Starting phenix.real_space_refine
on Sat Jun  7 23:50:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iqe_60789/06_2025/9iqe_60789.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iqe_60789/06_2025/9iqe_60789.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iqe_60789/06_2025/9iqe_60789.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iqe_60789/06_2025/9iqe_60789.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iqe_60789/06_2025/9iqe_60789.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iqe_60789/06_2025/9iqe_60789.cif"
  }
  resolution = 3.78
  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=   0.005 sd=   0.058
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      33      5.16       5
     C    5781      2.51       5
     N    1612      2.21       5
     O    1690      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9118
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 4348
          Classifications: {'peptide': 574}
          Link IDs: {'PTRANS': 19, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 4743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 619, 4743
          Classifications: {'peptide': 619}
          Link IDs: {'PTRANS': 18, 'TRANS': 600}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.74, per 1000 atoms: 0.63
  Number of scatterers: 9118
  At special positions: 0
  Unit cell: (70.72, 91.52, 147.264, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      33     16.00
     P       2     15.00
     O    1690      8.00
     N    1612      7.00
     C    5781      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.45
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2194

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 5 sheets defined
      70.8% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 0 through 10
      removed outlier: 4.078A  pdb=" N   GLN A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 45
      Proline residue:  A  35  - end of helix
    Processing helix  chain 'A' and resid 50 through 100
      removed outlier: 3.512A  pdb=" N   THR A 100 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 110
    Processing helix  chain 'A' and resid 110 through 135
      removed outlier: 4.272A  pdb=" N   THR A 116 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   ASP A 121 " --> pdb=" O   ARG A 117 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   VAL A 122 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ILE A 125 " --> pdb=" O   ASP A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 153
    Processing helix  chain 'A' and resid 158 through 203
      Proline residue:  A 166  - end of helix
      Proline residue:  A 181  - end of helix
      removed outlier: 3.525A  pdb=" N   GLY A 203 " --> pdb=" O   ASP A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 210
      removed outlier: 3.509A  pdb=" N   PHE A 210 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 240
    Processing helix  chain 'A' and resid 241 through 267
    Processing helix  chain 'A' and resid 270 through 293
      removed outlier: 4.134A  pdb=" N   LEU A 274 " --> pdb=" O   GLN A 270 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 313
      removed outlier: 4.179A  pdb=" N   ARG A 300 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 382
      removed outlier: 4.092A  pdb=" N   ILE A 378 " --> pdb=" O   LYS A 374 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   SER A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 410
    Processing helix  chain 'A' and resid 425 through 430
    Processing helix  chain 'A' and resid 437 through 448
    Processing helix  chain 'A' and resid 450 through 455
    Processing helix  chain 'A' and resid 459 through 462
    Processing helix  chain 'A' and resid 473 through 487
    Processing helix  chain 'A' and resid 498 through 502
      removed outlier: 3.800A  pdb=" N   ALA A 501 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 519
    Processing helix  chain 'A' and resid 529 through 533
    Processing helix  chain 'A' and resid 552 through 560
    Processing helix  chain 'A' and resid 560 through 571
    Processing helix  chain 'B' and resid 17 through 29
    Processing helix  chain 'B' and resid 32 through 70
      Proline residue:  B  53  - end of helix
    Processing helix  chain 'B' and resid 77 through 88
      removed outlier: 3.707A  pdb=" N   ARG B  88 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 98
    Processing helix  chain 'B' and resid 109 through 158
    Processing helix  chain 'B' and resid 161 through 168
      removed outlier: 4.203A  pdb=" N   PHE B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 178
      removed outlier: 4.120A  pdb=" N   SER B 175 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 213
      removed outlier: 3.590A  pdb=" N   ASP B 182 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   MET B 190 " --> pdb=" O   ASN B 186 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   LEU B 196 " --> pdb=" O   ILE B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 222
      removed outlier: 3.848A  pdb=" N   PHE B 219 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 262
      removed outlier: 3.561A  pdb=" N   ALA B 226 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      Proline residue:  B 240  - end of helix
