Starting phenix.real_space_refine
on Tue Apr 29 02:14:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uve_42617/04_2025/8uve_42617.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uve_42617/04_2025/8uve_42617.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uve_42617/04_2025/8uve_42617.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uve_42617/04_2025/8uve_42617.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uve_42617/04_2025/8uve_42617.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uve_42617/04_2025/8uve_42617.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.059
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      51      5.16       5
     Na      2      4.78       5
     C    5730      2.51       5
     N    1249      2.21       5
     O    1339      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8373
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 3887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3887
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 33, 'TRANS': 463}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 4011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 4011
          Classifications: {'peptide': 513}
          Link IDs: {'PTRANS': 34, 'TRANS': 478}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 219
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 219
          Unusual residues: {' NA': 1, 'C14': 3, 'CLR': 6, 'SIN': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
    Chain: "A"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 256
          Unusual residues: {' NA': 1, '3PE': 2, 'C14': 3, 'CLR': 4, 'SIN': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
  Time building chain proxies: 6.23, per 1000 atoms: 0.74
  Number of scatterers: 8373
  At special positions: 0
  Unit cell: (88.275, 106.425, 84.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      51     16.00
     P       2     15.00
     Na      2     11.00
     O    1339      8.00
     N    1249      7.00
     C    5730      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: 2.48
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1892

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 0 sheets defined
      82.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 14
      removed outlier: 3.566A  pdb=" N   ALA B  14 " --> pdb=" O   LYS B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 34
      Proline residue:  B  24  - end of helix
      Proline residue:  B  29  - end of helix
      removed outlier: 3.735A  pdb=" N   PHE B  32 " --> pdb=" O   LEU B  28 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU B  34 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 55
    Processing helix  chain 'B' and resid 58 through 64
    Processing helix  chain 'B' and resid 64 through 73
      removed outlier: 3.836A  pdb=" N   VAL B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      Proline residue:  B  71  - end of helix
    Processing helix  chain 'B' and resid 77 through 82
    Processing helix  chain 'B' and resid 83 through 86
      removed outlier: 3.539A  pdb=" N   PHE B  86 " --> pdb=" O   PRO B  83 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 83 through 86'
    Processing helix  chain 'B' and resid 87 through 106
      removed outlier: 3.581A  pdb=" N   TRP B 106 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 121
      removed outlier: 3.632A  pdb=" N   ARG B 111 " --> pdb=" O   ASN B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 140
    Processing helix  chain 'B' and resid 143 through 163
      Proline residue:  B 153  - end of helix
    Processing helix  chain 'B' and resid 225 through 246
      removed outlier: 4.686A  pdb=" N   ILE B 238 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      Proline residue:  B 239  - end of helix
    Processing helix  chain 'B' and resid 253 through 267
      removed outlier: 3.861A  pdb=" N   LEU B 257 " --> pdb=" O   THR B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 301
      Proline residue:  B 284  - end of helix
    Processing helix  chain 'B' and resid 320 through 336
      removed outlier: 3.547A  pdb=" N   GLY B 336 " --> pdb=" O   TYR B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 359
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 377 through 390
      removed outlier: 3.660A  pdb=" N   THR B 381 " --> pdb=" O   SER B 377 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ILE B 388 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   PHE B 390 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 404
      removed outlier: 4.093A  pdb=" N   PHE B 403 " --> pdb=" O   LEU B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 425
    Processing helix  chain 'B' and resid 426 through 446
      removed outlier: 3.573A  pdb=" N   ILE B 430 " --> pdb=" O   PRO B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 456
    Processing helix  chain 'B' and resid 463 through 479
