Starting phenix.real_space_refine
on Thu Feb 13 15:47:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tpp_41480/02_2025/8tpp_41480.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tpp_41480/02_2025/8tpp_41480.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tpp_41480/02_2025/8tpp_41480.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tpp_41480/02_2025/8tpp_41480.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tpp_41480/02_2025/8tpp_41480.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tpp_41480/02_2025/8tpp_41480.cif"
  }
  resolution = 3.64
  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=   0.002
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
     Ca      4      9.91       5
     S      38      5.16       5
     C    5968      2.51       5
     N    1524      2.21       5
     O    1582      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9116
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4556
          Classifications: {'peptide': 584}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 23, 'TRANS': 560}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 191
          Unresolved non-hydrogen angles: 241
          Unresolved non-hydrogen dihedrals: 169
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 145
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.59, per 1000 atoms: 0.94
  Number of scatterers: 9116
  At special positions: 0
  Unit cell: (86.45, 139.23, 100.1, 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)
     Ca      4     19.99
     S      38     16.00
     O    1582      8.00
     N    1524      7.00
     C    5968      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: 2.27
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2220

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      74.1% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 31
      No H-bonds generated for 'chain 'A' and resid 29 through 31'
    Processing helix  chain 'A' and resid 32 through 47
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.552A  pdb=" N   PHE A  76 " --> pdb=" O   SER A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.728A  pdb=" N   ASP A 107 " --> pdb=" O   GLN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 125
    Processing helix  chain 'A' and resid 126 through 130
    Processing helix  chain 'A' and resid 152 through 164
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 3.701A  pdb=" N   ILE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 199
      removed outlier: 3.841A  pdb=" N   ALA A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 217 through 246
    Processing helix  chain 'A' and resid 250 through 254
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.637A  pdb=" N   ARG A 284 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 319
      removed outlier: 3.614A  pdb=" N   PHE A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 358
      Proline residue:  A 341  - end of helix
    Processing helix  chain 'A' and resid 362 through 392
      removed outlier: 5.143A  pdb=" N   ALA A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 408
    Processing helix  chain 'A' and resid 431 through 451
      removed outlier: 3.923A  pdb=" N   ASN A 435 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   THR A 443 " --> pdb=" O   TYR A 439 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA A 444 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE A 449 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 465
      removed outlier: 3.658A  pdb=" N   TYR A 457 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 493
    Processing helix  chain 'A' and resid 500 through 518
      removed outlier: 3.766A  pdb=" N   SER A 518 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 545
      removed outlier: 3.564A  pdb=" N   CYS A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG A 537 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 585
      removed outlier: 3.626A  pdb=" N   ALA A 564 " --> pdb=" O   PRO A 560 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   SER A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA A 578 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN A 585 " --> pdb=" O   TYR A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 625
    Processing helix  chain 'A' and resid 630 through 642
    Processing helix  chain 'A' and resid 701 through 715
    Processing helix  chain 'B' and resid 29 through 31
      No H-bonds generated for 'chain 'B' and resid 29 through 31'
    Processing helix  chain 'B' and resid 32 through 47
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 3.551A  pdb=" N   PHE B  76 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.728A  pdb=" N   ASP B 107 " --> pdb=" O   GLN B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 125
    Processing helix  chain 'B' and resid 126 through 130
    Processing helix  chain 'B' and resid 152 through 164
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.700A  pdb=" N   ILE B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 199