    Processing helix  chain 'B' and resid 262 through 268
    Processing helix  chain 'B' and resid 271 through 299
    Processing helix  chain 'B' and resid 299 through 325
    Processing helix  chain 'B' and resid 329 through 372
      removed outlier: 3.606A  pdb=" N   ILE B 333 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      Proline residue:  B 346  - end of helix
      removed outlier: 4.350A  pdb=" N   GLN B 349 " --> pdb=" O   GLN B 345 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR B 354 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   ASN B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   THR B 356 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 438
    Processing helix  chain 'B' and resid 456 through 458
      No H-bonds generated for 'chain 'B' and resid 456 through 458'
    Processing helix  chain 'B' and resid 459 through 468
      removed outlier: 3.732A  pdb=" N   ALA B 465 " --> pdb=" O   GLU B 461 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   SER B 466 " --> pdb=" O   SER B 462 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE B 467 " --> pdb=" O   LEU B 463 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   GLY B 468 " --> pdb=" O   ARG B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 487
    Processing helix  chain 'B' and resid 493 through 504
      removed outlier: 3.605A  pdb=" N   ILE B 498 " --> pdb=" O   GLU B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 511
      removed outlier: 4.222A  pdb=" N   HIS B 511 " --> pdb=" O   ASP B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 544
    Processing helix  chain 'B' and resid 559 through 572
    Processing helix  chain 'B' and resid 585 through 590
      removed outlier: 3.573A  pdb=" N   ILE B 589 " --> pdb=" O   ARG B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 615
    Processing helix  chain 'B' and resid 617 through 627
      removed outlier: 3.998A  pdb=" N   HIS B 626 " --> pdb=" O   MET B 622 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   LEU B 627 " --> pdb=" O   THR B 623 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 354
      removed outlier: 5.868A  pdb=" N   ALA A 339 " --> pdb=" O   ASP A 353 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ALA A 339 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   SER A 389 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414
      removed outlier: 6.379A  pdb=" N   GLY A 412 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   ASP A 496 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL A 414 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLY A 368 " --> pdb=" O   SER A 527 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ASP A 543 " --> pdb=" O   VAL A 547 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   VAL A 547 " --> pdb=" O   ASP A 543 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424
      removed outlier: 4.082A  pdb=" N   GLY A 423 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 410 through 413
      removed outlier: 5.242A  pdb=" N   LEU B 410 " --> pdb=" O   HIS B 395 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 469 through 470
      removed outlier: 6.374A  pdb=" N   VAL B 470 " --> pdb=" O   ASP B 552 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU B 549 " --> pdb=" O   PHE B 580 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   ILE B 582 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LEU B 551 " --> pdb=" O   ILE B 582 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   ALA B 421 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   MET B 598 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   VAL B 423 " --> pdb=" O   MET B 598 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   ASP B 599 " --> pdb=" O   ILE B 603 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   ILE B 603 " --> pdb=" O   ASP B 599 " (cutoff:3.500A)

    638 hydrogen bonds defined for protein.
    1884 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: 3.01

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3080
        1.34 -     1.46: 1763
        1.46 -     1.58: 4367
        1.58 -     1.69: 3
        1.69 -     1.81: 61
  Bond restraints: 9274
  Sorted by residual:
  bond pdb=" N   LEU A 240 "
       pdb=" CA  LEU A 240 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.12e-02 7.97e+03 6.25e+00
  bond pdb=" CA  SER B 587 "
       pdb=" CB  SER B 587 "
    ideal  model  delta    sigma   weight residual
    1.529  1.490  0.039 1.55e-02 4.16e+03 6.23e+00
  bond pdb=" N   ASP B  61 "
       pdb=" CA  ASP B  61 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.027 1.19e-02 7.06e+03 5.33e+00
  bond pdb=" N   LEU A 157 "
       pdb=" CA  LEU A 157 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.42e-02 4.96e+03 5.01e+00
  bond pdb=" N   LEU B  97 "
       pdb=" CA  LEU B  97 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.027 1.27e-02 6.20e+03 4.57e+00
  ... (remaining 9269 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 12363
        1.88 -     3.75: 198
        3.75 -     5.63: 48
        5.63 -     7.50: 16
        7.50 -     9.38: 3
  Bond angle restraints: 12628
  Sorted by residual:
  angle pdb=" N   LEU A 240 "
        pdb=" CA  LEU A 240 "
        pdb=" C   LEU A 240 "
