Starting phenix.real_space_refine
on Tue Mar  3 17:15:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b4l_12002/03_2026/7b4l_12002.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b4l_12002/03_2026/7b4l_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_2026/7b4l_12002.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b4l_12002/03_2026/7b4l_12002.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b4l_12002/03_2026/7b4l_12002.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b4l_12002/03_2026/7b4l_12002.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.68, per 1000 atoms: 0.24
  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: 0.92
  Conformation dependent library (CDL) restraints added in 257.7 milliseconds
  

  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: 0.16
  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: 1.02

  Time building geometry restraints manager: 1.10 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: 0.01
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:             2.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.940
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.560
-------------------------------------------------------------------------------
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= 0.231
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.001   ARG B 157 
 TYR   0.007   0.001   TYR B 123 
 PHE   0.009   0.001   PHE B 401 
 TRP   0.012   0.002   TRP A 378 
 HIS   0.001   0.000   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 7122)
  covalent geometry    : angle       1.04846 ( 9572)
  hydrogen bonds       : bond        0.26939 (  498)
  hydrogen bonds       : angle       8.22316 ( 1488)

*********************** 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  : 0.229 
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: 0.7814 (mmtt)
REVERT: A  489 ASP cc_start: 0.7389 (m-30) cc_final: 0.7154 (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: 0.7821 (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: 0.0781
  time to fit residues: 12.6410
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  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0570
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.4019 r_free = 0.4019 target = 0.160813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.143942 restraints weight = 9014.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 1.79
r_work: 0.3719 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3597 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3597
-------------------------------------------------------------------------------
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 = 0.50   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 = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3618
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7122  Z= 0.137
  Angle     :  0.638   9.069   9572  Z= 0.320
  Chirality :  0.041   0.143   1146
  Planarity :  0.005   0.055   1122
  Dihedral  : 14.647  99.696   1236
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  7.00 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.29), residues: 882
  helix:  1.02 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -2.12 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  86 
 TYR   0.005   0.001   TYR B 123 
 PHE   0.012   0.001   PHE B 154 
 TRP   0.014   0.001   TRP A  98 
 HIS   0.001   0.000   HIS B 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7122)
  covalent geometry    : angle       0.63759 ( 9572)
  hydrogen bonds       : bond        0.05009 (  498)
  hydrogen bonds       : angle       4.68759 ( 1488)

*********************** 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
  104 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7088 (t70)
REVERT: A  198 LYS cc_start: 0.8567 (ttpt) cc_final: 0.7733 (mmtt)
REVERT: A  253 MET cc_start: 0.9046 (mmm) cc_final: 0.8699 (mmm)
REVERT: A  489 ASP cc_start: 0.7856 (m-30) cc_final: 0.7622 (m-30)
REVERT: B   85 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7111 (t70)
REVERT: B  198 LYS cc_start: 0.8566 (ttpt) cc_final: 0.7728 (mmtt)
REVERT: B  253 MET cc_start: 0.9045 (mmm) cc_final: 0.8690 (mmm)
REVERT: B  489 ASP cc_start: 0.7871 (m-30) cc_final: 0.7633 (m-30)
  outliers start: 10
  outliers final: 4
  residues processed: 98
  average time/residue: 0.0726
  time to fit residues: 10.1806
Evaluate side-chains
  87 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
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 B residue   85 ASP
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  417 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0050
   chunk 44 optimal weight:    0.0980
   chunk 77 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7398

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.160613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.144244 restraints weight = 8702.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 1.72
r_work: 0.3729 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3607 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3607
-------------------------------------------------------------------------------
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 = 0.62   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 = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2076

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= 0.125
  Angle     :  0.571   8.676   9572  Z= 0.286
  Chirality :  0.040   0.123   1146
  Planarity :  0.005   0.057   1122
  Dihedral  : 13.869  83.623   1236
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  :  8.96 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.29), residues: 882
  helix:  1.17 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -2.00 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 157 
 TYR   0.005   0.001   TYR A 123 
 PHE   0.013   0.001   PHE B 323 
 TRP   0.012   0.001   TRP A  98 
 HIS   0.002   0.001   HIS B 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7122)
  covalent geometry    : angle       0.57092 ( 9572)
  hydrogen bonds       : bond        0.04431 (  498)
  hydrogen bonds       : angle       4.32796 ( 1488)

