Starting phenix.real_space_refine
on Wed Mar 12 07:06:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b4l_12002/03_2025/7b4l_12002.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b4l_12002/03_2025/7b4l_12002.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b4l_12002/03_2025/7b4l_12002.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b4l_12002/03_2025/7b4l_12002.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b4l_12002/03_2025/7b4l_12002.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b4l_12002/03_2025/7b4l_12002.cif"
  }
  resolution = 3.1
  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=   0.100
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       4      5.49       5
     S      36      5.16       5
     Na      2      4.78       5
     C    4740      2.51       5
     N    1068      2.21       5
     O    1180      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7030
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3300
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3300
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 202
          Unusual residues: {' NA': 1, 'C14': 3, 'POV': 2, 'UND': 5}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
    Chain: "B"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 202
          Unusual residues: {' NA': 1, 'C14': 3, 'POV': 2, 'UND': 5}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb="NA    NA A 601 " occ=0.50
    residue:
      pdb="NA    NA B 602 " occ=0.50
    residue:
      pdb=" O   HOH A 711 " occ=0.50
    residue:
      pdb=" O   HOH B 711 " occ=0.50
  Time building chain proxies: 4.86, per 1000 atoms: 0.69
  Number of scatterers: 7030
  At special positions: 0
  Unit cell: (97.643, 91.205, 77.256, 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      36     16.00
     P       4     15.00
     Na      2     11.00
     O    1180      8.00
     N    1068      7.00
     C    4740      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: 2.00
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      84.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 106
      removed outlier: 3.510A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 110
    Processing helix  chain 'A' and resid 113 through 134
    Processing helix  chain 'A' and resid 144 through 159
      removed outlier: 3.982A  pdb=" N   GLY A 148 " --> pdb=" O   PRO A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
    Processing helix  chain 'A' and resid 169 through 190
    Processing helix  chain 'A' and resid 193 through 200
      removed outlier: 3.517A  pdb=" N   LYS A 199 " --> pdb=" O   LYS A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 224
      Proline residue:  A 211  - end of helix
    Processing helix  chain 'A' and resid 230 through 241
      removed outlier: 3.523A  pdb=" N   ILE A 236 " --> pdb=" O   GLN A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 260
      removed outlier: 3.644A  pdb=" N   VAL A 249 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
      Proline residue:  A 251  - end of helix
      removed outlier: 3.764A  pdb=" N   LEU A 255 " --> pdb=" O   PRO A 251 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 274
      removed outlier: 3.610A  pdb=" N   ALA A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 295
      removed outlier: 3.737A  pdb=" N   ILE A 280 " --> pdb=" O   SER A 276 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE A 292 " --> pdb=" O   THR A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 327
      removed outlier: 3.623A  pdb=" N   ASN A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY A 306 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A 307 " --> pdb=" O   VAL A 303 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   TYR A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE A 327 " --> pdb=" O   PHE A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 358
    Processing helix  chain 'A' and resid 361 through 378
      removed outlier: 3.558A  pdb=" N   LEU A 365 " --> pdb=" O   GLY A 361 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY A 377 " --> pdb=" O   LEU A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 406