      ideal   model   delta    sigma   weight residual
     112.97  107.48    5.49 1.06e+00 8.90e-01 2.68e+01
  angle pdb=" C   ALA B 554 "
        pdb=" N   THR B 555 "
        pdb=" CA  THR B 555 "
      ideal   model   delta    sigma   weight residual
     121.18  130.33   -9.15 1.98e+00 2.55e-01 2.14e+01
  angle pdb=" C   VAL A 486 "
        pdb=" N   ILE A 487 "
        pdb=" CA  ILE A 487 "
      ideal   model   delta    sigma   weight residual
     121.97  114.70    7.27 1.80e+00 3.09e-01 1.63e+01
  angle pdb=" CA  THR A  36 "
        pdb=" CB  THR A  36 "
        pdb=" OG1 THR A  36 "
      ideal   model   delta    sigma   weight residual
     109.60  103.85    5.75 1.50e+00 4.44e-01 1.47e+01
  angle pdb=" N   LEU A 157 "
        pdb=" CA  LEU A 157 "
        pdb=" C   LEU A 157 "
      ideal   model   delta    sigma   weight residual
     114.12  109.37    4.75 1.39e+00 5.18e-01 1.17e+01
  ... (remaining 12623 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.73: 5249
       31.73 -    63.45: 248
       63.45 -    95.18: 13
       95.18 -   126.91: 0
      126.91 -   158.63: 1
  Dihedral angle restraints: 5511
    sinusoidal: 2102
      harmonic: 3409
  Sorted by residual:
  dihedral pdb=" C2' ADP B 701 "
           pdb=" C1' ADP B 701 "
           pdb=" N9  ADP B 701 "
           pdb=" C4  ADP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      91.55  -67.09  158.63     1      2.00e+01 2.50e-03 4.64e+01
  dihedral pdb=" CA  GLU B 553 "
           pdb=" C   GLU B 553 "
           pdb=" N   ALA B 554 "
           pdb=" CA  ALA B 554 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.55   23.45     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  LEU B  29 "
           pdb=" C   LEU B  29 "
           pdb=" N   PRO B  30 "
           pdb=" CA  PRO B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.75  -22.25     0      5.00e+00 4.00e-02 1.98e+01
  ... (remaining 5508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1222
       0.053 -    0.105: 257
       0.105 -    0.158: 35
       0.158 -    0.211: 3
       0.211 -    0.263: 3
  Chirality restraints: 1520
  Sorted by residual:
  chirality pdb=" CG  LEU A 445 "
            pdb=" CB  LEU A 445 "
            pdb=" CD1 LEU A 445 "
            pdb=" CD2 LEU A 445 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  THR B 191 "
            pdb=" CA  THR B 191 "
            pdb=" OG1 THR B 191 "
            pdb=" CG2 THR B 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.30    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  LEU A 240 "
            pdb=" N   LEU A 240 "
            pdb=" C   LEU A 240 "
            pdb=" CB  LEU A 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1517 not shown)

  Planarity restraints: 1617
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 415 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.36e+00
        pdb=" N   PRO B 416 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 416 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 416 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 354 "   -0.009 2.00e-02 2.50e+03   1.21e-02 2.91e+00
        pdb=" CG  TYR B 354 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 354 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 354 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 354 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 354 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 354 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 354 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 358 "    0.026 5.00e-02 4.00e+02   3.97e-02 2.52e+00
        pdb=" N   PRO A 359 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 359 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 359 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1614 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1191
        2.75 -     3.29: 9942
        3.29 -     3.83: 16075
        3.83 -     4.36: 17322
        4.36 -     4.90: 30455
  Nonbonded interactions: 74985
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 270 "
            pdb=" OG  SER A 273 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   LEU B 174 "
            pdb=" OG1 THR B 178 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   PHE A 421 "
            pdb=" ND2 ASN A 428 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" O   SER B 213 "
            pdb=" OG1 THR B 217 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   ASN B 515 "
            pdb=" OG1 THR B 519 "
     model   vdw
     2.295 3.040
  ... (remaining 74980 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.100
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.740
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
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      :  0.003   0.041   9274  Z= 0.150
  Angle     :  0.663   9.378  12628  Z= 0.349
  Chirality :  0.043   0.263   1520
  Planarity :  0.004   0.046   1617
  Dihedral  : 16.844 158.632   3317
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.78 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 24.24 %
    Favored  : 70.64 %
  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:  1.33 (0.25), residues: 1189
  helix:  1.46 (0.19), residues: 777
  sheet:  0.34 (0.73), residues: 58
