonds defined for protein.
    1401 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.80

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1464
        1.30 -     1.43: 2855
        1.43 -     1.57: 5100
        1.57 -     1.70: 57
        1.70 -     1.84: 70
  Bond restraints: 9546
  Sorted by residual:
  bond pdb=" CB  HIS A 201 "
       pdb=" CG  HIS A 201 "
    ideal  model  delta    sigma   weight residual
    1.497  1.388  0.109 1.40e-02 5.10e+03 6.08e+01
  bond pdb=" CB  HIS B 201 "
       pdb=" CG  HIS B 201 "
    ideal  model  delta    sigma   weight residual
    1.497  1.389  0.108 1.40e-02 5.10e+03 6.00e+01
  bond pdb=" CB  PHE B 501 "
       pdb=" CG  PHE B 501 "
    ideal  model  delta    sigma   weight residual
    1.502  1.380  0.122 2.30e-02 1.89e+03 2.84e+01
  bond pdb=" CB  PHE A 501 "
       pdb=" CG  PHE A 501 "
    ideal  model  delta    sigma   weight residual
    1.502  1.381  0.121 2.30e-02 1.89e+03 2.78e+01
  bond pdb=" CB  HIS A 549 "
       pdb=" CG  HIS A 549 "
    ideal  model  delta    sigma   weight residual
    1.497  1.562 -0.065 1.40e-02 5.10e+03 2.17e+01
  ... (remaining 9541 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 11080
        2.38 -     4.77: 1540
        4.77 -     7.15: 194
        7.15 -     9.54: 36
        9.54 -    11.92: 6
  Bond angle restraints: 12856
  Sorted by residual:
  angle pdb=" C   SER A 386 "
        pdb=" N   PRO A 387 "
        pdb=" CA  PRO A 387 "
      ideal   model   delta    sigma   weight residual
     119.56  128.94   -9.38 1.02e+00 9.61e-01 8.46e+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  128.84   -9.28 1.02e+00 9.61e-01 8.29e+01
  angle pdb=" N   ILE A 222 "
        pdb=" CA  ILE A 222 "
        pdb=" C   ILE A 222 "
      ideal   model   delta    sigma   weight residual
     111.45  103.71    7.74 9.30e-01 1.16e+00 6.93e+01
  angle pdb=" N   ILE B 222 "
        pdb=" CA  ILE B 222 "
        pdb=" C   ILE B 222 "
      ideal   model   delta    sigma   weight residual
     111.45  103.78    7.67 9.30e-01 1.16e+00 6.81e+01
  angle pdb=" N   TYR A 521 "
        pdb=" CA  TYR A 521 "
        pdb=" C   TYR A 521 "
      ideal   model   delta    sigma   weight residual
     108.60  120.52  -11.92 1.46e+00 4.69e-01 6.67e+01
  ... (remaining 12851 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.28: 5462
       16.28 -    32.57: 183
       32.57 -    48.85: 37
       48.85 -    65.13: 20
       65.13 -    81.41: 6
  Dihedral angle restraints: 5708
    sinusoidal: 2376
      harmonic: 3332
  Sorted by residual:
  dihedral pdb=" C   ASN A 406 "
           pdb=" N   ASN A 406 "
           pdb=" CA  ASN A 406 "
           pdb=" CB  ASN A 406 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.18    9.58     0      2.50e+00 1.60e-01 1.47e+01
  dihedral pdb=" C   ASN B 406 "
           pdb=" N   ASN B 406 "
           pdb=" CA  ASN B 406 "
           pdb=" CB  ASN B 406 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.11    9.51     0      2.50e+00 1.60e-01 1.45e+01
  dihedral pdb=" CA  GLU A 202 "
           pdb=" CB  GLU A 202 "
           pdb=" CG  GLU A 202 "
           pdb=" CD  GLU A 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    4.59   55.41     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 5705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 765
       0.076 -    0.153: 463
       0.153 -    0.229: 148
       0.229 -    0.305: 10
       0.305 -    0.381: 8
  Chirality restraints: 1394
  Sorted by residual:
  chirality pdb=" CA  PHE A 220 "
            pdb=" N   PHE A 220 "
            pdb=" C   PHE A 220 "
            pdb=" CB  PHE A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.64e+00
  chirality pdb=" CA  PHE B 220 "
            pdb=" N   PHE B 220 "
            pdb=" C   PHE B 220 "
            pdb=" CB  PHE B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CA  ILE B 515 "
            pdb=" N   ILE B 515 "
            pdb=" C   ILE B 515 "
            pdb=" CB  ILE B 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.80   -0.37 2.00e-01 2.50e+01 3.37e+00
  ... (remaining 1391 not shown)

  Planarity restraints: 1576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 419 "    0.062 2.00e-02 2.50e+03   3.23e-02 2.09e+01