      removed outlier: 3.641A  pdb=" N   ILE A 388 " --> pdb=" O   GLU A 384 " (cutoff:3.500A)
      Proline residue:  A 398  - end of helix
    Processing helix  chain 'A' and resid 418 through 440
      removed outlier: 3.570A  pdb=" N   VAL A 425 " --> pdb=" O   CYS A 421 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL A 440 " --> pdb=" O   THR A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 456
    Processing helix  chain 'A' and resid 461 through 468
    Processing helix  chain 'A' and resid 469 through 479
    Processing helix  chain 'A' and resid 481 through 517
      removed outlier: 4.086A  pdb=" N   ASP A 485 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASP A 489 " --> pdb=" O   ASP A 485 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ILE A 498 " --> pdb=" O   ALA A 494 " (cutoff:3.500A)
      Proline residue:  A 503  - end of helix
      Proline residue:  A 514  - end of helix
    Processing helix  chain 'B' and resid 82 through 106
      removed outlier: 3.510A  pdb=" N   ILE B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 110
    Processing helix  chain 'B' and resid 113 through 134
    Processing helix  chain 'B' and resid 144 through 159
      removed outlier: 3.982A  pdb=" N   GLY B 148 " --> pdb=" O   PRO B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 164
    Processing helix  chain 'B' and resid 169 through 190
    Processing helix  chain 'B' and resid 193 through 200
      removed outlier: 3.517A  pdb=" N   LYS B 199 " --> pdb=" O   LYS B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 224
      Proline residue:  B 211  - end of helix
    Processing helix  chain 'B' and resid 230 through 241
      removed outlier: 3.523A  pdb=" N   ILE B 236 " --> pdb=" O   GLN B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 260
      removed outlier: 3.644A  pdb=" N   VAL B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      Proline residue:  B 251  - end of helix
      removed outlier: 3.764A  pdb=" N   LEU B 255 " --> pdb=" O   PRO B 251 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU B 256 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 274
      removed outlier: 3.611A  pdb=" N   ALA B 274 " --> pdb=" O   LEU B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 295
      removed outlier: 3.737A  pdb=" N   ILE B 280 " --> pdb=" O   SER B 276 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE B 292 " --> pdb=" O   THR B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 327
      removed outlier: 3.623A  pdb=" N   ASN B 302 " --> pdb=" O   SER B 298 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY B 306 " --> pdb=" O   ASN B 302 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL B 307 " --> pdb=" O   VAL B 303 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL B 310 " --> pdb=" O   GLY B 306 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   TYR B 326 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE B 327 " --> pdb=" O   PHE B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 358
    Processing helix  chain 'B' and resid 361 through 378
      removed outlier: 3.558A  pdb=" N   LEU B 365 " --> pdb=" O   GLY B 361 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY B 377 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 406
      removed outlier: 3.641A  pdb=" N   ILE B 388 " --> pdb=" O   GLU B 384 " (cutoff:3.500A)
      Proline residue:  B 398  - end of helix
    Processing helix  chain 'B' and resid 418 through 440
      removed outlier: 3.570A  pdb=" N   VAL B 425 " --> pdb=" O   CYS B 421 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL B 440 " --> pdb=" O   THR B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 456
    Processing helix  chain 'B' and resid 461 through 468
    Processing helix  chain 'B' and resid 469 through 479
    Processing helix  chain 'B' and resid 481 through 517
      removed outlier: 4.086A  pdb=" N   ASP B 485 " --> pdb=" O   LYS B 481 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASP B 489 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ILE B 498 " --> pdb=" O   ALA B 494 " (cutoff:3.500A)
      Proline residue:  B 503  - end of helix
      Proline residue:  B 514  - end of helix

    498 hydrogen bonds defined for protein.