      removed outlier: 3.841A  pdb=" N   ALA B 186 " --> pdb=" O   GLY B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 217 through 246
    Processing helix  chain 'B' and resid 250 through 254
    Processing helix  chain 'B' and resid 280 through 289
      removed outlier: 3.637A  pdb=" N   ARG B 284 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 319
      removed outlier: 3.614A  pdb=" N   PHE B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 358
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 362 through 392
      removed outlier: 5.144A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 408
    Processing helix  chain 'B' and resid 431 through 451
      removed outlier: 3.922A  pdb=" N   ASN B 435 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   THR B 443 " --> pdb=" O   TYR B 439 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA B 444 " --> pdb=" O   PHE B 440 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE B 449 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 465
      removed outlier: 3.658A  pdb=" N   TYR B 457 " --> pdb=" O   VAL B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 493
    Processing helix  chain 'B' and resid 500 through 518
      removed outlier: 3.766A  pdb=" N   SER B 518 " --> pdb=" O   VAL B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 545
      removed outlier: 3.565A  pdb=" N   CYS B 527 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG B 537 " --> pdb=" O   TRP B 533 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 585
      removed outlier: 3.625A  pdb=" N   ALA B 564 " --> pdb=" O   PRO B 560 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   SER B 577 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA B 578 " --> pdb=" O   ILE B 574 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASN B 585 " --> pdb=" O   TYR B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 625
    Processing helix  chain 'B' and resid 630 through 642
    Processing helix  chain 'B' and resid 701 through 715
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 59
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267
      removed outlier: 4.010A  pdb=" N   HIS A 265 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA A 267 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 59
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 267
      removed outlier: 4.010A  pdb=" N   HIS B 265 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA B 267 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)

    648 hydrogen bonds defined for protein.
    1902 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: 2.66

  Time building geometry restraints manager: 2.58 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2860
        1.34 -     1.46: 2385
        1.46 -     1.58: 4035
        1.58 -     1.70: 0
        1.70 -     1.82: 62
  Bond restraints: 9342
  Sorted by residual:
  bond pdb=" C   ILE B 201 "
       pdb=" N   PRO B 202 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.020 1.28e-02 6.10e+03 2.44e+00
  bond pdb=" C   ILE A 201 "
       pdb=" N   PRO A 202 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 1.28e-02 6.10e+03 2.31e+00
  bond pdb=" C   ILE A 394 "
       pdb=" N   PRO A 395 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.20e-02 6.94e+03 2.20e+00
  bond pdb=" C   ILE B 394 "
       pdb=" N   PRO B 395 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.20e-02 6.94e+03 2.17e+00
  bond pdb=" CB  GLU B  62 "
       pdb=" CG  GLU B  62 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.11e+00
  ... (remaining 9337 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 12366
        1.36 -     2.72: 266
        2.72 -     4.07: 50
        4.07 -     5.43: 13
        5.43 -     6.79: 11
  Bond angle restraints: 12706
  Sorted by residual:
  angle pdb=" N   THR A 340 "
        pdb=" CA  THR A 340 "
        pdb=" C   THR A 340 "
      ideal   model   delta    sigma   weight residual
     109.81  116.05   -6.24 2.21e+00 2.05e-01 7.98e+00
  angle pdb=" N   THR B 340 "
        pdb=" CA  THR B 340 "
        pdb=" C   THR B 340 "
      ideal   model   delta    sigma   weight residual
     109.81  116.00   -6.19 2.21e+00 2.05e-01 7.85e+00
  angle pdb=" CA  GLU A  62 "
        pdb=" CB  GLU A  62 "
        pdb=" CG  GLU A  62 "
      ideal   model   delta    sigma   weight residual
     114.10  118.87   -4.77 2.00e+00 2.50e-01 5.70e+00
  angle pdb=" CA  GLU B  62 "
        pdb=" CB  GLU B  62 "
        pdb=" CG  GLU B  62 "
      ideal   model   delta    sigma   weight residual
     114.10  118.87   -4.77 2.00e+00 2.50e-01 5.69e+00
  angle pdb=" N   GLU A 264 "
        pdb=" CA  GLU A 264 "
        pdb=" C   GLU A 264 "
      ideal   model   delta    sigma   weight residual
     112.93  109.97    2.96 1.33e+00 5.65e-01 4.94e+00
  ... (remaining 12701 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 4668
       17.46 -    34.92: 594