    Processing helix  chain 'B' and resid 483 through 502
      Proline residue:  B 493  - end of helix
      removed outlier: 3.621A  pdb=" N   ILE B 500 " --> pdb=" O   ALA B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 517
      Proline residue:  B 512  - end of helix
    Processing helix  chain 'B' and resid 527 through 535
    Processing helix  chain 'B' and resid 540 through 566
      removed outlier: 4.008A  pdb=" N   LEU B 550 " --> pdb=" O   ARG B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 571
    Processing helix  chain 'A' and resid 2 through 14
    Processing helix  chain 'A' and resid 14 through 28
      Proline residue:  A  24  - end of helix
    Processing helix  chain 'A' and resid 28 through 34
      removed outlier: 3.972A  pdb=" N   PHE A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 55
    Processing helix  chain 'A' and resid 58 through 64
    Processing helix  chain 'A' and resid 64 through 73
      removed outlier: 3.891A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      Proline residue:  A  71  - end of helix
    Processing helix  chain 'A' and resid 77 through 82
    Processing helix  chain 'A' and resid 83 through 86
      removed outlier: 3.552A  pdb=" N   PHE A  86 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 83 through 86'
    Processing helix  chain 'A' and resid 87 through 106
      removed outlier: 3.577A  pdb=" N   TRP A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 121
      removed outlier: 3.710A  pdb=" N   GLY A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 140
    Processing helix  chain 'A' and resid 143 through 163
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 220 through 247
      removed outlier: 3.973A  pdb=" N   ASP A 224 " --> pdb=" O   SER A 220 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ILE A 238 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
      removed outlier: 3.853A  pdb=" N   THR A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 267
      removed outlier: 4.004A  pdb=" N   LEU A 257 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 301
      Proline residue:  A 284  - end of helix
    Processing helix  chain 'A' and resid 320 through 334
    Processing helix  chain 'A' and resid 339 through 359
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 377 through 389
      removed outlier: 3.822A  pdb=" N   ILE A 388 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   LEU A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 4.228A  pdb=" N   PHE A 403 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 425
    Processing helix  chain 'A' and resid 426 through 446
    Processing helix  chain 'A' and resid 447 through 456
    Processing helix  chain 'A' and resid 463 through 479
    Processing helix  chain 'A' and resid 483 through 502
      Proline residue:  A 493  - end of helix
    Processing helix  chain 'A' and resid 506 through 517
      Proline residue:  A 512  - end of helix
    Processing helix  chain 'A' and resid 527 through 535
    Processing helix  chain 'A' and resid 540 through 566
      removed outlier: 4.035A  pdb=" N   LEU A 550 " --> pdb=" O   ARG A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 572

    532 hydrogen bonds defined for protein.
    1578 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: 2.44

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1240
        1.32 -     1.44: 2204
        1.44 -     1.57: 5084
        1.57 -     1.69: 4
        1.69 -     1.81: 88
  Bond restraints: 8620
  Sorted by residual:
  bond pdb=" C11 3PE A 705 "
       pdb=" O13 3PE A 705 "
    ideal  model  delta    sigma   weight residual
    1.408  1.457 -0.049 2.00e-02 2.50e+03 5.94e+00
  bond pdb=" C1  3PE A 709 "
       pdb=" O11 3PE A 709 "
    ideal  model  delta    sigma   weight residual
    1.409  1.457 -0.048 2.00e-02 2.50e+03 5.84e+00
  bond pdb=" C11 3PE A 709 "
       pdb=" O13 3PE A 709 "
    ideal  model  delta    sigma   weight residual
    1.408  1.456 -0.048 2.00e-02 2.50e+03 5.80e+00
  bond pdb=" O13 3PE A 709 "
       pdb=" P   3PE A 709 "
    ideal  model  delta    sigma   weight residual
    1.654  1.607  0.047 2.00e-02 2.50e+03 5.52e+00
  bond pdb=" O13 3PE A 705 "
       pdb=" P   3PE A 705 "
    ideal  model  delta    sigma   weight residual
    1.654  1.608  0.046 2.00e-02 2.50e+03 5.38e+00
  ... (remaining 8615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 11556
        2.12 -     4.24: 168
        4.24 -     6.36: 31
        6.36 -     8.48: 2
        8.48 -    10.60: 1
  Bond angle restraints: 11758
  Sorted by residual:
  angle pdb=" CB  MET B 131 "
        pdb=" CG  MET B 131 "
        pdb=" SD  MET B 131 "
      ideal   model   delta    sigma   weight residual
     112.70  102.10   10.60 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" C   TYR B  85 "
        pdb=" N   PHE B  86 "
        pdb=" CA  PHE B  86 "
      ideal   model   delta    sigma   weight residual