*********************** 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
  118 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7073 (t0)
REVERT: A  198 LYS cc_start: 0.8637 (ttpt) cc_final: 0.7712 (mmtt)
REVERT: A  253 MET cc_start: 0.9031 (mmm) cc_final: 0.8785 (mmm)
REVERT: A  489 ASP cc_start: 0.7876 (m-30) cc_final: 0.7593 (m-30)
REVERT: B   85 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7086 (t0)
REVERT: B  198 LYS cc_start: 0.8632 (ttpt) cc_final: 0.7703 (mmtt)
REVERT: B  253 MET cc_start: 0.9026 (mmm) cc_final: 0.8775 (mmm)
REVERT: B  489 ASP cc_start: 0.7883 (m-30) cc_final: 0.7597 (m-30)
  outliers start: 26
  outliers final: 16
  residues processed: 102
  average time/residue: 0.0710
  time to fit residues: 10.3317
Evaluate side-chains
  100 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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  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 41 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   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 478 HIS
B 478 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.160939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.143986 restraints weight = 9003.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.78
r_work: 0.3720 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
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 = 0.60   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: 0.7846
moved from start:          0.2308

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= 0.125
  Angle     :  0.555   8.568   9572  Z= 0.277
  Chirality :  0.040   0.122   1146
  Planarity :  0.005   0.062   1122
  Dihedral  : 13.266  63.553   1236
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 10.78 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.29), residues: 882
  helix:  1.29 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.94 (0.48), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 414 
 TYR   0.007   0.001   TYR B 123 
 PHE   0.012   0.001   PHE B 401 
 TRP   0.011   0.001   TRP A  98 
 HIS   0.002   0.001   HIS B 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7122)
  covalent geometry    : angle       0.55473 ( 9572)
  hydrogen bonds       : bond        0.04128 (  498)
  hydrogen bonds       : angle       4.24238 ( 1488)

*********************** 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
  114 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7307 (t0)
REVERT: A  198 LYS cc_start: 0.8668 (ttpt) cc_final: 0.7676 (mmtt)
REVERT: A  324 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8460 (mt)
REVERT: A  489 ASP cc_start: 0.7903 (m-30) cc_final: 0.7595 (m-30)
REVERT: B   85 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7322 (t0)
REVERT: B  198 LYS cc_start: 0.8663 (ttpt) cc_final: 0.7671 (mmtt)
REVERT: B  324 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8462 (mt)
REVERT: B  489 ASP cc_start: 0.7901 (m-30) cc_final: 0.7592 (m-30)
  outliers start: 22
  outliers final: 12
  residues processed: 104
  average time/residue: 0.0666
  time to fit residues: 9.9915
Evaluate side-chains
  96 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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  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  482 GLN
Chi-restraints excluded: chain B residue   85 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  429 VAL
Chi-restraints excluded: chain B residue  438 LEU
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 63 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.161274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.144353 restraints weight = 9009.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 1.79
r_work: 0.3727 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3605 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3605
-------------------------------------------------------------------------------
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 = 0.57   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 = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7122  Z= 0.116
  Angle     :  0.560   8.142   9572  Z= 0.276
  Chirality :  0.039   0.120   1146
  Planarity :  0.004   0.059   1122
  Dihedral  : 12.721  60.437   1236
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 10.36 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.29), residues: 882
  helix:  1.42 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.84 (0.48), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 187 
 TYR   0.007   0.001   TYR A 123 
 PHE   0.010   0.001   PHE B 401 
 TRP   0.010   0.001   TRP A  98 
 HIS   0.002   0.000   HIS B 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7122)
  covalent geometry    : angle       0.56037 ( 9572)
  hydrogen bonds       : bond        0.03951 (  498)
  hydrogen bonds       : angle       4.13620 ( 1488)