       34.92 -    52.38: 139
       52.38 -    69.84: 23
       69.84 -    87.30: 8
  Dihedral angle restraints: 5432
    sinusoidal: 2026
      harmonic: 3406
  Sorted by residual:
  dihedral pdb=" CG  ARG B 490 "
           pdb=" CD  ARG B 490 "
           pdb=" NE  ARG B 490 "
           pdb=" CZ  ARG B 490 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.09  -44.09     2      1.50e+01 4.44e-03 1.03e+01
  dihedral pdb=" CG  ARG A 490 "
           pdb=" CD  ARG A 490 "
           pdb=" NE  ARG A 490 "
           pdb=" CZ  ARG A 490 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.03  -44.03     2      1.50e+01 4.44e-03 1.03e+01
  dihedral pdb=" CG  ARG B 284 "
           pdb=" CD  ARG B 284 "
           pdb=" NE  ARG B 284 "
           pdb=" CZ  ARG B 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.71  -42.71     2      1.50e+01 4.44e-03 9.81e+00
  ... (remaining 5429 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1159
       0.045 -    0.091: 234
       0.091 -    0.136: 49
       0.136 -    0.181: 2
       0.181 -    0.226: 2
  Chirality restraints: 1446
  Sorted by residual:
  chirality pdb=" CB  VAL B 134 "
            pdb=" CA  VAL B 134 "
            pdb=" CG1 VAL B 134 "
            pdb=" CG2 VAL B 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CB  VAL A 134 "
            pdb=" CA  VAL A 134 "
            pdb=" CG1 VAL A 134 "
            pdb=" CG2 VAL A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  THR A 340 "
            pdb=" N   THR A 340 "
            pdb=" C   THR A 340 "
            pdb=" CB  THR A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.36e-01
  ... (remaining 1443 not shown)

  Planarity restraints: 1592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A  62 "   -0.007 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" CD  GLU A  62 "    0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLU A  62 "   -0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU A  62 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  62 "    0.007 2.00e-02 2.50e+03   1.51e-02 2.27e+00
        pdb=" CD  GLU B  62 "   -0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  62 "    0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  62 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 201 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO B 202 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 202 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 202 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1589 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1617
        2.76 -     3.30: 8695
        3.30 -     3.83: 15211
        3.83 -     4.37: 15299
        4.37 -     4.90: 28303
  Nonbonded interactions: 69125
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 188 "
            pdb=" OD2 ASP B 539 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OH  TYR A 188 "
            pdb=" OD2 ASP A 539 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OH  TYR B  26 "
            pdb=" O   ALA B  36 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OH  TYR A  26 "
            pdb=" O   ALA A  36 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG1 THR B 555 "
            pdb=" O   SER B 557 "
     model   vdw
     2.349 3.040
  ... (remaining 69120 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: 0.05
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:             2.270
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.610
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
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      :  0.003   0.032   9342  Z= 0.175
  Angle     :  0.526   6.790  12706  Z= 0.281
  Chirality :  0.038   0.226   1446
  Planarity :  0.004   0.036   1592
  Dihedral  : 16.551  87.300   3212
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 23.92 %
    Favored  : 75.97 %
  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:  2.18 (0.26), residues: 1132
  helix:  2.43 (0.18), residues: 800
  sheet: -0.42 (0.82), residues: 44
  loop : -1.19 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 611 
 PHE   0.014   0.001   PHE A 379 
 TYR   0.008   0.001   TYR A 188 
 ARG   0.006   0.000   ARG A 710 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.983 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1825
  time to fit residues: 20.2509
Evaluate side-chains
  68 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.3980
   chunk 87 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 105 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 698 GLN
B  58 HIS
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 698 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.128873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.103394 restraints weight = 13872.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.105405 restraints weight = 9242.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.106710 restraints weight = 7254.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.0875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9342  Z= 0.217