     122.62  118.63    3.99 1.63e+00 3.76e-01 6.01e+00
  angle pdb=" C   ILE B 364 "
        pdb=" CA  ILE B 364 "
        pdb=" CB  ILE B 364 "
      ideal   model   delta    sigma   weight residual
     110.13  112.22   -2.09 9.70e-01 1.06e+00 4.65e+00
  angle pdb=" C   VAL B 425 "
        pdb=" N   PRO B 426 "
        pdb=" CA  PRO B 426 "
      ideal   model   delta    sigma   weight residual
     119.84  122.47   -2.63 1.25e+00 6.40e-01 4.43e+00
  angle pdb=" C   VAL A 425 "
        pdb=" N   PRO A 426 "
        pdb=" CA  PRO A 426 "
      ideal   model   delta    sigma   weight residual
     119.84  122.46   -2.62 1.25e+00 6.40e-01 4.40e+00
  ... (remaining 11753 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.30: 5247
       24.30 -    48.60: 254
       48.60 -    72.90: 39
       72.90 -    97.19: 7
       97.19 -   121.49: 7
  Dihedral angle restraints: 5554
    sinusoidal: 2644
      harmonic: 2910
  Sorted by residual:
  dihedral pdb=" CA  PHE A 363 "
           pdb=" C   PHE A 363 "
           pdb=" N   ILE A 364 "
           pdb=" CA  ILE A 364 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.25   28.75     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  PHE A  86 "
           pdb=" C   PHE A  86 "
           pdb=" N   LEU A  87 "
           pdb=" CA  LEU A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.24   20.76     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" C10 CLR A 710 "
           pdb=" C1  CLR A 710 "
           pdb=" C2  CLR A 710 "
           pdb=" C3  CLR A 710 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.83   64.66 -121.49     1      3.00e+01 1.11e-03 1.62e+01
  ... (remaining 5551 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 993
       0.039 -    0.079: 295
       0.079 -    0.118: 81
       0.118 -    0.157: 15
       0.157 -    0.196: 2
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" C2  3PE A 705 "
            pdb=" C1  3PE A 705 "
            pdb=" C3  3PE A 705 "
            pdb=" O21 3PE A 705 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.33   -0.20 2.00e-01 2.50e+01 9.65e-01
  chirality pdb=" C2  3PE A 709 "
            pdb=" C1  3PE A 709 "
            pdb=" C3  3PE A 709 "
            pdb=" O21 3PE A 709 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.35   -0.17 2.00e-01 2.50e+01 7.33e-01
  chirality pdb=" CA  MET B 131 "
            pdb=" N   MET B 131 "
            pdb=" C   MET B 131 "
            pdb=" CB  MET B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.02e-01
  ... (remaining 1383 not shown)

  Planarity restraints: 1361
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 152 "    0.055 5.00e-02 4.00e+02   8.23e-02 1.08e+01
        pdb=" N   PRO B 153 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO B 153 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B 153 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 528 "    0.046 5.00e-02 4.00e+02   6.90e-02 7.61e+00
        pdb=" N   PRO B 529 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 529 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 529 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  86 "    0.020 2.00e-02 2.50e+03   1.79e-02 5.59e+00
        pdb=" CG  PHE B  86 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  86 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  86 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  86 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  86 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  86 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1358 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1480
        2.76 -     3.30: 8227
        3.30 -     3.83: 14518
        3.83 -     4.37: 17236
        4.37 -     4.90: 29649
  Nonbonded interactions: 71110
  Sorted by model distance:
  nonbonded pdb=" O   ALA B  63 "
            pdb=" OH  TYR B  85 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OE1 GLU B 480 "
            pdb=" N   MET B 522 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   LEU A 561 "
            pdb=" OG1 THR A 565 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OH  TYR A 240 "
            pdb=" O   PHE A 521 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OH  TYR B 240 "
            pdb=" O   PHE B 521 "
     model   vdw
     2.275 3.040
  ... (remaining 71105 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 219 or resid 225 through 303 or resid 319 throug \ 
h 576 or resid 701 through 704 or resid 706 through 708))
  selection = (chain 'B' and (resid 6 through 576 or resid 701 through 704 or resid 706 throug \ 
h 708))
}

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:             1.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.910
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.040
  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:12.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
