Starting phenix.real_space_refine
on Wed Feb 12 07:03:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b4l_12002/02_2025/7b4l_12002.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b4l_12002/02_2025/7b4l_12002.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b4l_12002/02_2025/7b4l_12002.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b4l_12002/02_2025/7b4l_12002.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b4l_12002/02_2025/7b4l_12002.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b4l_12002/02_2025/7b4l_12002.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.100
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      36      5.16       5
     Na      2      4.78       5
     C    4740      2.51       5
     N    1068      2.21       5
     O    1180      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7030
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3300
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3300
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 202
          Unusual residues: {' NA': 1, 'C14': 3, 'POV': 2, 'UND': 5}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
    Chain: "B"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 202
          Unusual residues: {' NA': 1, 'C14': 3, 'POV': 2, 'UND': 5}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb="NA    NA A 601 " occ=0.50
    residue:
      pdb="NA    NA B 602 " occ=0.50
    residue:
      pdb=" O   HOH A 711 " occ=0.50
    residue:
      pdb=" O   HOH B 711 " occ=0.50
  Time building chain proxies: 4.84, per 1000 atoms: 0.69
  Number of scatterers: 7030
  At special positions: 0
  Unit cell: (97.643, 91.205, 77.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       4     15.00
     Na      2     11.00
     O    1180      8.00
     N    1068      7.00
     C    4740      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.91
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      84.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  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: 1.89

  Time building geometry restraints manager: 2.13 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 116
        2.69 -     3.24: 6962
        3.24 -     3.80: 10296
        3.80 -     4.35: 14397
        4.35 -     4.90: 24237
  Nonbonded interactions: 56008
  Sorted by model distance:
  nonbonded pdb=" O   SER B 497 "
            pdb=" OG1 THR B 501 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   SER A 497 "
            pdb=" OG1 THR A 501 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   PHE B 445 "
            pdb=" NZ  LYS B 450 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" O   PHE A 445 "
            pdb=" NZ  LYS A 450 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   LYS B 450 "
            pdb=" OG  SER B 454 "
     model   vdw
     2.297 3.040
  ... (remaining 56003 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 79 through 521 or resid 604 through 605 or resid 607 throu \ 
gh 610))
  selection = (chain 'B' and (resid 79 through 521 or resid 604 through 605 or resid 607 throu \ 
gh 610))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.480
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.720
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   7122  Z= 0.310
  Angle     :  1.048  12.169   9572  Z= 0.442
  Chirality :  0.039   0.187   1146
  Planarity :  0.005   0.053   1122
  Dihedral  : 16.182 100.208   2672
  Min Nonbonded Distance : 2.141

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

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

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

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

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A  149 MET cc_start: 0.8974 (mtt) cc_final: 0.8530 (mtm)
REVERT: A  198 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7817 (mmtt)
REVERT: A  489 ASP cc_start: 0.7389 (m-30) cc_final: 0.7153 (m-30)
REVERT: B  149 MET cc_start: 0.8975 (mtt) cc_final: 0.8530 (mtm)
REVERT: B  198 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7824 (mmtt)
REVERT: B  489 ASP cc_start: 0.7391 (m-30) cc_final: 0.7153 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1891
  time to fit residues: 30.1993
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  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.9184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.159289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.142438 restraints weight = 8920.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 1.77
r_work: 0.3701 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3580 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3602
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3602
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1662

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

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

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

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

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

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7126 (t0)
REVERT: A  198 LYS cc_start: 0.8565 (ttpt) cc_final: 0.7733 (mmtt)
REVERT: A  253 MET cc_start: 0.9089 (mmm) cc_final: 0.8762 (mmm)
REVERT: A  489 ASP cc_start: 0.7869 (m-30) cc_final: 0.7643 (m-30)
REVERT: B   85 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7127 (t0)
REVERT: B  198 LYS cc_start: 0.8573 (ttpt) cc_final: 0.7742 (mmtt)
REVERT: B  253 MET cc_start: 0.9089 (mmm) cc_final: 0.8754 (mmm)
REVERT: B  489 ASP cc_start: 0.7891 (m-30) cc_final: 0.7662 (m-30)
  outliers start: 12
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1942
  time to fit residues: 25.1065
Evaluate side-chains
  90 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  429 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0980
   chunk 2 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 77 optimal weight:    6.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4023 r_free = 0.4023 target = 0.161177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.144184 restraints weight = 8935.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 1.78
r_work: 0.3726 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3605 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3605
-------------------------------------------------------------------------------
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 = 0.59   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 = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2033