  loop : -0.17 (0.36), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 620 
 HIS   0.004   0.001   HIS A  88 
 PHE   0.016   0.001   PHE B 336 
 TYR   0.030   0.001   TYR B 354 
 ARG   0.005   0.000   ARG B 618 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12773 (  638)
  hydrogen bonds       : angle       5.62541 ( 1884)
  covalent geometry    : bond        0.00294 ( 9274)
  covalent geometry    : angle       0.66253 (12628)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 148
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.8514 (m-80) cc_final: 0.8001 (m-80)
REVERT: A  180 MET cc_start: 0.8899 (tpp) cc_final: 0.8660 (mmt)
REVERT: A  195 ARG cc_start: 0.7943 (tpp80) cc_final: 0.7498 (tpp80)
REVERT: A  215 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8585 (tt)
REVERT: A  374 LYS cc_start: 0.8904 (pttp) cc_final: 0.8516 (ptpp)
REVERT: A  419 TYR cc_start: 0.8676 (t80) cc_final: 0.8398 (t80)
REVERT: A  543 ASP cc_start: 0.8538 (t0) cc_final: 0.8287 (t0)
REVERT: B   15 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7434 (ptm-80)
REVERT: B  160 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7941 (mp)
REVERT: B  228 LEU cc_start: 0.9309 (mm) cc_final: 0.9048 (mm)
REVERT: B  248 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8152 (t0)
REVERT: B  281 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6976 (mp0)
REVERT: B  353 MET cc_start: 0.7977 (pp-130) cc_final: 0.7484 (ptt)
REVERT: B  455 ILE cc_start: 0.8772 (pt) cc_final: 0.8527 (mp)
REVERT: B  472 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8445 (tp40)
REVERT: B  599 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7214 (m-30)
REVERT: B  609 HIS cc_start: 0.8682 (t70) cc_final: 0.8257 (t70)
REVERT: B  619 TYR cc_start: 0.9129 (t80) cc_final: 0.8625 (t80)
REVERT: B  630 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.6096 (mm)
  outliers start: 49
  outliers final: 36
  residues processed: 182
  average time/residue: 0.1845
  time to fit residues: 48.8197
Evaluate side-chains
  176 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 133
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  342 CYS
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  271 HIS
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  387 ARG
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  599 ASP
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  630 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0040
   chunk 30 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 92 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   overall best weight:    0.7594

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
B 158 HIS
B 334 GLN
** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.119164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.093305 restraints weight = 18594.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.096459 restraints weight = 9769.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.098512 restraints weight = 6406.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.0808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9274  Z= 0.130
  Angle     :  0.610  12.887  12628  Z= 0.304
  Chirality :  0.042   0.175   1520
  Planarity :  0.004   0.045   1617
  Dihedral  :  9.440 159.541   1395
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.70 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 22.15 %
    Favored  : 72.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.25), residues: 1189
  helix:  1.63 (0.19), residues: 775
  sheet:  0.34 (0.70), residues: 68
  loop : -0.06 (0.37), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  15 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.015   0.001   PHE B 343 
 TYR   0.015   0.001   TYR B 339 
 ARG   0.004   0.000   ARG A 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04275 (  638)
  hydrogen bonds       : angle       4.66531 ( 1884)
  covalent geometry    : bond        0.00278 ( 9274)
  covalent geometry    : angle       0.60966 (12628)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 154
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.8475 (m-80) cc_final: 0.7941 (m-80)
REVERT: A  135 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7706 (mpt)
REVERT: A  142 MET cc_start: 0.8791 (tpp) cc_final: 0.8582 (tpp)
REVERT: A  180 MET cc_start: 0.8897 (tpp) cc_final: 0.8665 (mmt)
REVERT: A  273 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8213 (p)
REVERT: A  374 LYS cc_start: 0.8762 (pttp) cc_final: 0.8326 (ptpp)
REVERT: A  419 TYR cc_start: 0.8561 (t80) cc_final: 0.8304 (t80)
REVERT: A  478 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8278 (mt0)
REVERT: A  543 ASP cc_start: 0.8442 (t0) cc_final: 0.8230 (t0)
REVERT: B   15 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7472 (ptm-80)
REVERT: B  160 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8025 (mp)
REVERT: B  228 LEU cc_start: 0.9256 (mm) cc_final: 0.9037 (mm)
REVERT: B  271 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7181 (m90)
REVERT: B  281 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7058 (mp0)
REVERT: B  455 ILE cc_start: 0.8705 (pt) cc_final: 0.8470 (mp)
REVERT: B  472 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8436 (tp40)
REVERT: B  599 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7350 (m-30)