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      :  0.004   0.049   8620  Z= 0.182
  Angle     :  0.623  10.604  11758  Z= 0.293
  Chirality :  0.041   0.196   1386
  Planarity :  0.006   0.082   1361
  Dihedral  : 14.477 121.493   3662
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.28), residues: 998
  helix:  1.88 (0.20), residues: 765
  sheet:  None (None), residues: 0
  loop :  0.29 (0.45), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 231 
 HIS   0.004   0.001   HIS A 109 
 PHE   0.041   0.001   PHE B  86 
 TYR   0.017   0.001   TYR B 508 
 ARG   0.005   0.000   ARG B 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11269 (  532)
  hydrogen bonds       : angle       4.78880 ( 1578)
  covalent geometry    : bond        0.00390 ( 8620)
  covalent geometry    : angle       0.62268 (11758)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.418 
Fit side-chains
REVERT: B  118 MET cc_start: 0.8172 (mtt) cc_final: 0.7870 (mtm)
REVERT: B  231 TRP cc_start: 0.5846 (m100) cc_final: 0.5072 (m-90)
REVERT: B  508 TYR cc_start: 0.7499 (t80) cc_final: 0.7045 (t80)
REVERT: A  228 ARG cc_start: 0.7408 (mtm180) cc_final: 0.7047 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 1.0341
  time to fit residues: 156.5912
Evaluate side-chains
  118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0060
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
B 538 HIS
A 552 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.148663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112091 restraints weight = 10789.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.96
r_work: 0.3319 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8620  Z= 0.132
  Angle     :  0.591   8.309  11758  Z= 0.282
  Chirality :  0.041   0.162   1386
  Planarity :  0.006   0.072   1361
  Dihedral  :  9.039  84.955   1866
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  8.14 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.28), residues: 998
  helix:  1.94 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop :  0.48 (0.46), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 231 
 HIS   0.008   0.001   HIS B 457 
 PHE   0.017   0.001   PHE B  86 
 TYR   0.014   0.001   TYR B 508 
 ARG   0.005   0.000   ARG B 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03641 (  532)
  hydrogen bonds       : angle       3.94604 ( 1578)
  covalent geometry    : bond        0.00320 ( 8620)
  covalent geometry    : angle       0.59139 (11758)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.874 
Fit side-chains
REVERT: B  141 TRP cc_start: 0.6530 (m100) cc_final: 0.6328 (m100)
REVERT: B  413 GLU cc_start: 0.7546 (tp30) cc_final: 0.7243 (tp30)
REVERT: B  508 TYR cc_start: 0.7510 (t80) cc_final: 0.6979 (t80)
REVERT: A  228 ARG cc_start: 0.7387 (mtm180) cc_final: 0.7152 (mtm110)
REVERT: A  325 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7385 (mtm110)
REVERT: A  572 GLN cc_start: 0.7936 (mm110) cc_final: 0.7612 (mm110)
  outliers start: 19
  outliers final: 8
  residues processed: 136
  average time/residue: 1.0221
  time to fit residues: 150.0533
Evaluate side-chains
  129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 40 optimal weight:    0.3980
   chunk 9 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.148135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.111526 restraints weight = 10964.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.97
r_work: 0.3317 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8620  Z= 0.125
  Angle     :  0.549   6.542  11758  Z= 0.266
  Chirality :  0.040   0.189   1386
  Planarity :  0.006   0.070   1361
  Dihedral  :  8.679  86.754   1866
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 10.50 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.28), residues: 998
  helix:  2.00 (0.19), residues: 773
  sheet:  None (None), residues: 0
  loop :  0.58 (0.47), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 231 
 HIS   0.007   0.001   HIS B 457 
 PHE   0.016   0.001   PHE A 352 
 TYR   0.011   0.001   TYR B 508 
 ARG   0.005   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03460 (  532)
  hydrogen bonds       : angle       3.82025 ( 1578)
  covalent geometry    : bond        0.00303 ( 8620)
  covalent geometry    : angle       0.54917 (11758)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.986 
Fit side-chains
REVERT: B  413 GLU cc_start: 0.7521 (tp30) cc_final: 0.7213 (tp30)
REVERT: B  508 TYR cc_start: 0.7483 (t80) cc_final: 0.6918 (t80)
REVERT: A  228 ARG cc_start: 0.7358 (mtm180) cc_final: 0.7115 (mtm110)
  outliers start: 20
  outliers final: 8
  residues processed: 138
  average time/residue: 1.0230
  time to fit residues: 153.4657
Evaluate side-chains
  125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 0 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0050