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= 0.173
  Angle     :  0.565   8.490   9572  Z= 0.284
  Chirality :  0.040   0.122   1146
  Planarity :  0.005   0.058   1122
  Dihedral  : 14.001  85.837   1236
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  :  8.40 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.29), residues: 882
  helix:  1.15 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -2.17 (0.47), residues: 178

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

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

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7104 (t0)
REVERT: A  198 LYS cc_start: 0.8647 (ttpt) cc_final: 0.7730 (mmtt)
REVERT: A  253 MET cc_start: 0.9030 (mmm) cc_final: 0.8800 (mmm)
REVERT: A  489 ASP cc_start: 0.7867 (m-30) cc_final: 0.7588 (m-30)
REVERT: B   85 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7096 (t0)
REVERT: B  198 LYS cc_start: 0.8650 (ttpt) cc_final: 0.7734 (mmtt)
REVERT: B  253 MET cc_start: 0.9020 (mmm) cc_final: 0.8782 (mmm)
REVERT: B  489 ASP cc_start: 0.7877 (m-30) cc_final: 0.7589 (m-30)
  outliers start: 26
  outliers final: 16
  residues processed: 105
  average time/residue: 0.1646
  time to fit residues: 24.4882
Evaluate side-chains
  102 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
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 45 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0060
   chunk 54 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0970
   chunk 43 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0970
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.3592

-------------------------------------------------------------------------------
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 = 0.4057 r_free = 0.4057 target = 0.164274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.147413 restraints weight = 8936.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 1.78
r_work: 0.3761 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3657 r_free = 0.3657    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3657 r_free = 0.3657    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7122  Z= 0.139
  Angle     :  0.521   7.380   9572  Z= 0.260
  Chirality :  0.038   0.122   1146
  Planarity :  0.005   0.063   1122
  Dihedral  : 12.718  60.825   1236
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 10.92 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.29), residues: 882
  helix:  1.49 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -2.00 (0.47), residues: 176

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

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

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7368 (t0)
REVERT: A  198 LYS cc_start: 0.8685 (ttpt) cc_final: 0.7719 (mmtt)
REVERT: A  324 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8386 (mt)
REVERT: A  489 ASP cc_start: 0.7819 (m-30) cc_final: 0.7518 (m-30)
REVERT: B   85 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7375 (t0)
REVERT: B  198 LYS cc_start: 0.8676 (ttpt) cc_final: 0.7708 (mmtt)
REVERT: B  324 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8388 (mt)
REVERT: B  489 ASP cc_start: 0.7823 (m-30) cc_final: 0.7519 (m-30)
  outliers start: 22
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1861
  time to fit residues: 28.5551
Evaluate side-chains
  98 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
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  439 MET
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue  158 ASN
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  482 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 25 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0050
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.6996

-------------------------------------------------------------------------------
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 = 0.162167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.145673 restraints weight = 8723.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 1.74
r_work: 0.3738 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3616 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2539

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= 0.169
  Angle     :  0.547   9.683   9572  Z= 0.270
  Chirality :  0.039   0.117   1146
  Planarity :  0.004   0.059   1122
  Dihedral  : 12.493  59.909   1236
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 11.48 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.29), residues: 882
  helix:  1.54 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.78 (0.48), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.002   0.000   HIS A 224 
 PHE   0.012   0.001   PHE B 323 
 TYR   0.007   0.001   TYR B 123 
 ARG   0.003   0.000   ARG B 157 

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

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7421 (t0)
REVERT: A  195 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7749 (pttm)
REVERT: A  198 LYS cc_start: 0.8618 (ttpt) cc_final: 0.7688 (mmtt)
REVERT: A  253 MET cc_start: 0.8773 (mmm) cc_final: 0.8186 (mmm)
REVERT: A  324 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8487 (mt)
REVERT: A  489 ASP cc_start: 0.7807 (m-30) cc_final: 0.7503 (m-30)
REVERT: B   85 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7422 (t0)
REVERT: B  195 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7736 (pttm)
REVERT: B  198 LYS cc_start: 0.8620 (ttpt) cc_final: 0.7687 (mmtt)
REVERT: B  253 MET cc_start: 0.8766 (mmm) cc_final: 0.8174 (mmm)
REVERT: B  324 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8484 (mt)
REVERT: B  489 ASP cc_start: 0.7800 (m-30) cc_final: 0.7496 (m-30)
  outliers start: 22
  outliers final: 12
  residues processed: 105
  average time/residue: 0.1746
  time to fit residues: 25.4020
Evaluate side-chains
  107 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
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  195 LYS
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  438 LEU
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue  158 ASN
Chi-restraints excluded: chain B residue  195 LYS
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  438 LEU
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  482 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 65 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.160608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.143504 restraints weight = 8935.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 1.79
r_work: 0.3712 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3587 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2572