  Angle     :  0.525   6.940  12706  Z= 0.271
  Chirality :  0.039   0.161   1446
  Planarity :  0.004   0.038   1592
  Dihedral  :  3.617  14.959   1238
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.51 %
    Favored  : 75.32 %
  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:  2.61 (0.25), residues: 1132
  helix:  2.73 (0.18), residues: 806
  sheet: -0.11 (0.81), residues: 44
  loop : -1.08 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B 611 
 PHE   0.014   0.001   PHE A 379 
 TYR   0.010   0.001   TYR A 188 
 ARG   0.006   0.000   ARG B 710 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7856 (tm-30)
REVERT: A  125 LYS cc_start: 0.7577 (ttmt) cc_final: 0.7274 (tppt)
REVERT: B  125 LYS cc_start: 0.7520 (ttmt) cc_final: 0.7279 (tppt)
  outliers start: 20
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1768
  time to fit residues: 25.6474
Evaluate side-chains
  83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 115 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0020
   chunk 25 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 435 ASN
A 633 GLN
A 714 GLN
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.129480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.103972 restraints weight = 14009.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.106002 restraints weight = 9388.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.107324 restraints weight = 7351.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9342  Z= 0.172
  Angle     :  0.496   6.256  12706  Z= 0.255
  Chirality :  0.038   0.144   1446
  Planarity :  0.003   0.034   1592
  Dihedral  :  3.596  14.387   1238
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.19 %
    Favored  : 74.89 %
  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:  2.63 (0.25), residues: 1132
  helix:  2.73 (0.18), residues: 806
  sheet:  0.09 (0.80), residues: 44
  loop : -1.08 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.012   0.001   PHE A 379 
 TYR   0.010   0.001   TYR A 188 
 ARG   0.006   0.000   ARG B 710 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 80
  time to evaluate  : 1.020 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7791 (tm-30)
REVERT: A  125 LYS cc_start: 0.7537 (ttmt) cc_final: 0.7269 (tppt)
REVERT: B  125 LYS cc_start: 0.7523 (ttmt) cc_final: 0.7268 (tppt)
  outliers start: 27
  outliers final: 14
  residues processed: 97
  average time/residue: 0.1512
  time to fit residues: 23.2229
Evaluate side-chains
  87 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 76 optimal weight:    0.4980
   chunk 7 optimal weight:    7.9990
   chunk 115 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 94 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 633 GLN
B 714 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.129662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.104568 restraints weight = 13805.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.106458 restraints weight = 9220.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.107874 restraints weight = 7227.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9342  Z= 0.166
  Angle     :  0.486   6.269  12706  Z= 0.248
  Chirality :  0.037   0.144   1446
  Planarity :  0.003   0.034   1592
  Dihedral  :  3.561  14.723   1238
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 23.70 %
    Favored  : 74.13 %
  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:  2.61 (0.25), residues: 1132
  helix:  2.74 (0.18), residues: 810
  sheet:  0.28 (0.81), residues: 44
  loop : -1.24 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 
 PHE   0.012   0.001   PHE A 396 
 TYR   0.009   0.001   TYR A 188 
 ARG   0.005   0.000   ARG B 710 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7503 (ttmt) cc_final: 0.7257 (tppt)
REVERT: B  125 LYS cc_start: 0.7525 (ttmt) cc_final: 0.7277 (tppt)
  outliers start: 20
  outliers final: 15
  residues processed: 91
  average time/residue: 0.1658
  time to fit residues: 23.4906
Evaluate side-chains
  89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0010
   chunk 40 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0470
   chunk 56 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 36 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.8686

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 143 HIS
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.128738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.103595 restraints weight = 13980.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.105588 restraints weight = 9300.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.106890 restraints weight = 7279.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9342  Z= 0.196
  Angle     :  0.499   6.308  12706  Z= 0.256
  Chirality :  0.038   0.145   1446
  Planarity :  0.003   0.034   1592
  Dihedral  :  3.561  14.833   1238
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 23.92 %
