Starting phenix.real_space_refine
on Mon May 12 00:47:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u56_41913/05_2025/8u56_41913.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u56_41913/05_2025/8u56_41913.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u56_41913/05_2025/8u56_41913.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u56_41913/05_2025/8u56_41913.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u56_41913/05_2025/8u56_41913.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u56_41913/05_2025/8u56_41913.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.036
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: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5814      2.51       5
     N    1300      2.21       5
     O    1418      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8588
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4253
          Classifications: {'peptide': 541}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 521}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'LMN': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'Y01:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.76, per 1000 atoms: 0.90
  Number of scatterers: 8588
  At special positions: 0
  Unit cell: (101.215, 124.276, 75.5908, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1418      8.00
     N    1300      7.00
     C    5814      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 967.2 milliseconds
  

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      91.5% alpha, 0.0% 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 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 41 through 62
    Processing helix  chain 'A' and resid 66 through 80
      removed outlier: 3.631A  pdb=" N   LYS A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLY A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LEU A  73 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 93
    Processing helix  chain 'A' and resid 94 through 98
    Processing helix  chain 'A' and resid 99 through 125
    Processing helix  chain 'A' and resid 129 through 143
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 159
    Processing helix  chain 'A' and resid 164 through 194
      removed outlier: 3.901A  pdb=" N   TYR A 168 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ILE A 169 " --> pdb=" O   TYR A 165 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   TYR A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 204 through 216
    Processing helix  chain 'A' and resid 217 through 234
    Processing helix  chain 'A' and resid 238 through 265
      removed outlier: 3.672A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   SER A 253 " --> pdb=" O   GLY A 249 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   GLY A 254 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL A 265 " --> pdb=" O   GLY A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 288
    Processing helix  chain 'A' and resid 288 through 302
    Processing helix  chain 'A' and resid 306 through 323
    Processing helix  chain 'A' and resid 326 through 336
      removed outlier: 4.120A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 3.617A  pdb=" N   ALA A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 368 through 370
      No H-bonds generated for 'chain 'A' and resid 368 through 370'
    Processing helix  chain 'A' and resid 371 through 404
    Processing helix  chain 'A' and resid 405 through 409
    Processing helix  chain 'A' and resid 411 through 436
      removed outlier: 3.576A  pdb=" N   PHE A 434 " --> pdb=" O   MET A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 473
    Processing helix  chain 'A' and resid 482 through 501
      removed outlier: 3.994A  pdb=" N   ILE A 491 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
      Proline residue:  A 492  - end of helix
      removed outlier: 3.729A  pdb=" N   VAL A 496 " --> pdb=" O   PRO A 492 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLY A 497 " --> pdb=" O   ALA A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 543
    Processing helix  chain 'A' and resid 655 through 682
    Processing helix  chain 'A' and resid 689 through 712
      removed outlier: 5.869A  pdb=" N   GLY A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
      removed outlier: 5.383A  pdb=" N   PHE A 705 " --> pdb=" O   PHE A 701 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE A 706 " --> pdb=" O   GLY A 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 40
      No H-bonds generated for 'chain 'B' and resid 38 through 40'
    Processing helix  chain 'B' and resid 41 through 62
    Processing helix  chain 'B' and resid 66 through 80
      removed outlier: 3.629A  pdb=" N   LYS B  71 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLY B  72 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LEU B  73 " --> pdb=" O   GLN B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 93
    Processing helix  chain 'B' and resid 94 through 98
    Processing helix  chain 'B' and resid 99 through 125
    Processing helix  chain 'B' and resid 129 through 143
      Proline residue:  B 138  - end of helix
    Processing helix  chain 'B' and resid 149 through 159
    Processing helix  chain 'B' and resid 164 through 194
      removed outlier: 3.900A  pdb=" N   TYR B 168 " --> pdb=" O   GLU B 164 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ILE B 169 " --> pdb=" O   TYR B 165 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   TYR B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      Proline residue:  B 174  - end of helix
      Proline residue:  B 182  - end of helix
    Processing helix  chain 'B' and resid 204 through 216
    Processing helix  chain 'B' and resid 217 through 234
    Processing helix  chain 'B' and resid 238 through 265
      removed outlier: 3.670A  pdb=" N   PHE B 244 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   SER B 253 " --> pdb=" O   GLY B 249 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   GLY B 254 " --> pdb=" O   ASN B 250 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL B 265 " --> pdb=" O   GLY B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 288
    Processing helix  chain 'B' and resid 288 through 302
    Processing helix  chain 'B' and resid 306 through 323
    Processing helix  chain 'B' and resid 326 through 336
      removed outlier: 4.120A  pdb=" N   ALA B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 367
      removed outlier: 3.617A  pdb=" N   ALA B 355 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      Proline residue:  B 356  - end of helix
    Processing helix  chain 'B' and resid 368 through 370
      No H-bonds generated for 'chain 'B' and resid 368 through 370'
    Processing helix  chain 'B' and resid 371 through 404
    Processing helix  chain 'B' and resid 405 through 409
    Processing helix  chain 'B' and resid 411 through 436
      removed outlier: 3.577A  pdb=" N   PHE B 434 " --> pdb=" O   MET B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 473
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 3.992A  pdb=" N   ILE B 491 " --> pdb=" O   SER B 487 " (cutoff:3.500A)
      Proline residue:  B 492  - end of helix
      removed outlier: 3.728A  pdb=" N   VAL B 496 " --> pdb=" O   PRO B 492 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLY B 497 " --> pdb=" O   ALA B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 543
    Processing helix  chain 'B' and resid 655 through 682
    Processing helix  chain 'B' and resid 689 through 712
      removed outlier: 5.870A  pdb=" N   GLY B 704 " --> pdb=" O   ASN B 700 " (cutoff:3.500A)
      removed outlier: 5.383A  pdb=" N   PHE B 705 " --> pdb=" O   PHE B 701 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE B 706 " --> pdb=" O   GLY B 702 " (cutoff:3.500A)

    722 hydrogen bonds defined for protein.