    1488 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: 1.90

  Time building geometry restraints manager: 2.32 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1016
        1.31 -     1.43: 1700
        1.43 -     1.56: 4346
        1.56 -     1.69: 8
        1.69 -     1.81: 52
  Bond restraints: 7122
  Sorted by residual:
  bond pdb=" C31 POV A 602 "
       pdb=" O31 POV A 602 "
    ideal  model  delta    sigma   weight residual
    1.327  1.399 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C31 POV B 603 "
       pdb=" O31 POV B 603 "
    ideal  model  delta    sigma   weight residual
    1.327  1.399 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C31 POV B 601 "
       pdb=" O31 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.398 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" C31 POV A 611 "
       pdb=" O31 POV A 611 "
    ideal  model  delta    sigma   weight residual
    1.327  1.398 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" C21 POV B 603 "
       pdb=" O21 POV B 603 "
    ideal  model  delta    sigma   weight residual
    1.330  1.400 -0.070 2.00e-02 2.50e+03 1.22e+01
  ... (remaining 7117 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 9129
        2.43 -     4.87: 386
        4.87 -     7.30: 31
        7.30 -     9.74: 18
        9.74 -    12.17: 8
  Bond angle restraints: 9572
  Sorted by residual:
  angle pdb=" O11 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O12 POV B 601 "
      ideal   model   delta    sigma   weight residual
      97.67  109.84  -12.17 3.00e+00 1.11e-01 1.65e+01
  angle pdb=" O11 POV A 611 "
        pdb=" P   POV A 611 "
        pdb=" O12 POV A 611 "
      ideal   model   delta    sigma   weight residual
      97.67  109.82  -12.15 3.00e+00 1.11e-01 1.64e+01
  angle pdb=" O13 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O14 POV B 601 "
      ideal   model   delta    sigma   weight residual
     121.11  109.21   11.90 3.00e+00 1.11e-01 1.57e+01
  angle pdb=" O13 POV A 611 "
        pdb=" P   POV A 611 "
        pdb=" O14 POV A 611 "
      ideal   model   delta    sigma   weight residual
     121.11  109.21   11.90 3.00e+00 1.11e-01 1.57e+01
  angle pdb=" O13 POV A 602 "
        pdb=" P   POV A 602 "
        pdb=" O14 POV A 602 "
      ideal   model   delta    sigma   weight residual
     121.11  109.62   11.49 3.00e+00 1.11e-01 1.47e+01
  ... (remaining 9567 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.04: 3824
       20.04 -    40.08: 326
       40.08 -    60.13: 86
       60.13 -    80.17: 10
       80.17 -   100.21: 2
  Dihedral angle restraints: 4248
    sinusoidal: 1778
      harmonic: 2470
  Sorted by residual:
  dihedral pdb=" CA  TYR B 326 "
           pdb=" C   TYR B 326 "
           pdb=" N   PHE B 327 "
           pdb=" CA  PHE B 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.16  -18.84     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  TYR A 326 "
           pdb=" C   TYR A 326 "
           pdb=" N   PHE A 327 "
           pdb=" CA  PHE A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.16  -18.84     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  PHE A 327 "
           pdb=" C   PHE A 327 "
           pdb=" N   PRO A 328 "
           pdb=" CA  PRO A 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.65   18.35     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 4245 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 787
       0.037 -    0.075: 307
       0.075 -    0.112: 38
       0.112 -    0.149: 10
       0.149 -    0.187: 4
  Chirality restraints: 1146
  Sorted by residual:
  chirality pdb=" CB  THR B 417 "
            pdb=" CA  THR B 417 "
            pdb=" OG1 THR B 417 "
            pdb=" CG2 THR B 417 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 8.73e-01
  chirality pdb=" CB  THR A 417 "
            pdb=" CA  THR A 417 "
            pdb=" OG1 THR A 417 "
            pdb=" CG2 THR A 417 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" CG  LEU B 483 "
            pdb=" CB  LEU B 483 "
            pdb=" CD1 LEU B 483 "
            pdb=" CD2 LEU B 483 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.36e-01
  ... (remaining 1143 not shown)

  Planarity restraints: 1122
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 110 "   -0.035 5.00e-02 4.00e+02   5.28e-02 4.45e+00
        pdb=" N   PRO A 111 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 111 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 111 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 110 "   -0.035 5.00e-02 4.00e+02   5.27e-02 4.44e+00
        pdb=" N   PRO B 111 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B 111 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 111 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 502 "   -0.025 5.00e-02 4.00e+02   3.86e-02 2.38e+00