    Favored  : 72.94 %
  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:  2.59 (0.25), residues: 1132
  helix:  2.71 (0.18), residues: 810
  sheet:  0.33 (0.83), residues: 44
  loop : -1.23 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 
 PHE   0.013   0.001   PHE A 396 
 TYR   0.009   0.001   TYR A 188 
 ARG   0.007   0.000   ARG B 710 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 0.931 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7518 (ttmt) cc_final: 0.7274 (tppt)
REVERT: A  380 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.7062 (mtp)
REVERT: B  125 LYS cc_start: 0.7541 (ttmt) cc_final: 0.7316 (tppt)
  outliers start: 29
  outliers final: 21
  residues processed: 95
  average time/residue: 0.1674
  time to fit residues: 24.4223
Evaluate side-chains
  95 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 107 optimal weight:    0.5980
   chunk 110 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 102 optimal weight:    0.0980
   chunk 44 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.129744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.104786 restraints weight = 13801.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.106790 restraints weight = 9126.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.108112 restraints weight = 7133.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9342  Z= 0.159
  Angle     :  0.483   6.270  12706  Z= 0.246
  Chirality :  0.037   0.145   1446
  Planarity :  0.003   0.033   1592
  Dihedral  :  3.531  14.815   1238
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 23.92 %
    Favored  : 72.94 %
  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:  2.65 (0.25), residues: 1132
  helix:  2.76 (0.18), residues: 810
  sheet:  0.47 (0.85), residues: 44
  loop : -1.24 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 611 
 PHE   0.011   0.001   PHE B 379 
 TYR   0.010   0.001   TYR A 188 
 ARG   0.005   0.000   ARG B 710 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7498 (ttmt) cc_final: 0.7243 (tppt)
REVERT: A  380 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.7046 (mtp)
REVERT: B  125 LYS cc_start: 0.7504 (ttmt) cc_final: 0.7272 (tppt)
  outliers start: 29
  outliers final: 22
  residues processed: 95
  average time/residue: 0.1617
  time to fit residues: 24.1448
Evaluate side-chains
  96 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 79 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0050
   chunk 114 optimal weight:    0.1980
   chunk 86 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.130779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.105492 restraints weight = 14102.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.107587 restraints weight = 9364.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.108955 restraints weight = 7265.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9342  Z= 0.143
  Angle     :  0.475   6.275  12706  Z= 0.241
  Chirality :  0.037   0.144   1446
  Planarity :  0.003   0.033   1592
  Dihedral  :  3.490  14.622   1238
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 24.68 %
    Favored  : 72.73 %
  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:  2.68 (0.25), residues: 1132
  helix:  2.82 (0.17), residues: 810
  sheet:  0.52 (0.86), residues: 44
  loop : -1.37 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 611 
 PHE   0.010   0.001   PHE B 379 
 TYR   0.009   0.001   TYR A 188 
 ARG   0.005   0.000   ARG B 710 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7465 (ttmt) cc_final: 0.7215 (tppt)
REVERT: A  380 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.7013 (mtp)
REVERT: B  125 LYS cc_start: 0.7482 (ttmt) cc_final: 0.7254 (tppt)
  outliers start: 24
  outliers final: 18
  residues processed: 93
  average time/residue: 0.1811
  time to fit residues: 26.3521
Evaluate side-chains
  92 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  602 LEU
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0170
   chunk 100 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 73 optimal weight:    0.5980
   chunk 87 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.130603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.105407 restraints weight = 14142.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.107439 restraints weight = 9350.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.108797 restraints weight = 7296.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9342  Z= 0.153
  Angle     :  0.485   6.303  12706  Z= 0.246
  Chirality :  0.037   0.144   1446
  Planarity :  0.003   0.033   1592
  Dihedral  :  3.466  14.539   1238
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 24.89 %
    Favored  : 72.51 %
  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:  2.67 (0.25), residues: 1132
  helix:  2.81 (0.17), residues: 810
  sheet:  0.59 (0.87), residues: 44
  loop : -1.40 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 611 
 PHE   0.012   0.001   PHE A 379 