   chunk 34 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.4794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.149374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.112969 restraints weight = 10813.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.96
r_work: 0.3317 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8620  Z= 0.112
  Angle     :  0.527   5.966  11758  Z= 0.257
  Chirality :  0.040   0.203   1386
  Planarity :  0.006   0.070   1361
  Dihedral  :  8.442  87.863   1866
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.08 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.61 (0.28), residues: 998
  helix:  2.08 (0.19), residues: 773
  sheet:  None (None), residues: 0
  loop :  0.62 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 231 
 HIS   0.008   0.001   HIS B 457 
 PHE   0.015   0.001   PHE A 352 
 TYR   0.010   0.001   TYR B 508 
 ARG   0.005   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03211 (  532)
  hydrogen bonds       : angle       3.72963 ( 1578)
  covalent geometry    : bond        0.00267 ( 8620)
  covalent geometry    : angle       0.52738 (11758)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.981 
Fit side-chains
REVERT: B  413 GLU cc_start: 0.7566 (tp30) cc_final: 0.7271 (tp30)
REVERT: B  508 TYR cc_start: 0.7432 (t80) cc_final: 0.6808 (t80)
REVERT: A  228 ARG cc_start: 0.7330 (mtm180) cc_final: 0.7094 (mtm110)
REVERT: A  325 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7427 (mtm110)
  outliers start: 23
  outliers final: 9
  residues processed: 139
  average time/residue: 0.9057
  time to fit residues: 136.9069
Evaluate side-chains
  127 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 93 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.9184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.146962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.110184 restraints weight = 10791.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.95
r_work: 0.3298 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8620  Z= 0.142
  Angle     :  0.560   7.713  11758  Z= 0.273
  Chirality :  0.041   0.220   1386
  Planarity :  0.006   0.069   1361
  Dihedral  :  8.515  89.241   1866
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 12.15 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.28), residues: 998
  helix:  2.08 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop :  0.57 (0.46), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 231 
 HIS   0.007   0.001   HIS B 457 
 PHE   0.018   0.001   PHE A 352 
 TYR   0.012   0.001   TYR B 508 
 ARG   0.004   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  532)
  hydrogen bonds       : angle       3.81740 ( 1578)
  covalent geometry    : bond        0.00358 ( 8620)
  covalent geometry    : angle       0.56042 (11758)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.823 
Fit side-chains
REVERT: B   86 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7494 (t80)
REVERT: B  413 GLU cc_start: 0.7488 (tp30) cc_final: 0.7209 (tp30)
REVERT: B  508 TYR cc_start: 0.7494 (t80) cc_final: 0.6882 (t80)
REVERT: A  445 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7646 (mm-30)
  outliers start: 23
  outliers final: 13
  residues processed: 133
  average time/residue: 0.8426
  time to fit residues: 122.4621
Evaluate side-chains
  131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.147920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.110768 restraints weight = 10836.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.05
r_work: 0.3273 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8620  Z= 0.125
  Angle     :  0.545   8.505  11758  Z= 0.265
  Chirality :  0.040   0.248   1386
  Planarity :  0.006   0.068   1361
  Dihedral  :  8.443  89.485   1866
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 13.33 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.66 (0.28), residues: 998
  helix:  2.13 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop :  0.58 (0.46), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 231 
 HIS   0.007   0.001   HIS B 457 
 PHE   0.016   0.001   PHE A 352 
 TYR   0.011   0.001   TYR B 508 
 ARG   0.003   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03376 (  532)
  hydrogen bonds       : angle       3.75133 ( 1578)
  covalent geometry    : bond        0.00307 ( 8620)
  covalent geometry    : angle       0.54501 (11758)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.943 
Fit side-chains
REVERT: B   86 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7327 (t80)
REVERT: B  413 GLU cc_start: 0.7476 (tp30) cc_final: 0.7228 (tp30)
REVERT: B  508 TYR cc_start: 0.7455 (t80) cc_final: 0.6792 (t80)
REVERT: A  228 ARG cc_start: 0.7065 (mtm110) cc_final: 0.6825 (mpp80)
REVERT: A  445 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7576 (mm-30)
  outliers start: 25
  outliers final: 15
  residues processed: 139
  average time/residue: 0.9138
  time to fit residues: 138.4702
Evaluate side-chains
  131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 95 optimal weight:    0.4980