    2142 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: 2.47

  Time building geometry restraints manager: 2.55 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1250
        1.32 -     1.44: 2387
        1.44 -     1.57: 5067
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 8794
  Sorted by residual:
  bond pdb=" CD1 TYR A 320 "
       pdb=" CE1 TYR A 320 "
    ideal  model  delta    sigma   weight residual
    1.382  1.337  0.045 3.00e-02 1.11e+03 2.25e+00
  bond pdb=" CD1 TYR B 320 "
       pdb=" CE1 TYR B 320 "
    ideal  model  delta    sigma   weight residual
    1.382  1.338  0.044 3.00e-02 1.11e+03 2.11e+00
  bond pdb=" CB  TYR A 320 "
       pdb=" CG  TYR A 320 "
    ideal  model  delta    sigma   weight residual
    1.512  1.481  0.031 2.20e-02 2.07e+03 2.02e+00
  bond pdb=" C   LEU B 665 "
       pdb=" O   LEU B 665 "
    ideal  model  delta    sigma   weight residual
    1.237  1.220  0.017 1.19e-02 7.06e+03 2.01e+00
  bond pdb=" C   SER B 251 "
       pdb=" O   SER B 251 "
    ideal  model  delta    sigma   weight residual
    1.236  1.253 -0.018 1.29e-02 6.01e+03 1.92e+00
  ... (remaining 8789 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 11371
        2.02 -     4.04: 484
        4.04 -     6.05: 75
        6.05 -     8.07: 8
        8.07 -    10.09: 4
  Bond angle restraints: 11942
  Sorted by residual:
  angle pdb=" C   GLU A 242 "
        pdb=" N   ASN A 243 "
        pdb=" CA  ASN A 243 "
      ideal   model   delta    sigma   weight residual
     121.58  111.49   10.09 1.95e+00 2.63e-01 2.68e+01
  angle pdb=" C   GLU B 242 "
        pdb=" N   ASN B 243 "
        pdb=" CA  ASN B 243 "
      ideal   model   delta    sigma   weight residual
     121.58  111.49   10.09 1.95e+00 2.63e-01 2.68e+01
  angle pdb=" C   VAL A 698 "
        pdb=" N   PHE A 699 "
        pdb=" CA  PHE A 699 "
      ideal   model   delta    sigma   weight residual
     120.44  115.63    4.81 1.36e+00 5.41e-01 1.25e+01
  angle pdb=" CA  PHE A 221 "
        pdb=" CB  PHE A 221 "
        pdb=" CG  PHE A 221 "
      ideal   model   delta    sigma   weight residual
     113.80  117.32   -3.52 1.00e+00 1.00e+00 1.24e+01
  angle pdb=" CA  PHE B 221 "
        pdb=" CB  PHE B 221 "
        pdb=" CG  PHE B 221 "
      ideal   model   delta    sigma   weight residual
     113.80  117.32   -3.52 1.00e+00 1.00e+00 1.24e+01
  ... (remaining 11937 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.86: 5020
       23.86 -    47.73: 156
       47.73 -    71.59: 30
       71.59 -    95.45: 2
       95.45 -   119.31: 6
  Dihedral angle restraints: 5214
    sinusoidal: 2076
      harmonic: 3138
  Sorted by residual:
  dihedral pdb=" CA  GLN A 143 "
           pdb=" C   GLN A 143 "
           pdb=" N   SER A 144 "
           pdb=" CA  SER A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.38  -26.62     0      5.00e+00 4.00e-02 2.83e+01
  dihedral pdb=" CA  GLN B 143 "
           pdb=" C   GLN B 143 "
           pdb=" N   SER B 144 "
           pdb=" CA  SER B 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.60  -26.40     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  TYR B 516 "
           pdb=" C   TYR B 516 "
           pdb=" N   GLY B 517 "
           pdb=" CA  GLY B 517 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.84   23.16     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 5211 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1048
       0.052 -    0.103: 314
       0.103 -    0.155: 74
       0.155 -    0.206: 4
       0.206 -    0.258: 8
  Chirality restraints: 1448
  Sorted by residual:
  chirality pdb=" CA  ASN B 243 "
            pdb=" N   ASN B 243 "
            pdb=" C   ASN B 243 "
            pdb=" CB  ASN B 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ASN A 243 "
            pdb=" N   ASN A 243 "
            pdb=" C   ASN A 243 "
            pdb=" CB  ASN A 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CB  VAL B 425 "
            pdb=" CA  VAL B 425 "
            pdb=" CG1 VAL B 425 "
            pdb=" CG2 VAL B 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 1445 not shown)

  Planarity restraints: 1406
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 320 "    0.056 2.00e-02 2.50e+03   2.89e-02 1.67e+01
        pdb=" CG  TYR B 320 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 320 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 320 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 320 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 320 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 320 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR B 320 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 320 "    0.056 2.00e-02 2.50e+03   2.85e-02 1.63e+01
        pdb=" CG  TYR A 320 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 320 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 320 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 320 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 320 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 320 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR A 320 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 221 "    0.029 2.00e-02 2.50e+03   2.24e-02 8.75e+00