 TYR   0.010   0.001   TYR A 383 
 ARG   0.008   0.000   ARG B 710 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7389 (ttmt) cc_final: 0.7178 (tppt)
REVERT: A  380 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.7016 (mtp)
REVERT: B  125 LYS cc_start: 0.7473 (ttmt) cc_final: 0.7247 (tppt)
  outliers start: 24
  outliers final: 20
  residues processed: 94
  average time/residue: 0.1522
  time to fit residues: 22.6293
Evaluate side-chains
  95 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  602 LEU
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 111 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 101 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.126844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.101712 restraints weight = 14096.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.103647 restraints weight = 9452.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.104803 restraints weight = 7434.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9342  Z= 0.266
  Angle     :  0.547   6.379  12706  Z= 0.281
  Chirality :  0.039   0.149   1446
  Planarity :  0.004   0.034   1592
  Dihedral  :  3.605  14.750   1238
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 24.03 %
    Favored  : 72.73 %
  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:  2.43 (0.25), residues: 1132
  helix:  2.63 (0.18), residues: 812
  sheet:  0.49 (0.85), residues: 44
  loop : -1.49 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 159 
 HIS   0.005   0.001   HIS B 611 
 PHE   0.017   0.001   PHE A 396 
 TYR   0.012   0.002   TYR B 360 
 ARG   0.007   0.000   ARG B 710 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 1.249 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7296 (tppt)
REVERT: A  263 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.7416 (p-90)
REVERT: B  263 TRP cc_start: 0.8016 (OUTLIER) cc_final: 0.7334 (p-90)
  outliers start: 30
  outliers final: 22
  residues processed: 99
  average time/residue: 0.1565
  time to fit residues: 24.4883
Evaluate side-chains
  98 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  263 TRP
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0970
   chunk 16 optimal weight:    0.6980
   chunk 112 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.128554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.103274 restraints weight = 14206.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.105278 restraints weight = 9444.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.106613 restraints weight = 7384.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9342  Z= 0.178
  Angle     :  0.522   7.008  12706  Z= 0.262
  Chirality :  0.037   0.145   1446
  Planarity :  0.003   0.036   1592
  Dihedral  :  3.597  14.872   1238
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 24.68 %
    Favored  : 72.62 %
  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:  2.50 (0.25), residues: 1132
  helix:  2.68 (0.18), residues: 812
  sheet:  0.52 (0.86), residues: 44
  loop : -1.46 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 
 PHE   0.013   0.001   PHE A 379 
 TYR   0.012   0.001   TYR B 383 
 ARG   0.007   0.000   ARG B 710 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 1.142 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7481 (ttmt) cc_final: 0.7248 (tppt)
REVERT: A  263 TRP cc_start: 0.8020 (OUTLIER) cc_final: 0.7364 (p-90)
  outliers start: 25
  outliers final: 23
  residues processed: 95
  average time/residue: 0.1683
  time to fit residues: 24.9497
Evaluate side-chains
  96 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 109 optimal weight:    0.0670
   chunk 13 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 65 optimal weight:    6.9990
   chunk 6 optimal weight:    0.7980
   chunk 111 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0070
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.5136

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.128613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.103346 restraints weight = 14093.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.105371 restraints weight = 9416.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.106700 restraints weight = 7375.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.121   9342  Z= 0.243
  Angle     :  0.853  59.199  12706  Z= 0.505
  Chirality :  0.044   0.892   1446
  Planarity :  0.004   0.080   1592
  Dihedral  :  3.601  14.855   1238
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 24.89 %
    Favored  : 72.62 %
  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:  2.48 (0.25), residues: 1132
  helix:  2.67 (0.17), residues: 814
  sheet:  0.52 (0.86), residues: 44
  loop : -1.53 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 
 PHE   0.013   0.001   PHE A 379 
 TYR   0.011   0.001   TYR B 383 
 ARG   0.006   0.000   ARG B 710 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2414.60 seconds
wall clock time: 44 minutes 14.86 seconds (2654.86 seconds total)