        pdb=" CG  TYR A 419 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 419 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 419 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 419 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 419 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 419 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 419 "    0.045 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 419 "   -0.061 2.00e-02 2.50e+03   3.20e-02 2.05e+01
        pdb=" CG  TYR B 419 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 419 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 419 "    0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 419 "    0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 419 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 419 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 419 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 540 "    0.056 2.00e-02 2.50e+03   2.68e-02 1.79e+01
        pdb=" CG  TRP B 540 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 540 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 540 "   -0.025 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 540 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 540 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 540 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 540 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 540 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 540 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1573 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.36: 13
        2.36 -     2.99: 5681
        2.99 -     3.63: 14462
        3.63 -     4.26: 24287
        4.26 -     4.90: 37307
  Nonbonded interactions: 81750
  Sorted by model distance:
  nonbonded pdb=" CB  ASP A 422 "
            pdb=" CB  ASP B 422 "
     model   vdw
     1.722 3.840
  nonbonded pdb=" O   ALA A  91 "
            pdb=" CZ  PHE B 421 "
     model   vdw
     1.923 3.340
  nonbonded pdb=" CZ  PHE A 421 "
            pdb=" O   ALA B  91 "
     model   vdw
     1.924 3.340
  nonbonded pdb=" OE2 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.099 2.230
  nonbonded pdb=" OE2 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.099 2.230
  ... (remaining 81745 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     28.700
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5053
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   0.122   9546  Z= 1.282
  Angle     :  1.722  11.922  12856  Z= 1.186
  Chirality :  0.099   0.381   1394
  Planarity :  0.009   0.041   1576
  Dihedral  : 10.181  81.415   3560
  Min Nonbonded Distance : 1.722

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  0.77 %
    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:  0.10 (0.23), residues: 1104
  helix:  0.31 (0.19), residues: 594
  sheet:  0.08 (0.47), residues: 124
  loop : -0.07 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.008   TRP B 540 
 HIS   0.010   0.002   HIS A 205 
 PHE   0.047   0.006   PHE A 274 
 TYR   0.062   0.010   TYR A 419 
 ARG   0.003   0.001   ARG B 384 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 341
  time to evaluate  : 1.081 
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: A  173 PHE cc_start: 0.4322 (m-80) cc_final: 0.3598 (m-80)
REVERT: A  316 ILE cc_start: 0.7263 (tp) cc_final: 0.6910 (tp)
REVERT: A  320 LEU cc_start: 0.8007 (mt) cc_final: 0.7510 (tp)
REVERT: A  412 MET cc_start: 0.2881 (tpp) cc_final: 0.1904 (tpp)
REVERT: A  434 MET cc_start: 0.4727 (tpp) cc_final: 0.4362 (tpp)
REVERT: B  173 PHE cc_start: 0.4309 (m-80) cc_final: 0.3592 (m-80)
REVERT: B  316 ILE cc_start: 0.7205 (tp) cc_final: 0.6845 (tp)
REVERT: B  320 LEU cc_start: 0.8018 (mt) cc_final: 0.7504 (tp)
REVERT: B  412 MET cc_start: 0.3080 (tpp) cc_final: 0.2131 (tpp)
REVERT: B  434 MET cc_start: 0.4728 (tpp) cc_final: 0.4340 (tpp)
  outliers start: 6
  outliers final: 2
  residues processed: 343
  average time/residue: 0.2305
  time to fit residues: 107.6702
Evaluate side-chains
  202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 200
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 152 ASN
A 252 ASN
A 297 ASN
A 538 ASN
B 152 ASN
B 252 ASN
B 297 ASN