*********************** 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
  124 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7431 (t0)
REVERT: A  198 LYS cc_start: 0.8681 (ttpt) cc_final: 0.7796 (mmtt)
REVERT: A  253 MET cc_start: 0.8721 (mmm) cc_final: 0.8244 (mmm)
REVERT: A  324 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8514 (mt)
REVERT: A  489 ASP cc_start: 0.7830 (m-30) cc_final: 0.7527 (m-30)
REVERT: B   85 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7429 (t0)
REVERT: B  198 LYS cc_start: 0.8679 (ttpt) cc_final: 0.7791 (mmtt)
REVERT: B  253 MET cc_start: 0.8711 (mmm) cc_final: 0.8233 (mmm)
REVERT: B  324 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8514 (mt)
REVERT: B  489 ASP cc_start: 0.7832 (m-30) cc_final: 0.7529 (m-30)
  outliers start: 20
  outliers final: 12
  residues processed: 112
  average time/residue: 0.0653
  time to fit residues: 10.6263
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  : 0.238 
-------------------------------------------------------------------------------
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  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  482 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0030
   chunk 81 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.6990

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.161520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.144285 restraints weight = 9106.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3848 rms_B_bonded: 1.82
r_work: 0.3723 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3599 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3599
-------------------------------------------------------------------------------
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 = 0.61   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 = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7122  Z= 0.122
  Angle     :  0.564   8.142   9572  Z= 0.278
  Chirality :  0.039   0.125   1146
  Planarity :  0.004   0.057   1122
  Dihedral  : 12.509  59.812   1236
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.29), residues: 882
  helix:  1.49 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.76 (0.48), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 157 
 TYR   0.008   0.001   TYR B 123 
 PHE   0.010   0.001   PHE B 401 
 TRP   0.010   0.001   TRP A  98 
 HIS   0.002   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7122)
  covalent geometry    : angle       0.56421 ( 9572)
  hydrogen bonds       : bond        0.03933 (  498)
  hydrogen bonds       : angle       4.12206 ( 1488)

*********************** 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
  104 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7519 (t0)
REVERT: A  195 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7702 (pttm)
REVERT: A  198 LYS cc_start: 0.8598 (ttpt) cc_final: 0.7695 (mmtt)
REVERT: A  253 MET cc_start: 0.8780 (mmm) cc_final: 0.8368 (mmm)
REVERT: A  324 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8427 (mt)
REVERT: A  489 ASP cc_start: 0.7867 (m-30) cc_final: 0.7554 (m-30)
REVERT: B   85 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7515 (t0)
REVERT: B  195 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7690 (pttm)
REVERT: B  198 LYS cc_start: 0.8597 (ttpt) cc_final: 0.7683 (mmtt)
REVERT: B  253 MET cc_start: 0.8771 (mmm) cc_final: 0.8350 (mmm)
REVERT: B  324 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8427 (mt)
REVERT: B  489 ASP cc_start: 0.7871 (m-30) cc_final: 0.7557 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 94
  average time/residue: 0.0674
  time to fit residues: 9.2630
Evaluate side-chains
  96 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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  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  482 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0870
   chunk 50 optimal weight:    0.0270
   chunk 14 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 80 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0670
   chunk 59 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.2754

-------------------------------------------------------------------------------
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 = 0.4055 r_free = 0.4055 target = 0.163984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.147044 restraints weight = 8959.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.79
r_work: 0.3756 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3658 r_free = 0.3658    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3658 r_free = 0.3658    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7122  Z= 0.103
  Angle     :  0.533   7.564   9572  Z= 0.262
  Chirality :  0.038   0.127   1146
  Planarity :  0.004   0.054   1122
  Dihedral  : 12.138  59.706   1236
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.29), residues: 882
  helix:  1.65 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -1.46 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 157 
 TYR   0.007   0.001   TYR A 123 
 PHE   0.011   0.001   PHE A 323 
 TRP   0.010   0.001   TRP A  98 
 HIS   0.001   0.000   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 7122)
  covalent geometry    : angle       0.53304 ( 9572)
  hydrogen bonds       : bond        0.03672 (  498)
  hydrogen bonds       : angle       4.04477 ( 1488)