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= 0.213
  Angle     :  0.575  10.092   9572  Z= 0.283
  Chirality :  0.040   0.121   1146
  Planarity :  0.005   0.059   1122
  Dihedral  : 12.453  59.751   1236
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 11.76 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.29), residues: 882
  helix:  1.46 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.72 (0.48), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 233 
 HIS   0.003   0.001   HIS B 224 
 PHE   0.011   0.001   PHE B 401 
 TYR   0.006   0.001   TYR A 123 
 ARG   0.003   0.000   ARG B 157 

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

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7503 (t0)
REVERT: A  195 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7743 (pttm)
REVERT: A  198 LYS cc_start: 0.8675 (ttpt) cc_final: 0.7752 (mmtt)
REVERT: A  253 MET cc_start: 0.8833 (mmm) cc_final: 0.8362 (mmm)
REVERT: A  324 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8545 (mt)
REVERT: A  489 ASP cc_start: 0.7848 (m-30) cc_final: 0.7537 (m-30)
REVERT: B   85 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7432 (t0)
REVERT: B  195 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7736 (pttm)
REVERT: B  198 LYS cc_start: 0.8672 (ttpt) cc_final: 0.7740 (mmtt)
REVERT: B  253 MET cc_start: 0.8835 (mmm) cc_final: 0.8365 (mmm)
REVERT: B  324 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8540 (mt)
REVERT: B  489 ASP cc_start: 0.7844 (m-30) cc_final: 0.7536 (m-30)
  outliers start: 24
  outliers final: 14
  residues processed: 93
  average time/residue: 0.1500
  time to fit residues: 20.3948
Evaluate side-chains
  98 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  244 VAL
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  195 LYS
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain B residue  244 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0980
   chunk 5 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.163494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.146338 restraints weight = 8932.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3871 rms_B_bonded: 1.81
r_work: 0.3750 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3626 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    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 = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7122  Z= 0.149
  Angle     :  0.545   9.286   9572  Z= 0.264
  Chirality :  0.038   0.123   1146
  Planarity :  0.004   0.054   1122
  Dihedral  : 12.062  59.756   1236
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 5.88
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.29), residues: 882
  helix:  1.62 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.62 (0.49), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.001   0.000   HIS A 224 
 PHE   0.009   0.001   PHE A 401 
 TYR   0.006   0.001   TYR A 123 
 ARG   0.002   0.000   ARG B 187 

*********************** 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
  106 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  198 LYS cc_start: 0.8610 (ttpt) cc_final: 0.7669 (mmtt)
REVERT: A  253 MET cc_start: 0.8817 (mmm) cc_final: 0.8365 (mmm)
REVERT: A  324 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8341 (mt)
REVERT: A  489 ASP cc_start: 0.7802 (m-30) cc_final: 0.7484 (m-30)
REVERT: B  198 LYS cc_start: 0.8608 (ttpt) cc_final: 0.7662 (mmtt)
REVERT: B  253 MET cc_start: 0.8802 (mmm) cc_final: 0.8346 (mmm)
REVERT: B  324 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8342 (mt)
REVERT: B  489 ASP cc_start: 0.7814 (m-30) cc_final: 0.7499 (m-30)
  outliers start: 18
  outliers final: 8
  residues processed: 100
  average time/residue: 0.1412
  time to fit residues: 21.0305
Evaluate side-chains
  88 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
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  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  482 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 72 optimal weight:    0.2980
   chunk 40 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.162276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.145023 restraints weight = 8992.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 1.82
r_work: 0.3728 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
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 = 0.66   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 = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7122  Z= 0.181
  Angle     :  0.566   9.612   9572  Z= 0.273
  Chirality :  0.039   0.124   1146
  Planarity :  0.004   0.052   1122
  Dihedral  : 11.916  59.352   1236
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.89 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.29), residues: 882
  helix:  1.58 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.52 (0.50), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.002   0.001   HIS B 224 
 PHE   0.010   0.001   PHE A 401 
 TYR   0.006   0.001   TYR A 123 
 ARG   0.002   0.000   ARG A 414 