        pdb=" CG  PHE B 221 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 221 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 221 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 221 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 221 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 221 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1403 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 3367
        2.90 -     3.40: 9559
        3.40 -     3.90: 15526
        3.90 -     4.40: 17942
        4.40 -     4.90: 29501
  Nonbonded interactions: 75895
  Sorted by model distance:
  nonbonded pdb=" CG1 VAL B 348 "
            pdb=" CBQ LMN B 901 "
     model   vdw
     2.398 3.860
  nonbonded pdb=" CG1 VAL A 348 "
            pdb=" CBQ LMN A 901 "
     model   vdw
     2.399 3.860
  nonbonded pdb=" CE  MET A 264 "
            pdb=" CBL LMN A 901 "
     model   vdw
     2.448 3.860
  nonbonded pdb=" CE  MET B 264 "
            pdb=" CBL LMN B 901 "
     model   vdw
     2.449 3.860
  nonbonded pdb=" O   GLN B 520 "
            pdb=" OG1 THR B 524 "
     model   vdw
     2.476 3.040
  ... (remaining 75890 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  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 individual isotropic
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:             0.830
  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:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     23.800
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
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      :  0.007   0.049   8794  Z= 0.330
  Angle     :  0.963  10.090  11942  Z= 0.546
  Chirality :  0.053   0.258   1448
  Planarity :  0.008   0.072   1406
  Dihedral  : 13.549 119.315   3186
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.24), residues: 1058
  helix: -0.39 (0.15), residues: 894
  sheet:  None (None), residues: 0
  loop :  0.01 (0.54), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.005   TRP B 100 
 HIS   0.007   0.003   HIS B 310 
 PHE   0.050   0.005   PHE A 221 
 TYR   0.056   0.005   TYR B 320 
 ARG   0.004   0.001   ARG B 295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10975 (  722)
  hydrogen bonds       : angle       6.41557 ( 2142)
  covalent geometry    : bond        0.00707 ( 8794)
  covalent geometry    : angle       0.96323 (11942)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 311
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TYR cc_start: 0.7773 (m-10) cc_final: 0.7428 (m-10)
REVERT: A  246 ASP cc_start: 0.7917 (m-30) cc_final: 0.7551 (m-30)
REVERT: A  347 MET cc_start: 0.8862 (tmm) cc_final: 0.8661 (tmm)
REVERT: B  104 TYR cc_start: 0.7701 (m-10) cc_final: 0.7489 (m-10)
REVERT: B  136 LEU cc_start: 0.8481 (mt) cc_final: 0.8112 (mt)
REVERT: B  246 ASP cc_start: 0.7902 (m-30) cc_final: 0.7597 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 311
  average time/residue: 0.8659
  time to fit residues: 292.3092
Evaluate side-chains
  167 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0470
   chunk 98 optimal weight:    0.0770
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
A 310 HIS
A 409 GLN
A 672 ASN
A 716 HIS
B 310 HIS
B 409 GLN
B 716 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.137711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.111642 restraints weight = 15902.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.44
r_work: 0.3534 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8794  Z= 0.192
  Angle     :  0.755   7.920  11942  Z= 0.385
  Chirality :  0.043   0.177   1448
  Planarity :  0.005   0.040   1406
  Dihedral  :  7.024  79.260   1280
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 14.01 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.63 (0.26), residues: 1058
  helix:  1.20 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop :  0.92 (0.58), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 432 
 HIS   0.002   0.001   HIS A 412 
 PHE   0.032   0.002   PHE B 221 
 TYR   0.012   0.002   TYR A 168 
 ARG   0.006   0.001   ARG A 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05753 (  722)
  hydrogen bonds       : angle       5.33633 ( 2142)
  covalent geometry    : bond        0.00429 ( 8794)
  covalent geometry    : angle       0.75503 (11942)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 217
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.8270 (ptp-170) cc_final: 0.7716 (ptp-170)
REVERT: A  179 MET cc_start: 0.8408 (mtm) cc_final: 0.7970 (mtm)
REVERT: A  212 LEU cc_start: 0.8896 (tm) cc_final: 0.8578 (mt)
REVERT: A  213 ARG cc_start: 0.8762 (mtp85) cc_final: 0.8355 (mtp85)
REVERT: A  295 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.8001 (ttm-80)
REVERT: A  296 GLU cc_start: 0.8791 (tp30) cc_final: 0.8386 (tp30)
REVERT: A  352 PHE cc_start: 0.8370 (t80) cc_final: 0.7927 (t80)
REVERT: A  396 TRP cc_start: 0.7638 (t60) cc_final: 0.7218 (t60)
REVERT: A  413 MET cc_start: 0.8292 (ptm) cc_final: 0.7799 (ttp)
REVERT: A  417 ASN cc_start: 0.8826 (m-40) cc_final: 0.8269 (m110)
REVERT: A  469 PHE cc_start: 0.8244 (t80) cc_final: 0.7795 (t80)
REVERT: B  130 ARG cc_start: 0.8140 (ptp90) cc_final: 0.7758 (ptp-170)
REVERT: B  179 MET cc_start: 0.8463 (mtm) cc_final: 0.8166 (mtm)
REVERT: B  296 GLU cc_start: 0.8769 (tp30) cc_final: 0.8396 (tp30)
REVERT: B  352 PHE cc_start: 0.8396 (t80) cc_final: 0.7965 (t80)