        pdb=" N   PRO A 503 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 503 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 503 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1119 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 116
        2.69 -     3.24: 6962
        3.24 -     3.80: 10296
        3.80 -     4.35: 14397
        4.35 -     4.90: 24237
  Nonbonded interactions: 56008
  Sorted by model distance:
  nonbonded pdb=" O   SER B 497 "
            pdb=" OG1 THR B 501 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   SER A 497 "
            pdb=" OG1 THR A 501 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   PHE B 445 "
            pdb=" NZ  LYS B 450 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" O   PHE A 445 "
            pdb=" NZ  LYS A 450 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   LYS B 450 "
            pdb=" OG  SER B 454 "
     model   vdw
     2.297 3.040
  ... (remaining 56003 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: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 79 through 521 or resid 604 through 605 or resid 607 throu \ 
gh 610))
  selection = (chain 'B' and (resid 79 through 521 or resid 604 through 605 or resid 607 throu \ 
gh 610))
}

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=0.50 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:             1.250
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.480
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
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      :  0.005   0.072   7122  Z= 0.310
  Angle     :  1.048  12.169   9572  Z= 0.442
  Chirality :  0.039   0.187   1146
  Planarity :  0.005   0.053   1122
  Dihedral  : 16.182 100.208   2672
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.27), residues: 882
  helix: -0.07 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -2.28 (0.41), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 378 
 HIS   0.001   0.000   HIS A 224 
 PHE   0.009   0.001   PHE B 401 
 TYR   0.007   0.001   TYR B 123 
 ARG   0.006   0.001   ARG B 157 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A  149 MET cc_start: 0.8974 (mtt) cc_final: 0.8530 (mtm)
REVERT: A  198 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7817 (mmtt)
REVERT: A  489 ASP cc_start: 0.7389 (m-30) cc_final: 0.7153 (m-30)
REVERT: B  149 MET cc_start: 0.8975 (mtt) cc_final: 0.8530 (mtm)
REVERT: B  198 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7824 (mmtt)
REVERT: B  489 ASP cc_start: 0.7391 (m-30) cc_final: 0.7153 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1828
  time to fit residues: 29.3105
Evaluate side-chains
  88 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   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 = 0.4001 r_free = 0.4001 target = 0.159289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.142439 restraints weight = 8920.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 1.77
r_work: 0.3700 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3578 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3600
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3600 r_free = 0.3600    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3600 r_free = 0.3600    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3600
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7122  Z= 0.225
  Angle     :  0.644   9.346   9572  Z= 0.327
  Chirality :  0.042   0.153   1146
  Planarity :  0.005   0.056   1122
  Dihedral  : 14.816 100.310   1236
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  7.84 %
    Favored  : 90.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.29), residues: 882
  helix:  1.00 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -2.06 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 378 
 HIS   0.002   0.001   HIS A 224 
 PHE   0.012   0.001   PHE B 401 
 TYR   0.004   0.001   TYR A 123 
 ARG   0.002   0.000   ARG B 177 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7126 (t0)
REVERT: A  198 LYS cc_start: 0.8563 (ttpt) cc_final: 0.7727 (mmtt)
REVERT: A  253 MET cc_start: 0.9091 (mmm) cc_final: 0.8764 (mmm)
REVERT: A  489 ASP cc_start: 0.7883 (m-30) cc_final: 0.7651 (m-30)
REVERT: B   85 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7131 (t0)
REVERT: B  198 LYS cc_start: 0.8569 (ttpt) cc_final: 0.7734 (mmtt)
REVERT: B  253 MET cc_start: 0.9088 (mmm) cc_final: 0.8755 (mmm)
REVERT: B  489 ASP cc_start: 0.7900 (m-30) cc_final: 0.7668 (m-30)
  outliers start: 12
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1595
  time to fit residues: 21.2163
Evaluate side-chains
  90 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  429 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 44 optimal weight:    7.9990
   chunk 2 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 77 optimal weight:    7.9990