B 538 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5032
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9546  Z= 0.226
  Angle     :  0.648   5.772  12856  Z= 0.373
  Chirality :  0.045   0.182   1394
  Planarity :  0.004   0.031   1576
  Dihedral  :  4.807  19.818   1212
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  2.22 %
    Favored  : 97.40 %
  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:  0.72 (0.24), residues: 1104
  helix:  1.12 (0.20), residues: 588
  sheet:  0.14 (0.48), residues: 128
  loop : -0.25 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 424 
 HIS   0.004   0.001   HIS B 239 
 PHE   0.030   0.002   PHE B  22 
 TYR   0.025   0.002   TYR A 203 
 ARG   0.003   0.001   ARG A  23 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 299
  time to evaluate  : 1.083 
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  173 PHE cc_start: 0.4341 (m-80) cc_final: 0.4013 (m-80)
REVERT: A  195 LEU cc_start: 0.6959 (mm) cc_final: 0.6506 (mm)
REVERT: A  237 ILE cc_start: 0.8824 (mt) cc_final: 0.8590 (mt)
REVERT: A  310 ILE cc_start: 0.7565 (mt) cc_final: 0.6877 (tp)
REVERT: A  322 MET cc_start: 0.5830 (ttp) cc_final: 0.5398 (ttp)
REVERT: A  323 VAL cc_start: 0.7876 (t) cc_final: 0.7666 (t)
REVERT: A  434 MET cc_start: 0.4296 (tpp) cc_final: 0.3905 (tpp)
REVERT: B  173 PHE cc_start: 0.4333 (m-80) cc_final: 0.3983 (m-80)
REVERT: B  195 LEU cc_start: 0.6953 (mm) cc_final: 0.6523 (mm)
REVERT: B  237 ILE cc_start: 0.8823 (mt) cc_final: 0.8595 (mt)
REVERT: B  310 ILE cc_start: 0.7603 (mt) cc_final: 0.6951 (tp)
REVERT: B  322 MET cc_start: 0.5866 (ttp) cc_final: 0.5424 (ttp)
REVERT: B  434 MET cc_start: 0.4278 (tpp) cc_final: 0.3868 (tpp)
  outliers start: 4
  outliers final: 2
  residues processed: 303
  average time/residue: 0.1920
  time to fit residues: 83.6922
Evaluate side-chains
  222 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 220
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0670
   chunk 27 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 108 optimal weight:    0.8980
   chunk 89 optimal weight:    9.9990
   chunk 99 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    1.3522

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
B 252 ASN
B 327 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5103
moved from start:          0.4570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9546  Z= 0.202
  Angle     :  0.581   6.389  12856  Z= 0.332
  Chirality :  0.044   0.177   1394
  Planarity :  0.004   0.031   1576
  Dihedral  :  4.660  14.827   1212
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.83 %
    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:  0.54 (0.25), residues: 1104
  helix:  0.98 (0.20), residues: 596
  sheet:  0.13 (0.48), residues: 126
  loop : -0.40 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 424 
 HIS   0.003   0.001   HIS B 205 
 PHE   0.023   0.002   PHE B  22 
 TYR   0.033   0.002   TYR B 391 
 ARG   0.002   0.000   ARG A 444 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 268
  time to evaluate  : 1.310 
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  173 PHE cc_start: 0.4397 (m-80) cc_final: 0.3995 (m-80)
REVERT: A  195 LEU cc_start: 0.7036 (mm) cc_final: 0.6550 (mm)
REVERT: A  237 ILE cc_start: 0.8877 (mt) cc_final: 0.8595 (mt)
REVERT: A  310 ILE cc_start: 0.7214 (mt) cc_final: 0.6638 (tp)
REVERT: A  434 MET cc_start: 0.4301 (tpp) cc_final: 0.3947 (tpp)
REVERT: B  173 PHE cc_start: 0.4355 (m-80) cc_final: 0.3939 (m-80)
REVERT: B  195 LEU cc_start: 0.7042 (mm) cc_final: 0.6259 (mm)
REVERT: B  237 ILE cc_start: 0.8889 (mt) cc_final: 0.8596 (mt)
REVERT: B  310 ILE cc_start: 0.7518 (mt) cc_final: 0.6663 (tp)
REVERT: B  434 MET cc_start: 0.4211 (tpp) cc_final: 0.3900 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 269
  average time/residue: 0.1888
  time to fit residues: 73.9940
Evaluate side-chains
  193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 100 optimal weight:    7.9990
   chunk 106 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
A 325 GLN
A 327 GLN
B 252 ASN
B 327 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5202
moved from start:          0.5276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9546  Z= 0.257