REVERT: B  396 TRP cc_start: 0.7690 (t60) cc_final: 0.7357 (t60)
REVERT: B  413 MET cc_start: 0.8216 (ptm) cc_final: 0.7932 (ttp)
REVERT: B  417 ASN cc_start: 0.8765 (m-40) cc_final: 0.8246 (m110)
REVERT: B  469 PHE cc_start: 0.8237 (t80) cc_final: 0.7459 (t80)
  outliers start: 39
  outliers final: 2
  residues processed: 237
  average time/residue: 0.8860
  time to fit residues: 227.5814
Evaluate side-chains
  178 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 176
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain B residue  119 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 104 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 716 HIS
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 716 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.135631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.108936 restraints weight = 16305.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.54
r_work: 0.3493 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8794  Z= 0.208
  Angle     :  0.744  10.338  11942  Z= 0.369
  Chirality :  0.044   0.268   1448
  Planarity :  0.005   0.036   1406
  Dihedral  :  6.486  71.317   1280
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.00 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  2.19 (0.26), residues: 1058
  helix:  1.59 (0.17), residues: 884
  sheet:  None (None), residues: 0
  loop :  1.10 (0.57), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 363 
 HIS   0.001   0.001   HIS A 716 
 PHE   0.029   0.002   PHE A 384 
 TYR   0.013   0.002   TYR B 455 
 ARG   0.006   0.001   ARG B 657 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05323 (  722)
  hydrogen bonds       : angle       5.16754 ( 2142)
  covalent geometry    : bond        0.00486 ( 8794)
  covalent geometry    : angle       0.74436 (11942)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 190
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.8280 (ptp-170) cc_final: 0.7944 (ptp-170)
REVERT: A  413 MET cc_start: 0.8095 (ptm) cc_final: 0.7827 (ttp)
REVERT: A  417 ASN cc_start: 0.8809 (m-40) cc_final: 0.8232 (m110)
REVERT: A  430 MET cc_start: 0.7570 (mtp) cc_final: 0.7342 (mtp)
REVERT: A  458 TYR cc_start: 0.7667 (m-10) cc_final: 0.7461 (m-80)
REVERT: A  514 PHE cc_start: 0.7772 (m-80) cc_final: 0.7210 (m-80)
REVERT: B  130 ARG cc_start: 0.8261 (ptp90) cc_final: 0.7861 (ptp-170)
REVERT: B  296 GLU cc_start: 0.8760 (tp30) cc_final: 0.8330 (tp30)
REVERT: B  297 MET cc_start: 0.8576 (mmt) cc_final: 0.8302 (mpt)
REVERT: B  299 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7571 (mm-30)
REVERT: B  413 MET cc_start: 0.8086 (ptm) cc_final: 0.7805 (ttp)
REVERT: B  417 ASN cc_start: 0.8841 (m-40) cc_final: 0.8267 (m110)
REVERT: B  430 MET cc_start: 0.7537 (mtp) cc_final: 0.7320 (mtp)
REVERT: B  447 PHE cc_start: 0.8187 (t80) cc_final: 0.7983 (t80)
REVERT: B  514 PHE cc_start: 0.7759 (m-80) cc_final: 0.7179 (m-80)
REVERT: B  714 ASP cc_start: 0.8099 (t0) cc_final: 0.7895 (t0)
  outliers start: 32
  outliers final: 7
  residues processed: 210
  average time/residue: 0.9006
  time to fit residues: 205.0126
Evaluate side-chains
  174 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 167
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  288 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 337 ASN
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 716 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.134825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.108199 restraints weight = 16149.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.54
r_work: 0.3482 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8794  Z= 0.211
  Angle     :  0.709   7.495  11942  Z= 0.357
  Chirality :  0.044   0.299   1448
  Planarity :  0.005   0.048   1406
  Dihedral  :  6.509  73.097   1280
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 18.26 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 (0.26), residues: 1058
  helix:  1.74 (0.17), residues: 886
  sheet:  None (None), residues: 0
  loop :  1.29 (0.57), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 363 
 HIS   0.001   0.001   HIS A 412 
 PHE   0.031   0.002   PHE A 221 
 TYR   0.012   0.002   TYR B 455 
 ARG   0.009   0.001   ARG B 657 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05138 (  722)
  hydrogen bonds       : angle       5.08184 ( 2142)
  covalent geometry    : bond        0.00500 ( 8794)
  covalent geometry    : angle       0.70912 (11942)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 179
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.8367 (mtm-85)
REVERT: A  130 ARG cc_start: 0.8272 (ptp-170) cc_final: 0.7918 (ptp-170)
REVERT: A  215 LEU cc_start: 0.9335 (mt) cc_final: 0.9089 (mm)
REVERT: A  296 GLU cc_start: 0.8797 (tp30) cc_final: 0.8363 (tp30)
REVERT: A  370 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6718 (mmt)
REVERT: A  413 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7817 (ttp)
REVERT: A  414 LEU cc_start: 0.8414 (mt) cc_final: 0.8097 (mm)
REVERT: A  417 ASN cc_start: 0.8801 (m-40) cc_final: 0.8172 (m110)
REVERT: A  469 PHE cc_start: 0.8220 (t80) cc_final: 0.7864 (t80)
REVERT: B   41 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8367 (mtm-85)
REVERT: B  130 ARG cc_start: 0.8281 (ptp90) cc_final: 0.7885 (ptp-170)