   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 158 ASN
A 478 HIS
B 158 ASN
B 478 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.160538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.143576 restraints weight = 8947.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 1.78
r_work: 0.3722 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3599 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3618
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3618
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7122  Z= 0.184
  Angle     :  0.572   8.704   9572  Z= 0.287
  Chirality :  0.040   0.127   1146
  Planarity :  0.005   0.057   1122
  Dihedral  : 14.073  85.992   1236
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  :  8.68 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.29), residues: 882
  helix:  1.12 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -2.20 (0.47), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  98 
 HIS   0.002   0.001   HIS A 224 
 PHE   0.013   0.001   PHE B 323 
 TYR   0.005   0.001   TYR B 123 
 ARG   0.001   0.000   ARG B 157 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7105 (t0)
REVERT: A  198 LYS cc_start: 0.8651 (ttpt) cc_final: 0.7726 (mmtt)
REVERT: A  253 MET cc_start: 0.9031 (mmm) cc_final: 0.8804 (mmm)
REVERT: A  489 ASP cc_start: 0.7883 (m-30) cc_final: 0.7602 (m-30)
REVERT: B   85 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7107 (t0)
REVERT: B  198 LYS cc_start: 0.8652 (ttpt) cc_final: 0.7729 (mmtt)
REVERT: B  253 MET cc_start: 0.9026 (mmm) cc_final: 0.8795 (mmm)
REVERT: B  489 ASP cc_start: 0.7886 (m-30) cc_final: 0.7604 (m-30)
  outliers start: 26
  outliers final: 17
  residues processed: 104
  average time/residue: 0.1566
  time to fit residues: 23.1643
Evaluate side-chains
  101 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  120 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  407 GLU
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  482 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0030
   chunk 54 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 18 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 478 HIS
B 158 ASN
B 478 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.161876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.144918 restraints weight = 8974.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 1.78
r_work: 0.3733 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3609 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3630
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7122  Z= 0.163
  Angle     :  0.539   8.085   9572  Z= 0.269
  Chirality :  0.039   0.123   1146
  Planarity :  0.005   0.063   1122
  Dihedral  : 13.090  61.297   1236
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 10.22 %
    Favored  : 85.99 %
  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:  1.08 (0.29), residues: 882
  helix:  1.38 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.93 (0.48), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.002   0.001   HIS A 224 
 PHE   0.012   0.001   PHE A 401 
 TYR   0.007   0.001   TYR B 123 
 ARG   0.001   0.000   ARG B 414 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7325 (t0)
REVERT: A  198 LYS cc_start: 0.8666 (ttpt) cc_final: 0.7698 (mmtt)
REVERT: A  324 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8437 (mt)
REVERT: A  489 ASP cc_start: 0.7857 (m-30) cc_final: 0.7556 (m-30)
REVERT: B   85 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7335 (t0)
REVERT: B  198 LYS cc_start: 0.8664 (ttpt) cc_final: 0.7692 (mmtt)
REVERT: B  324 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8441 (mt)
REVERT: B  407 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7535 (mp0)
REVERT: B  489 ASP cc_start: 0.7846 (m-30) cc_final: 0.7543 (m-30)
  outliers start: 27
  outliers final: 16
  residues processed: 105
  average time/residue: 0.1774
  time to fit residues: 25.7417
Evaluate side-chains
  104 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  158 ASN
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue  158 ASN
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  407 GLU
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  482 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 49 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 44 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   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 158 ASN
A 478 HIS
B 158 ASN
B 478 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.161652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.144617 restraints weight = 8892.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3848 rms_B_bonded: 1.78