*********************** 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
  120 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.8125 (mmtp) cc_final: 0.7623 (pttm)
REVERT: A  198 LYS cc_start: 0.8593 (ttpt) cc_final: 0.7695 (mmtt)
REVERT: A  253 MET cc_start: 0.8770 (mmm) cc_final: 0.8221 (mmm)
REVERT: A  324 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8389 (mt)
REVERT: A  489 ASP cc_start: 0.7861 (m-30) cc_final: 0.7527 (m-30)
REVERT: B  195 LYS cc_start: 0.8099 (mmtp) cc_final: 0.7589 (pttm)
REVERT: B  198 LYS cc_start: 0.8590 (ttpt) cc_final: 0.7681 (mmtt)
REVERT: B  253 MET cc_start: 0.8749 (mmm) cc_final: 0.8185 (mmm)
REVERT: B  324 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8385 (mt)
REVERT: B  489 ASP cc_start: 0.7855 (m-30) cc_final: 0.7519 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 112
  average time/residue: 0.0702
  time to fit residues: 11.2131
Evaluate side-chains
  102 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  422 VAL
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  422 VAL
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 66 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 85 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0030
   chunk 50 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.163098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.146121 restraints weight = 9079.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 1.82
r_work: 0.3744 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3620 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3642
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7122  Z= 0.113
  Angle     :  0.546   7.918   9572  Z= 0.268
  Chirality :  0.039   0.126   1146
  Planarity :  0.004   0.051   1122
  Dihedral  : 12.015  59.921   1236
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.29), residues: 882
  helix:  1.64 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -1.39 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 157 
 TYR   0.006   0.001   TYR B 123 
 PHE   0.009   0.001   PHE A 401 
 TRP   0.009   0.001   TRP A  98 
 HIS   0.002   0.000   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7122)
  covalent geometry    : angle       0.54579 ( 9572)
  hydrogen bonds       : bond        0.03763 (  498)
  hydrogen bonds       : angle       4.05161 ( 1488)

*********************** 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: 16
    poor density    : 92
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7610 (pttm)
REVERT: A  198 LYS cc_start: 0.8590 (ttpt) cc_final: 0.7697 (mmtt)
REVERT: A  253 MET cc_start: 0.8777 (mmm) cc_final: 0.8344 (mmm)
REVERT: A  324 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8422 (mt)
REVERT: A  489 ASP cc_start: 0.7836 (m-30) cc_final: 0.7538 (m-30)
REVERT: B  195 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7584 (pttm)
REVERT: B  198 LYS cc_start: 0.8591 (ttpt) cc_final: 0.7688 (mmtt)
REVERT: B  253 MET cc_start: 0.8775 (mmm) cc_final: 0.8331 (mmm)
REVERT: B  324 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8423 (mt)
REVERT: B  489 ASP cc_start: 0.7838 (m-30) cc_final: 0.7538 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0673
  time to fit residues: 9.7976
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  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  422 VAL
Chi-restraints excluded: chain A residue  482 GLN
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  422 VAL
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 28 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0370
   chunk 11 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.1864

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.159078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.142652 restraints weight = 8950.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 1.76
r_work: 0.3700 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3578 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7122  Z= 0.149
  Angle     :  0.593   8.382   9572  Z= 0.292
  Chirality :  0.041   0.129   1146
  Planarity :  0.004   0.045   1122
  Dihedral  : 12.206  59.326   1236
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.29), residues: 882
  helix:  1.42 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.53 (0.49), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 414 
 TYR   0.006   0.001   TYR B 123 
 PHE   0.013   0.001   PHE A 401 
 TRP   0.012   0.001   TRP A 233 
 HIS   0.003   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 7122)
  covalent geometry    : angle       0.59298 ( 9572)
  hydrogen bonds       : bond        0.04199 (  498)
  hydrogen bonds       : angle       4.17785 ( 1488)