REVERT: B  606 ARG cc_start: 0.8315 (pmm-80) cc_final: 0.8089 (ptp90)
REVERT: B  619 TYR cc_start: 0.9264 (t80) cc_final: 0.8846 (t80)
  outliers start: 56
  outliers final: 30
  residues processed: 195
  average time/residue: 0.1857
  time to fit residues: 52.0373
Evaluate side-chains
  178 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 141
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 HIS
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  387 ARG
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  599 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    7.9990
   chunk 102 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 93 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 528 GLN
B 158 HIS
B 334 GLN
** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.114379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.088360 restraints weight = 19318.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.090926 restraints weight = 11230.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.092638 restraints weight = 7894.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9274  Z= 0.132
  Angle     :  0.627  14.791  12628  Z= 0.304
  Chirality :  0.043   0.268   1520
  Planarity :  0.004   0.048   1617
  Dihedral  :  8.455 158.995   1361
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.45 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 21.21 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.25), residues: 1189
  helix:  1.71 (0.19), residues: 778
  sheet:  0.53 (0.76), residues: 58
  loop : -0.04 (0.36), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A   3 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.015   0.001   PHE B 343 
 TYR   0.016   0.001   TYR B 517 
 ARG   0.002   0.000   ARG A 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (  638)
  hydrogen bonds       : angle       4.60102 ( 1884)
  covalent geometry    : bond        0.00287 ( 9274)
  covalent geometry    : angle       0.62749 (12628)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 159
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8992 (mp)
REVERT: A    9 TYR cc_start: 0.8305 (m-80) cc_final: 0.7820 (m-80)
REVERT: A  135 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7763 (mpt)
REVERT: A  142 MET cc_start: 0.8821 (tpp) cc_final: 0.8604 (tpp)
REVERT: A  273 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.7942 (p)
REVERT: A  294 MET cc_start: 0.8119 (mmt) cc_final: 0.7698 (mtt)
REVERT: B   15 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7446 (ptm-80)
REVERT: B  172 GLU cc_start: 0.6814 (tp30) cc_final: 0.6341 (tp30)
REVERT: B  248 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8221 (t0)
REVERT: B  281 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6960 (mp0)
REVERT: B  353 MET cc_start: 0.8111 (ppp) cc_final: 0.7376 (ptm)
REVERT: B  472 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8541 (tp40)
REVERT: B  599 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7144 (m-30)
  outliers start: 66
  outliers final: 41
  residues processed: 210
  average time/residue: 0.1864
  time to fit residues: 57.1730
Evaluate side-chains
  187 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 139
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  387 ARG
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  599 ASP
Chi-restraints excluded: chain B residue  603 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 117 optimal weight:    0.5980
   chunk 79 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 93 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0980
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 334 GLN
B 344 ASN
B 484 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.115010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.089053 restraints weight = 19187.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.091711 restraints weight = 11175.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.093323 restraints weight = 7835.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9274  Z= 0.124
  Angle     :  0.645  15.329  12628  Z= 0.308
  Chirality :  0.043   0.240   1520
  Planarity :  0.004   0.045   1617
  Dihedral  :  8.093 158.857   1355
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.53 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 23.09 %
    Favored  : 70.85 %
  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:  1.63 (0.25), residues: 1189
  helix:  1.71 (0.19), residues: 776
  sheet:  0.38 (0.72), residues: 58
  loop : -0.10 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A   3 
 HIS   0.004   0.001   HIS B 271 
 PHE   0.014   0.001   PHE B 343 
 TYR   0.025   0.001   TYR A 419 
 ARG   0.006   0.000   ARG B  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03937 (  638)
  hydrogen bonds       : angle       4.56380 ( 1884)
  covalent geometry    : bond        0.00264 ( 9274)
  covalent geometry    : angle       0.64461 (12628)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 155
  time to evaluate  : 1.031 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8972 (mp)
REVERT: A    9 TYR cc_start: 0.8293 (m-80) cc_final: 0.7798 (m-80)
REVERT: A  135 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7692 (mpt)
REVERT: A  273 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.7840 (p)