r_work: 0.3724 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3600 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3623 r_free = 0.3623    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3623 r_free = 0.3623    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7122  Z= 0.169
  Angle     :  0.546   8.025   9572  Z= 0.272
  Chirality :  0.039   0.119   1146
  Planarity :  0.004   0.060   1122
  Dihedral  : 12.765  60.671   1236
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 10.08 %
    Favored  : 86.69 %
  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:  1.18 (0.29), residues: 882
  helix:  1.44 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.87 (0.48), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.002   0.000   HIS A 224 
 PHE   0.010   0.001   PHE A 401 
 TYR   0.007   0.001   TYR B 123 
 ARG   0.001   0.000   ARG A 157 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7426 (t0)
REVERT: A  195 LYS cc_start: 0.8110 (mmtp) cc_final: 0.7685 (pttm)
REVERT: A  198 LYS cc_start: 0.8708 (ttpt) cc_final: 0.7773 (mmtt)
REVERT: A  253 MET cc_start: 0.8811 (mmm) cc_final: 0.8327 (mmm)
REVERT: A  324 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8453 (mt)
REVERT: A  489 ASP cc_start: 0.7833 (m-30) cc_final: 0.7529 (m-30)
REVERT: B   85 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7425 (t0)
REVERT: B  195 LYS cc_start: 0.8107 (mmtp) cc_final: 0.7676 (pttm)
REVERT: B  198 LYS cc_start: 0.8707 (ttpt) cc_final: 0.7768 (mmtt)
REVERT: B  253 MET cc_start: 0.8799 (mmm) cc_final: 0.8308 (mmm)
REVERT: B  324 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8451 (mt)
REVERT: B  489 ASP cc_start: 0.7827 (m-30) cc_final: 0.7525 (m-30)
  outliers start: 23
  outliers final: 14
  residues processed: 103
  average time/residue: 0.1627
  time to fit residues: 23.9710
Evaluate side-chains
  107 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  158 ASN
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue  158 ASN
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  482 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0980
   chunk 40 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0970
   chunk 50 optimal weight:    4.9990
   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 158 ASN
A 478 HIS
B 158 ASN
B 478 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.160925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.144404 restraints weight = 8821.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 1.73
r_work: 0.3726 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3603 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7122  Z= 0.178
  Angle     :  0.552   8.174   9572  Z= 0.274
  Chirality :  0.039   0.121   1146
  Planarity :  0.004   0.058   1122
  Dihedral  : 12.556  60.026   1236
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 11.34 %
    Favored  : 85.57 %
  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:  1.25 (0.29), residues: 882
  helix:  1.50 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.86 (0.48), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.002   0.001   HIS A 224 
 PHE   0.010   0.001   PHE A 401 
 TYR   0.006   0.001   TYR A 123 
 ARG   0.003   0.000   ARG A 157 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7675 (pttm)
REVERT: A  198 LYS cc_start: 0.8706 (ttpt) cc_final: 0.7767 (mmtt)
REVERT: A  253 MET cc_start: 0.8819 (mmm) cc_final: 0.8340 (mmm)
REVERT: A  324 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8417 (mt)
REVERT: A  489 ASP cc_start: 0.7821 (m-30) cc_final: 0.7516 (m-30)
REVERT: B  195 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7667 (pttm)
REVERT: B  198 LYS cc_start: 0.8708 (ttpt) cc_final: 0.7762 (mmtt)
REVERT: B  253 MET cc_start: 0.8813 (mmm) cc_final: 0.8327 (mmm)
REVERT: B  324 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8409 (mt)
REVERT: B  489 ASP cc_start: 0.7825 (m-30) cc_final: 0.7522 (m-30)
  outliers start: 22
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1583
  time to fit residues: 22.8375
Evaluate side-chains
  102 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ASN
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain B residue  158 ASN
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  482 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0970
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0010
   overall best weight:    0.2962

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 478 HIS
B 158 ASN
B 478 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.163641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.146792 restraints weight = 8960.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 1.79
r_work: 0.3754 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3631 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3652 r_free = 0.3652    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3652 r_free = 0.3652    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7122  Z= 0.136