  Angle     :  0.647   9.796  12856  Z= 0.357
  Chirality :  0.046   0.199   1394
  Planarity :  0.004   0.040   1576
  Dihedral  :  4.761  15.466   1212
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  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: 1104
  helix:  0.78 (0.20), residues: 602
  sheet:  0.17 (0.48), residues: 126
  loop : -0.50 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 475 
 HIS   0.005   0.001   HIS A 557 
 PHE   0.028   0.002   PHE A 491 
 TYR   0.016   0.002   TYR B 471 
 ARG   0.004   0.001   ARG A 444 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 PHE cc_start: 0.4583 (m-80) cc_final: 0.3934 (m-80)
REVERT: A  195 LEU cc_start: 0.7131 (mm) cc_final: 0.6724 (mm)
REVERT: A  208 ASN cc_start: 0.8458 (m-40) cc_final: 0.8256 (m-40)
REVERT: A  247 ARG cc_start: 0.5611 (mtp180) cc_final: 0.5380 (mtp180)
REVERT: A  310 ILE cc_start: 0.6926 (mt) cc_final: 0.6429 (tp)
REVERT: A  327 GLN cc_start: 0.5020 (tm130) cc_final: 0.4723 (tm-30)
REVERT: A  328 PHE cc_start: 0.4733 (m-80) cc_final: 0.4499 (m-80)
REVERT: A  393 ILE cc_start: 0.6662 (pt) cc_final: 0.5866 (mt)
REVERT: B  195 LEU cc_start: 0.7191 (mm) cc_final: 0.6721 (mm)
REVERT: B  208 ASN cc_start: 0.8396 (m-40) cc_final: 0.8161 (m-40)
REVERT: B  393 ILE cc_start: 0.6582 (pt) cc_final: 0.5835 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1929
  time to fit residues: 69.5999
Evaluate side-chains
  191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0170
   chunk 43 optimal weight:    8.9990
   chunk 90 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7620

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
A 327 GLN
A 428 GLN
A 537 ASN
** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 ASN
B 327 GLN
B 428 GLN
B 537 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5111
moved from start:          0.5760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9546  Z= 0.175
  Angle     :  0.581  15.339  12856  Z= 0.320
  Chirality :  0.044   0.184   1394
  Planarity :  0.004   0.045   1576
  Dihedral  :  4.560  14.839   1212
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.25), residues: 1104
  helix:  0.83 (0.20), residues: 596
  sheet:  0.04 (0.48), residues: 130
  loop : -0.34 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 424 
 HIS   0.004   0.001   HIS B 239 
 PHE   0.025   0.002   PHE B 491 
 TYR   0.020   0.001   TYR B 203 
 ARG   0.003   0.000   ARG B 294 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 LEU cc_start: 0.7059 (mm) cc_final: 0.6354 (mm)
REVERT: A  208 ASN cc_start: 0.8274 (m-40) cc_final: 0.8052 (m-40)
REVERT: A  310 ILE cc_start: 0.6982 (mt) cc_final: 0.6692 (tt)
REVERT: A  495 MET cc_start: 0.3947 (mpp) cc_final: 0.3685 (mpp)
REVERT: A  499 ASN cc_start: 0.6783 (p0) cc_final: 0.6451 (p0)
REVERT: B  195 LEU cc_start: 0.7080 (mm) cc_final: 0.6563 (mm)
REVERT: B  495 MET cc_start: 0.4179 (mpp) cc_final: 0.3924 (mpp)
REVERT: B  499 ASN cc_start: 0.6858 (p0) cc_final: 0.6489 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.1942
  time to fit residues: 68.0620
Evaluate side-chains
  198 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 106 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0370
   overall best weight:    1.2062

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 ASN
B 327 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5130
moved from start:          0.6049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9546  Z= 0.191
  Angle     :  0.567   6.457  12856  Z= 0.314
  Chirality :  0.043   0.157   1394
  Planarity :  0.004   0.044   1576
  Dihedral  :  4.582  16.325   1212
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.25), residues: 1104
  helix:  0.80 (0.20), residues: 592
  sheet:  0.07 (0.49), residues: 130
  loop : -0.50 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 475 
 HIS   0.004   0.001   HIS B 239 
 PHE   0.033   0.002   PHE A 491 
 TYR   0.025   0.002   TYR B 337 
 ARG   0.002   0.000   ARG B 247 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 ILE cc_start: 0.7115 (mt) cc_final: 0.6831 (tt)
REVERT: A  499 ASN cc_start: 0.6731 (p0) cc_final: 0.6343 (p0)
REVERT: B  195 LEU cc_start: 0.7055 (mm) cc_final: 0.6710 (mm)