REVERT: A  294 MET cc_start: 0.8097 (mmt) cc_final: 0.7702 (mtt)
REVERT: A  374 LYS cc_start: 0.8561 (pttp) cc_final: 0.8146 (ptpp)
REVERT: A  419 TYR cc_start: 0.8183 (t80) cc_final: 0.7937 (t80)
REVERT: B   15 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7461 (ptm-80)
REVERT: B  172 GLU cc_start: 0.6870 (tp30) cc_final: 0.6392 (tp30)
REVERT: B  248 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8212 (t0)
REVERT: B  281 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6893 (mp0)
REVERT: B  599 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7101 (m-30)
REVERT: B  619 TYR cc_start: 0.9107 (t80) cc_final: 0.8847 (t80)
  outliers start: 58
  outliers final: 38
  residues processed: 200
  average time/residue: 0.1718
  time to fit residues: 50.2291
Evaluate side-chains
  185 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 140
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   44 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  387 ARG
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  599 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 78 optimal weight:    0.0870
   chunk 36 optimal weight:    0.0030
   chunk 19 optimal weight:    3.9990
   chunk 46 optimal weight:    0.2980
   chunk 104 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:   20.0000
   chunk 62 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0370
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.2246

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

Flipped N/Q/H residues before XYZ refinement:
A 528 GLN
B 334 GLN
** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.116244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.089922 restraints weight = 19162.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.092828 restraints weight = 10776.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.094781 restraints weight = 7356.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9274  Z= 0.119
  Angle     :  0.646  15.772  12628  Z= 0.306
  Chirality :  0.043   0.240   1520
  Planarity :  0.004   0.045   1617
  Dihedral  :  7.813 158.543   1350
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.45 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 24.14 %
    Favored  : 69.91 %
  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:  1.66 (0.25), residues: 1189
  helix:  1.76 (0.19), residues: 776
  sheet:  0.37 (0.72), residues: 58
  loop : -0.17 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 475 
 HIS   0.004   0.000   HIS A  88 
 PHE   0.014   0.001   PHE B 343 
 TYR   0.016   0.001   TYR A 419 
 ARG   0.006   0.000   ARG B  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03798 (  638)
  hydrogen bonds       : angle       4.49672 ( 1884)
  covalent geometry    : bond        0.00243 ( 9274)
  covalent geometry    : angle       0.64638 (12628)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 159
  time to evaluate  : 1.100 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8850 (mp)
REVERT: A    9 TYR cc_start: 0.8351 (m-80) cc_final: 0.7891 (m-80)
REVERT: A   28 ASN cc_start: 0.8237 (m-40) cc_final: 0.7977 (m-40)
REVERT: A  135 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7630 (mpt)
REVERT: A  195 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7616 (tmm160)
REVERT: A  294 MET cc_start: 0.8106 (mmt) cc_final: 0.7807 (mtt)
REVERT: A  419 TYR cc_start: 0.8143 (t80) cc_final: 0.7882 (t80)
REVERT: B   15 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7496 (ptm-80)
REVERT: B  248 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8159 (t0)
REVERT: B  281 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6892 (mp0)
REVERT: B  599 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7139 (m-30)
  outliers start: 57
  outliers final: 38
  residues processed: 199
  average time/residue: 0.1729
  time to fit residues: 51.3035
Evaluate side-chains
  190 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 146
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   44 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  387 ARG
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  598 MET
Chi-restraints excluded: chain B residue  599 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 29 optimal weight:    0.0980
   chunk 28 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0980
   chunk 62 optimal weight:    8.9990
   chunk 110 optimal weight:    0.0980
   chunk 2 optimal weight:    2.9990
   chunk 96 optimal weight:    9.9990
   chunk 98 optimal weight:    9.9990
   chunk 97 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
B 334 GLN
** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.116989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.091417 restraints weight = 18906.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.094058 restraints weight = 11000.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.095817 restraints weight = 7751.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9274  Z= 0.118
  Angle     :  0.657  15.098  12628  Z= 0.307
  Chirality :  0.043   0.240   1520
  Planarity :  0.004   0.045   1617
  Dihedral  :  7.620 158.718   1348
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.20 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 26.12 %
    Favored  : 68.65 %