  Angle     :  0.522   7.580   9572  Z= 0.257
  Chirality :  0.038   0.129   1146
  Planarity :  0.004   0.054   1122
  Dihedral  : 12.154  59.966   1236
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.61 %
    Favored  : 85.15 %
  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:  1.44 (0.29), residues: 882
  helix:  1.62 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.74 (0.48), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.001   0.000   HIS A 224 
 PHE   0.009   0.001   PHE A 401 
 TYR   0.006   0.001   TYR A 123 
 ARG   0.006   0.000   ARG B 157 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.8090 (mmtp) cc_final: 0.7673 (pttm)
REVERT: A  198 LYS cc_start: 0.8625 (ttpt) cc_final: 0.7680 (mmtt)
REVERT: A  253 MET cc_start: 0.8807 (mmm) cc_final: 0.8339 (mmm)
REVERT: A  324 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8400 (mt)
REVERT: A  489 ASP cc_start: 0.7786 (m-30) cc_final: 0.7479 (m-30)
REVERT: B  195 LYS cc_start: 0.8078 (mmtp) cc_final: 0.7656 (pttm)
REVERT: B  198 LYS cc_start: 0.8623 (ttpt) cc_final: 0.7674 (mmtt)
REVERT: B  253 MET cc_start: 0.8800 (mmm) cc_final: 0.8324 (mmm)
REVERT: B  324 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8392 (mt)
REVERT: B  489 ASP cc_start: 0.7792 (m-30) cc_final: 0.7487 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 105
  average time/residue: 0.1665
  time to fit residues: 24.6017
Evaluate side-chains
  100 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ASN
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain B residue  158 ASN
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  482 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 36 optimal weight:    0.0060
   chunk 1 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0870
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.4974

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 478 HIS
B 158 ASN
B 478 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.163410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.146568 restraints weight = 9001.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 1.80
r_work: 0.3750 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3627 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3648
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3648 r_free = 0.3648    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3648 r_free = 0.3648    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3648
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7122  Z= 0.149
  Angle     :  0.526   7.486   9572  Z= 0.260
  Chirality :  0.038   0.126   1146
  Planarity :  0.004   0.053   1122
  Dihedral  : 11.970  59.956   1236
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.17 %
    Favored  : 84.87 %
  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:  1.49 (0.29), residues: 882
  helix:  1.65 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.69 (0.48), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.002   0.000   HIS A 224 
 PHE   0.009   0.001   PHE A 401 
 TYR   0.005   0.001   TYR A 123 
 ARG   0.004   0.000   ARG A 157 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.8101 (mmtp) cc_final: 0.7632 (pttm)
REVERT: A  198 LYS cc_start: 0.8603 (ttpt) cc_final: 0.7681 (mmtt)
REVERT: A  253 MET cc_start: 0.8782 (mmm) cc_final: 0.8320 (mmm)
REVERT: A  324 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8419 (mt)
REVERT: A  489 ASP cc_start: 0.7798 (m-30) cc_final: 0.7495 (m-30)
REVERT: B  195 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7604 (pttm)
REVERT: B  198 LYS cc_start: 0.8594 (ttpt) cc_final: 0.7664 (mmtt)
REVERT: B  253 MET cc_start: 0.8789 (mmm) cc_final: 0.8326 (mmm)
REVERT: B  324 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8417 (mt)
REVERT: B  489 ASP cc_start: 0.7801 (m-30) cc_final: 0.7499 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 100
  average time/residue: 0.1704
  time to fit residues: 24.0529
Evaluate side-chains
  102 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ASN
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain B residue  158 ASN
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  482 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 50 optimal weight:    0.1980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 325 GLN
A 478 HIS
B 158 ASN
B 325 GLN
B 478 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.163061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.146300 restraints weight = 9059.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 1.81
r_work: 0.3747 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3622 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7122  Z= 0.157
  Angle     :  0.529   7.613   9572  Z= 0.261
  Chirality :  0.039   0.130   1146
  Planarity :  0.004   0.049   1122