*********************** 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: 12
    poor density    : 96
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.8140 (mmtp) cc_final: 0.7556 (pttm)
REVERT: A  198 LYS cc_start: 0.8610 (ttpt) cc_final: 0.7683 (mmtt)
REVERT: A  253 MET cc_start: 0.8808 (mmm) cc_final: 0.8384 (mmm)
REVERT: A  324 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8426 (mt)
REVERT: A  489 ASP cc_start: 0.7964 (m-30) cc_final: 0.7675 (m-30)
REVERT: B  195 LYS cc_start: 0.8131 (mmtp) cc_final: 0.7548 (pttm)
REVERT: B  198 LYS cc_start: 0.8617 (ttpt) cc_final: 0.7681 (mmtt)
REVERT: B  253 MET cc_start: 0.8785 (mmm) cc_final: 0.8346 (mmm)
REVERT: B  324 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8428 (mt)
REVERT: B  489 ASP cc_start: 0.7962 (m-30) cc_final: 0.7669 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0705
  time to fit residues: 10.3250
Evaluate side-chains
  106 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  422 VAL
Chi-restraints excluded: chain A residue  482 GLN
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  422 VAL
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 66 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 49 optimal weight:    0.3980
   chunk 43 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 87 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.4029 r_free = 0.4029 target = 0.161768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.144708 restraints weight = 9080.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3848 rms_B_bonded: 1.81
r_work: 0.3726 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3601 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2882

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= 0.120
  Angle     :  0.555   8.009   9572  Z= 0.273
  Chirality :  0.039   0.128   1146
  Planarity :  0.004   0.043   1122
  Dihedral  : 11.997  59.840   1236
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.45 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.29), residues: 882
  helix:  1.51 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -1.42 (0.49), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 177 
 TYR   0.006   0.001   TYR A 123 
 PHE   0.010   0.001   PHE B 323 
 TRP   0.010   0.001   TRP B  98 
 HIS   0.002   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7122)
  covalent geometry    : angle       0.55537 ( 9572)
  hydrogen bonds       : bond        0.03835 (  498)
  hydrogen bonds       : angle       4.10268 ( 1488)

********************** 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  : 0.249 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7531 (pttm)
REVERT: A  198 LYS cc_start: 0.8594 (ttpt) cc_final: 0.7688 (mmtt)
REVERT: A  253 MET cc_start: 0.8770 (mmm) cc_final: 0.8357 (mmm)
REVERT: A  324 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8343 (mt)
REVERT: A  489 ASP cc_start: 0.7953 (m-30) cc_final: 0.7667 (m-30)
REVERT: B  195 LYS cc_start: 0.8122 (mmtp) cc_final: 0.7527 (pttm)
REVERT: B  198 LYS cc_start: 0.8600 (ttpt) cc_final: 0.7692 (mmtt)
REVERT: B  253 MET cc_start: 0.8728 (mmm) cc_final: 0.8174 (mmm)
REVERT: B  324 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8346 (mt)
REVERT: B  489 ASP cc_start: 0.7955 (m-30) cc_final: 0.7665 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 99
  average time/residue: 0.0703
  time to fit residues: 9.9378
Evaluate side-chains
  102 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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  422 VAL
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  422 VAL
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 5 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.160940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.143893 restraints weight = 9005.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 1.80
r_work: 0.3716 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3593 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2853

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= 0.135
  Angle     :  0.568   8.226   9572  Z= 0.279
  Chirality :  0.040   0.126   1146
  Planarity :  0.004   0.044   1122
  Dihedral  : 12.033  59.853   1236
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.45 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.29), residues: 882
  helix:  1.47 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.41 (0.49), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 157 
 TYR   0.005   0.001   TYR B 123 
 PHE   0.011   0.001   PHE A 401 
 TRP   0.010   0.001   TRP B  98 
 HIS   0.003   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7122)
  covalent geometry    : angle       0.56792 ( 9572)
  hydrogen bonds       : bond        0.03969 (  498)
  hydrogen bonds       : angle       4.12247 ( 1488)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1642.64 seconds
wall clock time: 28 minutes 45.06 seconds (1725.06 seconds total)