REVERT: B  278 ASN cc_start: 0.6607 (t0) cc_final: 0.6264 (t0)
REVERT: B  499 ASN cc_start: 0.6777 (p0) cc_final: 0.6381 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1980
  time to fit residues: 69.8018
Evaluate side-chains
  196 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0470
   chunk 77 optimal weight:    4.9990
   chunk 89 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 106 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 65 optimal weight:    0.2980
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.8482

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
B 227 ASN
B 252 ASN
B 327 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5107
moved from start:          0.6317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9546  Z= 0.178
  Angle     :  0.583   8.176  12856  Z= 0.319
  Chirality :  0.044   0.175   1394
  Planarity :  0.004   0.046   1576
  Dihedral  :  4.513  17.175   1212
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.25), residues: 1104
  helix:  0.82 (0.20), residues: 592
  sheet:  0.11 (0.49), residues: 130
  loop : -0.42 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 424 
 HIS   0.005   0.001   HIS B 239 
 PHE   0.029   0.002   PHE B 217 
 TYR   0.022   0.002   TYR B 337 
 ARG   0.003   0.000   ARG B 194 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 LEU cc_start: 0.7081 (mm) cc_final: 0.6638 (mm)
REVERT: A  247 ARG cc_start: 0.5651 (mtp180) cc_final: 0.5130 (mtp180)
REVERT: A  310 ILE cc_start: 0.7060 (mt) cc_final: 0.6818 (tt)
REVERT: A  434 MET cc_start: 0.4394 (tpp) cc_final: 0.4153 (tpp)
REVERT: A  499 ASN cc_start: 0.6723 (p0) cc_final: 0.6386 (p0)
REVERT: B  181 LEU cc_start: 0.7781 (tp) cc_final: 0.7525 (tp)
REVERT: B  434 MET cc_start: 0.4396 (tpp) cc_final: 0.4081 (tpp)
REVERT: B  499 ASN cc_start: 0.6713 (p0) cc_final: 0.6393 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1876
  time to fit residues: 67.1872
Evaluate side-chains
  198 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 1.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 72 optimal weight:    0.1980
   chunk 52 optimal weight:   30.0000
   chunk 9 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 96 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0020
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
B 252 ASN
B 327 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5088
moved from start:          0.6571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9546  Z= 0.172
  Angle     :  0.597  13.138  12856  Z= 0.321
  Chirality :  0.043   0.165   1394
  Planarity :  0.004   0.049   1576
  Dihedral  :  4.419  16.764   1212
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  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:  0.51 (0.25), residues: 1104
  helix:  1.02 (0.21), residues: 578
  sheet:  0.05 (0.49), residues: 130
  loop : -0.43 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 424 
 HIS   0.004   0.001   HIS B 239 
 PHE   0.030   0.002   PHE A 217 
 TYR   0.018   0.001   TYR A 203 
 ARG   0.003   0.000   ARG A 194 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 LEU cc_start: 0.7760 (tp) cc_final: 0.7554 (tp)
REVERT: A  310 ILE cc_start: 0.7085 (mt) cc_final: 0.6802 (tt)
REVERT: A  330 MET cc_start: 0.4159 (mpp) cc_final: 0.3803 (mmt)
REVERT: A  434 MET cc_start: 0.4281 (tpp) cc_final: 0.4025 (tpp)
REVERT: A  499 ASN cc_start: 0.6881 (p0) cc_final: 0.6553 (p0)
REVERT: B   49 PRO cc_start: 0.7822 (Cg_endo) cc_final: 0.7610 (Cg_exo)
REVERT: B  499 ASN cc_start: 0.6838 (p0) cc_final: 0.6546 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.1902
  time to fit residues: 66.8784
Evaluate side-chains
  193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 101 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0870
   chunk 30 optimal weight:    0.7980
   chunk 89 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0670
   chunk 104 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.5496

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

Flipped N/Q/H residues before XYZ refinement:
** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 ASN
A 252 ASN
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 ASN
B 327 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5092