REVERT: B  215 LEU cc_start: 0.9288 (mt) cc_final: 0.9062 (mm)
REVERT: B  370 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.6911 (mmm)
REVERT: B  413 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7730 (ttp)
REVERT: B  414 LEU cc_start: 0.8409 (mt) cc_final: 0.8112 (mm)
REVERT: B  417 ASN cc_start: 0.8800 (m-40) cc_final: 0.8155 (m110)
REVERT: B  430 MET cc_start: 0.7643 (mtp) cc_final: 0.7437 (mmm)
REVERT: B  469 PHE cc_start: 0.8212 (t80) cc_final: 0.7810 (t80)
REVERT: B  691 GLU cc_start: 0.8739 (mp0) cc_final: 0.8532 (mp0)
  outliers start: 38
  outliers final: 9
  residues processed: 201
  average time/residue: 0.8449
  time to fit residues: 184.9872
Evaluate side-chains
  179 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 166
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  413 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 54 optimal weight:    0.4980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 409 GLN
A 716 HIS
B 337 ASN
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.135501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.109006 restraints weight = 16201.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.54
r_work: 0.3497 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.4510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8794  Z= 0.197
  Angle     :  0.705   8.425  11942  Z= 0.353
  Chirality :  0.043   0.248   1448
  Planarity :  0.004   0.033   1406
  Dihedral  :  6.479  74.608   1280
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.64 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  2.51 (0.26), residues: 1058
  helix:  1.80 (0.17), residues: 884
  sheet:  None (None), residues: 0
  loop :  1.26 (0.58), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 363 
 HIS   0.001   0.001   HIS B 716 
 PHE   0.035   0.002   PHE B 384 
 TYR   0.023   0.002   TYR A 458 
 ARG   0.007   0.001   ARG B 657 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04998 (  722)
  hydrogen bonds       : angle       5.04810 ( 2142)
  covalent geometry    : bond        0.00465 ( 8794)
  covalent geometry    : angle       0.70542 (11942)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 176
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.8402 (mtm-85)
REVERT: A  130 ARG cc_start: 0.8343 (ptp-170) cc_final: 0.8023 (ptp-170)
REVERT: A  215 LEU cc_start: 0.9252 (mt) cc_final: 0.9010 (mm)
REVERT: A  246 ASP cc_start: 0.8597 (m-30) cc_final: 0.8232 (m-30)
REVERT: A  296 GLU cc_start: 0.8763 (tp30) cc_final: 0.8321 (tp30)
REVERT: A  370 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6896 (mmm)
REVERT: A  417 ASN cc_start: 0.8798 (m-40) cc_final: 0.8272 (m110)
REVERT: A  430 MET cc_start: 0.7598 (mmm) cc_final: 0.7268 (mmm)
REVERT: A  459 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8325 (mt)
REVERT: A  469 PHE cc_start: 0.8228 (t80) cc_final: 0.7861 (t80)
REVERT: A  514 PHE cc_start: 0.8009 (m-80) cc_final: 0.7711 (p90)
REVERT: B   41 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.8404 (mtm-85)
REVERT: B  130 ARG cc_start: 0.8314 (ptp90) cc_final: 0.7972 (ptp-170)
REVERT: B  215 LEU cc_start: 0.9265 (mt) cc_final: 0.8992 (mm)
REVERT: B  246 ASP cc_start: 0.8538 (m-30) cc_final: 0.8149 (m-30)
REVERT: B  296 GLU cc_start: 0.8721 (tp30) cc_final: 0.8358 (tp30)
REVERT: B  370 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.6917 (mmm)
REVERT: B  413 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7625 (ttp)
REVERT: B  417 ASN cc_start: 0.8798 (m-40) cc_final: 0.8248 (m110)
REVERT: B  459 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8296 (mt)
REVERT: B  657 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7674 (ttm-80)
  outliers start: 36
  outliers final: 10
  residues processed: 196
  average time/residue: 0.9135
  time to fit residues: 194.2644
Evaluate side-chains
  178 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 163
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  459 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 93 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0050
   chunk 69 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
A 409 GLN
A 716 HIS
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 716 HIS ** 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 = 0.4032 r_free = 0.4032 target = 0.136151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.109451 restraints weight = 15985.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.53
r_work: 0.3510 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.4717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   8794  Z= 0.189
  Angle     :  0.709   7.791  11942  Z= 0.358
  Chirality :  0.044   0.232   1448
  Planarity :  0.004   0.034   1406
  Dihedral  :  6.425  75.841   1280
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 20.49 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  2.58 (0.26), residues: 1058
  helix:  1.86 (0.17), residues: 886
  sheet:  None (None), residues: 0
  loop :  1.17 (0.57), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 460 
 HIS   0.002   0.001   HIS A 412 
 PHE   0.027   0.002   PHE A 221 
 TYR   0.014   0.002   TYR B 455 
 ARG   0.007   0.001   ARG A 657 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04882 (  722)
  hydrogen bonds       : angle       5.01131 ( 2142)