   chunk 71 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0570
   chunk 17 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.5700

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

Flipped N/Q/H residues before XYZ refinement:
B 457 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.148064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110453 restraints weight = 10912.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.11
r_work: 0.3263 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8620  Z= 0.118
  Angle     :  0.546   9.468  11758  Z= 0.266
  Chirality :  0.040   0.263   1386
  Planarity :  0.006   0.068   1361
  Dihedral  :  8.379  88.585   1866
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.62 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.70 (0.28), residues: 998
  helix:  2.15 (0.19), residues: 773
  sheet:  None (None), residues: 0
  loop :  0.62 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 231 
 HIS   0.006   0.001   HIS B 457 
 PHE   0.017   0.001   PHE A 403 
 TYR   0.010   0.001   TYR B 508 
 ARG   0.006   0.000   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  532)
  hydrogen bonds       : angle       3.74615 ( 1578)
  covalent geometry    : bond        0.00286 ( 8620)
  covalent geometry    : angle       0.54629 (11758)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.929 
Fit side-chains
REVERT: B   86 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7223 (t80)
REVERT: B  118 MET cc_start: 0.7965 (mtp) cc_final: 0.7548 (mtp)
REVERT: B  413 GLU cc_start: 0.7481 (tp30) cc_final: 0.7225 (tp30)
REVERT: B  508 TYR cc_start: 0.7409 (t80) cc_final: 0.6304 (t80)
REVERT: A  228 ARG cc_start: 0.7044 (mtm110) cc_final: 0.6808 (mpp80)
REVERT: A  445 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7560 (mm-30)
REVERT: A  553 LEU cc_start: 0.7754 (mt) cc_final: 0.7359 (tt)
  outliers start: 21
  outliers final: 14
  residues processed: 136
  average time/residue: 0.8376
  time to fit residues: 124.5584
Evaluate side-chains
  132 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  544 MET
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 28 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 84 optimal weight:    0.1980
   chunk 75 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 457 HIS
A 552 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.148595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.111698 restraints weight = 10813.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.08
r_work: 0.3287 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8620  Z= 0.118
  Angle     :  0.554  10.299  11758  Z= 0.269
  Chirality :  0.040   0.266   1386
  Planarity :  0.006   0.068   1361
  Dihedral  :  8.362  87.845   1866
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.33 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.70 (0.28), residues: 998
  helix:  2.16 (0.19), residues: 773
  sheet:  None (None), residues: 0
  loop :  0.61 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 231 
 HIS   0.011   0.001   HIS B 457 
 PHE   0.018   0.001   PHE A 403 
 TYR   0.012   0.001   TYR B 240 
 ARG   0.005   0.000   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03256 (  532)
  hydrogen bonds       : angle       3.76043 ( 1578)
  covalent geometry    : bond        0.00287 ( 8620)
  covalent geometry    : angle       0.55389 (11758)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.964 
Fit side-chains
REVERT: B   86 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7310 (t80)
REVERT: B  119 LEU cc_start: 0.8629 (tp) cc_final: 0.8327 (mm)
REVERT: B  413 GLU cc_start: 0.7530 (tp30) cc_final: 0.7287 (tp30)
REVERT: B  508 TYR cc_start: 0.7435 (t80) cc_final: 0.6290 (t80)
REVERT: A  228 ARG cc_start: 0.7144 (mtm110) cc_final: 0.6902 (mpp80)
REVERT: A  413 GLU cc_start: 0.7537 (tt0) cc_final: 0.7331 (tt0)
REVERT: A  445 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7704 (mm-30)
  outliers start: 18
  outliers final: 13
  residues processed: 130
  average time/residue: 0.8836
  time to fit residues: 125.5310
Evaluate side-chains
  131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  544 MET
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 79 optimal weight:    0.2980
   chunk 13 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.147066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.109330 restraints weight = 11169.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.04
r_work: 0.3274 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8620  Z= 0.125
  Angle     :  0.566  10.914  11758  Z= 0.277
  Chirality :  0.041   0.271   1386
  Planarity :  0.006   0.068   1361
  Dihedral  :  8.398  87.222   1866
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.09 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.28), residues: 998
  helix:  2.18 (0.19), residues: 773
  sheet:  None (None), residues: 0