moved from start:          0.6671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.112   9546  Z= 0.311
  Angle     :  1.019  67.300  12856  Z= 0.473
  Chirality :  0.047   0.289   1394
  Planarity :  0.004   0.053   1576
  Dihedral  :  4.475  20.464   1212
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.09 %
  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:  0.42 (0.25), residues: 1104
  helix:  0.92 (0.21), residues: 578
  sheet:  0.07 (0.49), residues: 130
  loop : -0.45 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 424 
 HIS   0.005   0.001   HIS A 239 
 PHE   0.051   0.003   PHE B 491 
 TYR   0.027   0.002   TYR A 130 
 ARG   0.003   0.000   ARG A 194 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 ILE cc_start: 0.7047 (mt) cc_final: 0.6809 (tt)
REVERT: A  434 MET cc_start: 0.4392 (tpp) cc_final: 0.4145 (tpp)
REVERT: A  499 ASN cc_start: 0.6863 (p0) cc_final: 0.6528 (p0)
REVERT: B   13 CYS cc_start: 0.5330 (p) cc_final: 0.5124 (p)
REVERT: B  264 SER cc_start: 0.7394 (p) cc_final: 0.7066 (p)
REVERT: B  265 ILE cc_start: 0.7434 (mt) cc_final: 0.6798 (mt)
REVERT: B  499 ASN cc_start: 0.6867 (p0) cc_final: 0.6551 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.1757
  time to fit residues: 60.2748
Evaluate side-chains
  189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 109 optimal weight:    0.0020
   chunk 100 optimal weight:   20.0000
   chunk 87 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 53 optimal weight:    6.9990
   chunk 69 optimal weight:    0.5980
   chunk 92 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
B 153 HIS
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5063
moved from start:          0.6827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   9546  Z= 0.187
  Angle     :  0.656  13.077  12856  Z= 0.349
  Chirality :  0.046   0.353   1394
  Planarity :  0.004   0.048   1576
  Dihedral  :  4.503  20.341   1212
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  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:  0.52 (0.25), residues: 1104
  helix:  1.01 (0.21), residues: 570
  sheet:  0.09 (0.49), residues: 130
  loop : -0.38 (0.33), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 424 
 HIS   0.012   0.001   HIS B 213 
 PHE   0.030   0.002   PHE B 217 
 TYR   0.019   0.001   TYR A 203 
 ARG   0.003   0.000   ARG A 194 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 ILE cc_start: 0.6967 (mt) cc_final: 0.6701 (tt)
REVERT: A  495 MET cc_start: 0.4169 (mpp) cc_final: 0.3590 (mpp)
REVERT: A  499 ASN cc_start: 0.6668 (p0) cc_final: 0.6383 (p0)
REVERT: B  491 PHE cc_start: 0.3313 (t80) cc_final: 0.2963 (t80)
REVERT: B  495 MET cc_start: 0.4252 (mpp) cc_final: 0.3533 (mpp)
REVERT: B  499 ASN cc_start: 0.6716 (p0) cc_final: 0.6430 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1727
  time to fit residues: 59.8921
Evaluate side-chains
  192 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 87 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 252 ASN
A 297 ASN
A 327 GLN
B 134 GLN
B 153 HIS
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.155248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.108499 restraints weight = 22667.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.111833 restraints weight = 15088.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.114033 restraints weight = 11196.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6701
moved from start:          0.7034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9546  Z= 0.197
  Angle     :  0.656   9.487  12856  Z= 0.353
  Chirality :  0.045   0.216   1394
  Planarity :  0.004   0.047   1576
  Dihedral  :  4.517  17.279   1212
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  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:  0.35 (0.25), residues: 1104
  helix:  0.85 (0.21), residues: 578
  sheet:  0.13 (0.50), residues: 130
  loop : -0.50 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 424 
 HIS   0.009   0.001   HIS B 213 
 PHE   0.031   0.002   PHE B  21 
 TYR   0.038   0.002   TYR A 203 
 ARG   0.003   0.000   ARG A 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2207.15 seconds
wall clock time: 41 minutes 29.72 seconds (2489.72 seconds total)