  covalent geometry    : bond        0.00452 ( 8794)
  covalent geometry    : angle       0.70909 (11942)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 180
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.8354 (ptp-170) cc_final: 0.8070 (ptp-170)
REVERT: A  159 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8129 (pm20)
REVERT: A  213 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8149 (ptm-80)
REVERT: A  370 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6830 (mmm)
REVERT: A  417 ASN cc_start: 0.8803 (m-40) cc_final: 0.8215 (m110)
REVERT: A  459 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8442 (mt)
REVERT: A  469 PHE cc_start: 0.8221 (t80) cc_final: 0.7869 (t80)
REVERT: A  657 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7652 (ttm110)
REVERT: B  130 ARG cc_start: 0.8319 (ptp90) cc_final: 0.7972 (ptp-170)
REVERT: B  159 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8168 (pm20)
REVERT: B  246 ASP cc_start: 0.8568 (m-30) cc_final: 0.8187 (m-30)
REVERT: B  296 GLU cc_start: 0.8737 (tp30) cc_final: 0.8367 (tp30)
REVERT: B  370 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6876 (mmm)
REVERT: B  413 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7647 (ttp)
REVERT: B  417 ASN cc_start: 0.8801 (m-40) cc_final: 0.8272 (m110)
REVERT: B  430 MET cc_start: 0.7416 (mmm) cc_final: 0.7025 (mmm)
REVERT: B  459 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8313 (mt)
REVERT: B  469 PHE cc_start: 0.8216 (t80) cc_final: 0.7857 (t80)
REVERT: B  657 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7694 (ttm110)
REVERT: B  714 ASP cc_start: 0.7937 (t0) cc_final: 0.7721 (t0)
  outliers start: 37
  outliers final: 12
  residues processed: 202
  average time/residue: 0.9166
  time to fit residues: 199.9636
Evaluate side-chains
  181 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  213 ARG
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  159 GLN
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  459 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 32 optimal weight:    0.9980
   chunk 84 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0670
   chunk 88 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 409 GLN
A 716 HIS
B 337 ASN
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 520 GLN
B 716 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.137666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.112013 restraints weight = 16062.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.49
r_work: 0.3541 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.4943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8794  Z= 0.170
  Angle     :  0.727   8.068  11942  Z= 0.364
  Chirality :  0.043   0.241   1448
  Planarity :  0.004   0.031   1406
  Dihedral  :  6.406  76.993   1280
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 22.61 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  2.66 (0.26), residues: 1058
  helix:  1.94 (0.17), residues: 884
  sheet:  None (None), residues: 0
  loop :  1.12 (0.57), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 460 
 HIS   0.001   0.001   HIS A 658 
 PHE   0.035   0.002   PHE A 384 
 TYR   0.014   0.002   TYR B 359 
 ARG   0.006   0.001   ARG A 657 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04738 (  722)
  hydrogen bonds       : angle       4.95709 ( 2142)
  covalent geometry    : bond        0.00398 ( 8794)
  covalent geometry    : angle       0.72720 (11942)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 182
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.8312 (ptp-170) cc_final: 0.8042 (ptp-170)
REVERT: A  417 ASN cc_start: 0.8783 (m-40) cc_final: 0.8271 (m110)
REVERT: A  430 MET cc_start: 0.7589 (mmm) cc_final: 0.7338 (mpp)
REVERT: A  459 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8432 (mt)
REVERT: A  469 PHE cc_start: 0.8230 (t80) cc_final: 0.7893 (t80)
REVERT: A  657 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7719 (ttm110)
REVERT: B  130 ARG cc_start: 0.8271 (ptp90) cc_final: 0.7977 (ptp-170)
REVERT: B  246 ASP cc_start: 0.8496 (m-30) cc_final: 0.8168 (m-30)
REVERT: B  296 GLU cc_start: 0.8638 (tp30) cc_final: 0.8269 (tp30)
REVERT: B  417 ASN cc_start: 0.8786 (m-40) cc_final: 0.8281 (m110)
REVERT: B  458 TYR cc_start: 0.7646 (m-10) cc_final: 0.6837 (m-10)
REVERT: B  459 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8496 (mt)
REVERT: B  469 PHE cc_start: 0.8217 (t80) cc_final: 0.7836 (t80)
REVERT: B  657 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7735 (ttm110)
  outliers start: 32
  outliers final: 11
  residues processed: 199
  average time/residue: 0.9339
  time to fit residues: 201.4086
Evaluate side-chains
  181 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 168
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  459 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0980
   chunk 80 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 716 HIS
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 716 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.134953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.108370 restraints weight = 16394.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.56
r_work: 0.3486 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8794  Z= 0.235