*********************** 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
  102 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.673 
Fit side-chains
REVERT: A  198 LYS cc_start: 0.8589 (ttpt) cc_final: 0.7695 (mmtt)
REVERT: A  253 MET cc_start: 0.8806 (mmm) cc_final: 0.8352 (mmm)
REVERT: A  324 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8372 (mt)
REVERT: A  489 ASP cc_start: 0.7854 (m-30) cc_final: 0.7557 (m-30)
REVERT: B  198 LYS cc_start: 0.8588 (ttpt) cc_final: 0.7681 (mmtt)
REVERT: B  253 MET cc_start: 0.8800 (mmm) cc_final: 0.8347 (mmm)
REVERT: B  324 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8369 (mt)
REVERT: B  489 ASP cc_start: 0.7853 (m-30) cc_final: 0.7555 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 98
  average time/residue: 0.1571
  time to fit residues: 22.0170
Evaluate side-chains
  96 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
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  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  482 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 50 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3984 r_free = 0.3984 target = 0.159576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.142347 restraints weight = 8952.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 1.84
r_work: 0.3684 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3577
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7122  Z= 0.161
  Angle     :  0.549   9.345   9572  Z= 0.265
  Chirality :  0.038   0.124   1146
  Planarity :  0.004   0.043   1122
  Dihedral  : 11.717  59.449   1236
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.31 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.29), residues: 882
  helix:  1.70 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.46 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.002   0.000   HIS A 224 
 PHE   0.009   0.001   PHE B 401 
 TYR   0.006   0.001   TYR B 123 
 ARG   0.001   0.000   ARG A 414 

*********************** 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
  105 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.8122 (mmtp) cc_final: 0.7595 (pttm)
REVERT: A  198 LYS cc_start: 0.8581 (ttpt) cc_final: 0.7663 (mmtt)
REVERT: A  253 MET cc_start: 0.8743 (mmm) cc_final: 0.8304 (mmm)
REVERT: A  489 ASP cc_start: 0.7735 (m-30) cc_final: 0.7425 (m-30)
REVERT: B  195 LYS cc_start: 0.8109 (mmtp) cc_final: 0.7583 (pttm)
REVERT: B  198 LYS cc_start: 0.8579 (ttpt) cc_final: 0.7664 (mmtt)
REVERT: B  253 MET cc_start: 0.8741 (mmm) cc_final: 0.8298 (mmm)
REVERT: B  324 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8342 (mt)
REVERT: B  489 ASP cc_start: 0.7732 (m-30) cc_final: 0.7421 (m-30)
  outliers start: 13
  outliers final: 10
  residues processed: 99
  average time/residue: 0.1644
  time to fit residues: 23.2073
Evaluate side-chains
  99 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  429 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 26 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 69 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3957 r_free = 0.3957 target = 0.157012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.139427 restraints weight = 9254.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 1.88
r_work: 0.3644 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3518 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2818

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= 0.220
  Angle     :  0.580   9.826   9572  Z= 0.282
  Chirality :  0.040   0.122   1146
  Planarity :  0.004   0.045   1122
  Dihedral  : 11.897  59.133   1236
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.01 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.29), residues: 882
  helix:  1.56 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.44 (0.50), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 233 
 HIS   0.003   0.001   HIS A 224 
 PHE   0.012   0.001   PHE B 401 
 TYR   0.006   0.001   TYR A 123 
 ARG   0.001   0.000   ARG A 414 

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

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  198 LYS cc_start: 0.8583 (ttpt) cc_final: 0.7676 (mmtt)
REVERT: A  253 MET cc_start: 0.8792 (mmm) cc_final: 0.8336 (mmm)
REVERT: A  324 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8378 (mt)
REVERT: A  489 ASP cc_start: 0.7889 (m-30) cc_final: 0.7583 (m-30)
REVERT: B  198 LYS cc_start: 0.8577 (ttpt) cc_final: 0.7674 (mmtt)
REVERT: B  253 MET cc_start: 0.8795 (mmm) cc_final: 0.8339 (mmm)
REVERT: B  324 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8395 (mt)
REVERT: B  489 ASP cc_start: 0.7887 (m-30) cc_final: 0.7578 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 98
  average time/residue: 0.1587
  time to fit residues: 22.3390
Evaluate side-chains
  100 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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  429 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  429 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 2 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0040
   chunk 57 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0000
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.160130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.142893 restraints weight = 8909.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 1.84
r_work: 0.3691 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3567 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3584
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3584 r_free = 0.3584    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3584 r_free = 0.3584    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7122  Z= 0.149
  Angle     :  0.542   9.323   9572  Z= 0.261
  Chirality :  0.038   0.131   1146
  Planarity :  0.004   0.044   1122
  Dihedral  : 11.616  59.063   1236
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.01 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.29), residues: 882
  helix:  1.73 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -1.27 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.001   0.000   HIS B 224 
 PHE   0.011   0.001   PHE B 323 
 TYR   0.005   0.001   TYR A 123 
 ARG   0.001   0.000   ARG A 414 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3448.85 seconds
wall clock time: 61 minutes 51.16 seconds (3711.16 seconds total)