  loop :  0.58 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 231 
 HIS   0.007   0.001   HIS B 457 
 PHE   0.019   0.001   PHE A 403 
 TYR   0.011   0.001   TYR B 508 
 ARG   0.005   0.000   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03335 (  532)
  hydrogen bonds       : angle       3.80683 ( 1578)
  covalent geometry    : bond        0.00307 ( 8620)
  covalent geometry    : angle       0.56640 (11758)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.928 
Fit side-chains
REVERT: B   86 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7383 (t80)
REVERT: B  118 MET cc_start: 0.8015 (mtp) cc_final: 0.7587 (mtp)
REVERT: B  119 LEU cc_start: 0.8686 (tp) cc_final: 0.8398 (mm)
REVERT: B  413 GLU cc_start: 0.7538 (tp30) cc_final: 0.7302 (tp30)
REVERT: B  508 TYR cc_start: 0.7441 (t80) cc_final: 0.6274 (t80)
REVERT: A  228 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6898 (mpp80)
REVERT: A  445 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7704 (mm-30)
REVERT: A  553 LEU cc_start: 0.7891 (mt) cc_final: 0.7475 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 132
  average time/residue: 0.8658
  time to fit residues: 124.7446
Evaluate side-chains
  129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  544 MET
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0010
   chunk 0 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.6186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.148397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.111301 restraints weight = 10864.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.05
r_work: 0.3274 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8620  Z= 0.123
  Angle     :  0.566  10.970  11758  Z= 0.278
  Chirality :  0.041   0.293   1386
  Planarity :  0.006   0.068   1361
  Dihedral  :  8.401  86.365   1866
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.45 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.28), residues: 998
  helix:  2.18 (0.19), residues: 773
  sheet:  None (None), residues: 0
  loop :  0.57 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 231 
 HIS   0.006   0.001   HIS B 457 
 PHE   0.015   0.001   PHE A 352 
 TYR   0.011   0.001   TYR B 240 
 ARG   0.005   0.000   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03320 (  532)
  hydrogen bonds       : angle       3.81697 ( 1578)
  covalent geometry    : bond        0.00303 ( 8620)
  covalent geometry    : angle       0.56569 (11758)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.974 
Fit side-chains
REVERT: B   86 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7266 (t80)
REVERT: B  118 MET cc_start: 0.7978 (mtp) cc_final: 0.7541 (mtp)
REVERT: B  119 LEU cc_start: 0.8641 (tp) cc_final: 0.8341 (mm)
REVERT: B  231 TRP cc_start: 0.5839 (m100) cc_final: 0.5516 (t-100)
REVERT: B  413 GLU cc_start: 0.7495 (tp30) cc_final: 0.7273 (tp30)
REVERT: B  508 TYR cc_start: 0.7368 (t80) cc_final: 0.6245 (t80)
REVERT: B  538 HIS cc_start: 0.7056 (m-70) cc_final: 0.6623 (m-70)
REVERT: A  228 ARG cc_start: 0.7045 (mtm110) cc_final: 0.6801 (mpp80)
REVERT: A  445 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7576 (mm-30)
REVERT: A  553 LEU cc_start: 0.7845 (mt) cc_final: 0.7448 (tt)
  outliers start: 17
  outliers final: 13
  residues processed: 128
  average time/residue: 0.9082
  time to fit residues: 126.7893
Evaluate side-chains
  129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  544 MET
Chi-restraints excluded: chain A residue  549 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0980
   chunk 58 optimal weight:    0.9990
   chunk 85 optimal weight:    0.5980
   chunk 18 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 79 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 552 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.147504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.109843 restraints weight = 11068.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.04
r_work: 0.3283 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8620  Z= 0.122
  Angle     :  0.565  11.300  11758  Z= 0.278
  Chirality :  0.041   0.284   1386
  Planarity :  0.006   0.068   1361
  Dihedral  :  8.388  85.676   1866
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.68 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.76 (0.28), residues: 998
  helix:  2.20 (0.19), residues: 773
  sheet:  None (None), residues: 0
  loop :  0.63 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B 231 
 HIS   0.006   0.001   HIS B 457 
 PHE   0.015   0.001   PHE A 352 
 TYR   0.016   0.001   TYR B 508 
 ARG   0.005   0.000   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03289 (  532)
  hydrogen bonds       : angle       3.81627 ( 1578)
  covalent geometry    : bond        0.00299 ( 8620)
  covalent geometry    : angle       0.56495 (11758)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6703.27 seconds
wall clock time: 116 minutes 39.39 seconds (6999.39 seconds total)