  Angle     :  0.784   8.703  11942  Z= 0.391
  Chirality :  0.045   0.248   1448
  Planarity :  0.004   0.027   1406
  Dihedral  :  6.342  77.859   1280
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 23.25 %
    Favored  : 73.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  2.47 (0.26), residues: 1058
  helix:  1.81 (0.17), residues: 886
  sheet:  None (None), residues: 0
  loop :  1.03 (0.56), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 100 
 HIS   0.002   0.001   HIS B 412 
 PHE   0.031   0.002   PHE A 701 
 TYR   0.015   0.002   TYR B 320 
 ARG   0.005   0.001   ARG A 657 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04933 (  722)
  hydrogen bonds       : angle       5.05462 ( 2142)
  covalent geometry    : bond        0.00570 ( 8794)
  covalent geometry    : angle       0.78408 (11942)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 168
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.8383 (ptp-170) cc_final: 0.8100 (ptp-170)
REVERT: A  159 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8167 (pm20)
REVERT: A  213 ARG cc_start: 0.8642 (ptm160) cc_final: 0.8330 (ptm-80)
REVERT: A  370 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6875 (mmm)
REVERT: A  417 ASN cc_start: 0.8812 (m-40) cc_final: 0.8253 (m110)
REVERT: A  459 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8408 (mt)
REVERT: A  539 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7934 (mp)
REVERT: A  657 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7655 (ttm-80)
REVERT: B  130 ARG cc_start: 0.8321 (ptp90) cc_final: 0.7961 (ptp-170)
REVERT: B  159 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8188 (pm20)
REVERT: B  213 ARG cc_start: 0.8700 (ptm160) cc_final: 0.8429 (ptm-80)
REVERT: B  296 GLU cc_start: 0.8750 (tp30) cc_final: 0.8364 (tp30)
REVERT: B  370 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6878 (mmm)
REVERT: B  417 ASN cc_start: 0.8801 (m-40) cc_final: 0.8259 (m110)
REVERT: B  430 MET cc_start: 0.7687 (mmm) cc_final: 0.7382 (mpp)
REVERT: B  459 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8398 (mt)
REVERT: B  469 PHE cc_start: 0.8227 (t80) cc_final: 0.7862 (t80)
REVERT: B  539 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8090 (mp)
REVERT: B  657 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7610 (ttm110)
REVERT: B  714 ASP cc_start: 0.7837 (t0) cc_final: 0.7139 (t0)
REVERT: B  716 HIS cc_start: 0.6098 (m90) cc_final: 0.5569 (m-70)
  outliers start: 31
  outliers final: 14
  residues processed: 189
  average time/residue: 0.9435
  time to fit residues: 192.6243
Evaluate side-chains
  178 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  159 GLN
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  539 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 86 optimal weight:    0.1980
   chunk 48 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 GLN
A 716 HIS
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 693 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.137511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.111554 restraints weight = 16200.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 2.49
r_work: 0.3534 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.5061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8794  Z= 0.182
  Angle     :  0.766   9.270  11942  Z= 0.383
  Chirality :  0.044   0.219   1448
  Planarity :  0.004   0.027   1406
  Dihedral  :  6.379  76.345   1280
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 24.10 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 (0.26), residues: 1058
  helix:  1.91 (0.17), residues: 882
  sheet:  None (None), residues: 0
  loop :  0.94 (0.57), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 460 
 HIS   0.001   0.000   HIS A 658 
 PHE   0.029   0.002   PHE B 384 
 TYR   0.020   0.002   TYR B 451 
 ARG   0.005   0.001   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04784 (  722)
  hydrogen bonds       : angle       5.02240 ( 2142)
  covalent geometry    : bond        0.00439 ( 8794)
  covalent geometry    : angle       0.76566 (11942)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 180
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.8298 (ptp-170) cc_final: 0.8035 (ptp-170)
REVERT: A  159 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8169 (pm20)
REVERT: A  370 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6898 (mmm)
REVERT: A  417 ASN cc_start: 0.8784 (m-40) cc_final: 0.8230 (m110)
REVERT: A  459 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8429 (mt)
REVERT: A  469 PHE cc_start: 0.8285 (t80) cc_final: 0.7862 (t80)
REVERT: A  657 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7713 (ttm-80)
REVERT: A  714 ASP cc_start: 0.7789 (t0) cc_final: 0.7283 (t0)
REVERT: B  130 ARG cc_start: 0.8280 (ptp90) cc_final: 0.7994 (ptp-170)
REVERT: B  159 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8204 (pm20)
REVERT: B  296 GLU cc_start: 0.8661 (tp30) cc_final: 0.8275 (tp30)
REVERT: B  370 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6918 (mmm)
REVERT: B  417 ASN cc_start: 0.8757 (m-40) cc_final: 0.8234 (m110)
REVERT: B  455 TYR cc_start: 0.7769 (m-80) cc_final: 0.7451 (m-80)
REVERT: B  459 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8396 (mt)