  Dihedral  : 11.851  59.980   1236
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.89 %
    Favored  : 84.87 %
  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:  1.49 (0.29), residues: 882
  helix:  1.66 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.53 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.002   0.000   HIS A 224 
 PHE   0.009   0.001   PHE A 401 
 TYR   0.005   0.001   TYR A 123 
 ARG   0.002   0.000   ARG B 157 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.8117 (mmtp) cc_final: 0.7645 (pttm)
REVERT: A  198 LYS cc_start: 0.8604 (ttpt) cc_final: 0.7691 (mmtt)
REVERT: A  253 MET cc_start: 0.8775 (mmm) cc_final: 0.8313 (mmm)
REVERT: A  324 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8418 (mt)
REVERT: A  489 ASP cc_start: 0.7803 (m-30) cc_final: 0.7511 (m-30)
REVERT: B  195 LYS cc_start: 0.8099 (mmtp) cc_final: 0.7619 (pttm)
REVERT: B  198 LYS cc_start: 0.8598 (ttpt) cc_final: 0.7676 (mmtt)
REVERT: B  253 MET cc_start: 0.8787 (mmm) cc_final: 0.8324 (mmm)
REVERT: B  324 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8423 (mt)
REVERT: B  489 ASP cc_start: 0.7792 (m-30) cc_final: 0.7500 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 102
  average time/residue: 0.1608
  time to fit residues: 23.0754
Evaluate side-chains
  104 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ASN
Chi-restraints excluded: chain A residue  164 ASP
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain B residue  158 ASN
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  482 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0060
   chunk 51 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 478 HIS
B 158 ASN
B 478 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.162380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.146012 restraints weight = 9057.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 1.77
r_work: 0.3747 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3626 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7122  Z= 0.166
  Angle     :  0.549   9.179   9572  Z= 0.266
  Chirality :  0.039   0.129   1146
  Planarity :  0.004   0.046   1122
  Dihedral  : 11.770  59.930   1236
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.17 %
    Favored  : 84.87 %
  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:  1.53 (0.29), residues: 882
  helix:  1.66 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.44 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.002   0.000   HIS A 224 
 PHE   0.009   0.001   PHE A 401 
 TYR   0.005   0.001   TYR B 123 
 ARG   0.001   0.000   ARG B 414 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.696 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7571 (pttm)
REVERT: A  198 LYS cc_start: 0.8617 (ttpt) cc_final: 0.7688 (mmtt)
REVERT: A  253 MET cc_start: 0.8797 (mmm) cc_final: 0.8349 (mmm)
REVERT: A  324 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8414 (mt)
REVERT: A  489 ASP cc_start: 0.7791 (m-30) cc_final: 0.7515 (m-30)
REVERT: B  195 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7553 (pttm)
REVERT: B  198 LYS cc_start: 0.8614 (ttpt) cc_final: 0.7679 (mmtt)
REVERT: B  253 MET cc_start: 0.8784 (mmm) cc_final: 0.8327 (mmm)
REVERT: B  324 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8414 (mt)
REVERT: B  489 ASP cc_start: 0.7782 (m-30) cc_final: 0.7505 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 99
  average time/residue: 0.1652
  time to fit residues: 23.2271
Evaluate side-chains
  100 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ASN
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  408 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain B residue  158 ASN
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  482 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 18 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 478 HIS
B 158 ASN
B 478 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.161467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.145233 restraints weight = 8900.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 1.74
r_work: 0.3741 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7122  Z= 0.182
  Angle     :  0.554   8.351   9572  Z= 0.269
  Chirality :  0.039   0.129   1146
  Planarity :  0.004   0.043   1122
  Dihedral  : 11.758  59.694   1236
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.43 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.29), residues: 882
  helix:  1.63 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.36 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.002   0.001   HIS A 224 
 PHE   0.011   0.001   PHE B 154 
 TYR   0.004   0.001   TYR A 123 
 ARG   0.001   0.000   ARG B 157 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3333.59 seconds
wall clock time: 58 minutes 5.62 seconds (3485.62 seconds total)