REVERT: B  469 PHE cc_start: 0.8285 (t80) cc_final: 0.7925 (t80)
REVERT: B  657 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7672 (ttm110)
REVERT: B  714 ASP cc_start: 0.7818 (t0) cc_final: 0.7136 (t0)
REVERT: B  716 HIS cc_start: 0.6201 (m90) cc_final: 0.5806 (m-70)
  outliers start: 24
  outliers final: 10
  residues processed: 194
  average time/residue: 0.9699
  time to fit residues: 203.2779
Evaluate side-chains
  183 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  159 GLN
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  459 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0870
   chunk 57 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 337 ASN
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 693 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.137129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.110787 restraints weight = 16074.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.52
r_work: 0.3525 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.5164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   8794  Z= 0.202
  Angle     :  0.796   9.198  11942  Z= 0.400
  Chirality :  0.044   0.233   1448
  Planarity :  0.004   0.032   1406
  Dihedral  :  6.320  77.031   1280
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 24.84 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 (0.26), residues: 1058
  helix:  1.83 (0.17), residues: 886
  sheet:  None (None), residues: 0
  loop :  1.01 (0.58), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 100 
 HIS   0.006   0.001   HIS A 716 
 PHE   0.027   0.002   PHE B 384 
 TYR   0.019   0.002   TYR A 451 
 ARG   0.006   0.001   ARG B 474 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04859 (  722)
  hydrogen bonds       : angle       5.06658 ( 2142)
  covalent geometry    : bond        0.00491 ( 8794)
  covalent geometry    : angle       0.79634 (11942)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 174
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.8301 (ptp-170) cc_final: 0.7985 (ptp-170)
REVERT: A  159 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8188 (pm20)
REVERT: A  215 LEU cc_start: 0.9217 (mt) cc_final: 0.8979 (mm)
REVERT: A  417 ASN cc_start: 0.8759 (m-40) cc_final: 0.8172 (m110)
REVERT: A  420 ILE cc_start: 0.8770 (mp) cc_final: 0.8278 (tp)
REVERT: A  459 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8411 (mt)
REVERT: A  469 PHE cc_start: 0.8307 (t80) cc_final: 0.7900 (t80)
REVERT: A  539 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7878 (mp)
REVERT: A  657 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7693 (ttm-80)
REVERT: B  130 ARG cc_start: 0.8267 (ptp90) cc_final: 0.7984 (ptp-170)
REVERT: B  159 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8213 (pm20)
REVERT: B  179 MET cc_start: 0.8695 (ttp) cc_final: 0.8416 (ptm)
REVERT: B  296 GLU cc_start: 0.8703 (tp30) cc_final: 0.8294 (tp30)
REVERT: B  370 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6876 (mmm)
REVERT: B  417 ASN cc_start: 0.8758 (m-40) cc_final: 0.8222 (m110)
REVERT: B  455 TYR cc_start: 0.7773 (m-80) cc_final: 0.7440 (m-80)
REVERT: B  458 TYR cc_start: 0.7648 (m-10) cc_final: 0.6947 (m-10)
REVERT: B  459 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8391 (mt)
REVERT: B  469 PHE cc_start: 0.8260 (t80) cc_final: 0.7898 (t80)
REVERT: B  539 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7942 (mp)
REVERT: B  657 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7647 (ttm110)
REVERT: B  714 ASP cc_start: 0.7838 (t0) cc_final: 0.7139 (t0)
REVERT: B  716 HIS cc_start: 0.6255 (m90) cc_final: 0.5939 (m-70)
  outliers start: 20
  outliers final: 10
  residues processed: 184
  average time/residue: 0.9299
  time to fit residues: 184.5492
Evaluate side-chains
  183 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  159 GLN
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  539 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 90 optimal weight:    0.3980
   chunk 93 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 409 GLN
B 693 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.144555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.119255 restraints weight = 16394.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.75
r_work: 0.3594 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.5181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8794  Z= 0.193
  Angle     :  0.790  10.987  11942  Z= 0.395
  Chirality :  0.045   0.227   1448
  Planarity :  0.004   0.034   1406
  Dihedral  :  6.305  75.397   1280
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 24.52 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 (0.26), residues: 1058
  helix:  1.84 (0.17), residues: 886
  sheet:  None (None), residues: 0
  loop :  0.99 (0.58), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 460 
 HIS   0.006   0.001   HIS A 716 
 PHE   0.037   0.002   PHE A 701 
 TYR   0.026   0.002   TYR A 458 
 ARG   0.006   0.001   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04813 (  722)
  hydrogen bonds       : angle       5.05828 ( 2142)
  covalent geometry    : bond        0.00471 ( 8794)
  covalent geometry    : angle       0.78973 (11942)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5784.09 seconds
wall clock time: 100 minutes 35.58 seconds (6035.58 seconds total)