  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:  1.65 (0.25), residues: 1189
  helix:  1.78 (0.19), residues: 776
  sheet:  0.36 (0.73), residues: 58
  loop : -0.23 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 475 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.028   0.001   PHE B 509 
 TYR   0.015   0.001   TYR B 517 
 ARG   0.005   0.000   ARG B  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  638)
  hydrogen bonds       : angle       4.44398 ( 1884)
  covalent geometry    : bond        0.00247 ( 9274)
  covalent geometry    : angle       0.65747 (12628)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 163
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8812 (mp)
REVERT: A    9 TYR cc_start: 0.8211 (m-80) cc_final: 0.7782 (m-80)
REVERT: A  135 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7556 (mpt)
REVERT: A  195 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7590 (tmm160)
REVERT: A  294 MET cc_start: 0.8031 (mmt) cc_final: 0.7779 (mtt)
REVERT: A  419 TYR cc_start: 0.8135 (t80) cc_final: 0.7912 (t80)
REVERT: B   15 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7308 (ptm160)
REVERT: B  172 GLU cc_start: 0.6796 (tp30) cc_final: 0.6382 (tp30)
REVERT: B  248 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8144 (t0)
REVERT: B  281 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6884 (mp0)
REVERT: B  353 MET cc_start: 0.7938 (ppp) cc_final: 0.7369 (ptm)
REVERT: B  472 GLN cc_start: 0.8361 (tp40) cc_final: 0.8044 (tp40)
REVERT: B  542 VAL cc_start: 0.9183 (t) cc_final: 0.8806 (t)
REVERT: B  599 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7014 (m-30)
  outliers start: 50
  outliers final: 38
  residues processed: 200
  average time/residue: 0.2047
  time to fit residues: 60.6135
Evaluate side-chains
  191 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 147
  time to evaluate  : 1.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   44 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  387 ARG
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  599 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 36 optimal weight:    0.4980
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
B 334 GLN
B 344 ASN
** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.113638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.087520 restraints weight = 19368.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.090166 restraints weight = 11380.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.091868 restraints weight = 7982.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9274  Z= 0.164
  Angle     :  0.671  13.674  12628  Z= 0.322
  Chirality :  0.044   0.357   1520
  Planarity :  0.004   0.043   1617
  Dihedral  :  7.623 158.230   1348
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.45 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 25.18 %
    Favored  : 68.76 %
  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 (0.25), residues: 1189
  helix:  1.68 (0.19), residues: 784
  sheet:  0.34 (0.72), residues: 59
  loop : -0.25 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 408 
 HIS   0.003   0.001   HIS A 337 
 PHE   0.023   0.002   PHE B 509 
 TYR   0.014   0.002   TYR A 563 
 ARG   0.004   0.000   ARG B  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03938 (  638)
  hydrogen bonds       : angle       4.44692 ( 1884)
  covalent geometry    : bond        0.00379 ( 9274)
  covalent geometry    : angle       0.67132 (12628)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 143
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.8273 (m-80) cc_final: 0.7829 (m-80)
REVERT: A  135 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7553 (mpt)
REVERT: A  195 ARG cc_start: 0.7876 (ttp-170) cc_final: 0.7614 (tmm160)
REVERT: A  294 MET cc_start: 0.8145 (mmt) cc_final: 0.7890 (mtt)
REVERT: B   15 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7474 (ptm-80)
REVERT: B  172 GLU cc_start: 0.6895 (tp30) cc_final: 0.6400 (tp30)
REVERT: B  248 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8235 (t0)
REVERT: B  281 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6965 (mp0)
REVERT: B  353 MET cc_start: 0.8213 (ppp) cc_final: 0.7579 (ptm)
REVERT: B  472 GLN cc_start: 0.8401 (tp40) cc_final: 0.7992 (tp40)
REVERT: B  599 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7076 (m-30)
REVERT: B  630 ILE cc_start: 0.5576 (OUTLIER) cc_final: 0.5196 (mm)
  outliers start: 58
  outliers final: 40
  residues processed: 186
  average time/residue: 0.1602
  time to fit residues: 44.5314
Evaluate side-chains
  182 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 136
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   44 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  344 ASN
Chi-restraints excluded: chain B residue  387 ARG
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  599 ASP
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  630 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 112 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0170
   chunk 38 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.6620

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 334 GLN
B 344 ASN
** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.115972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.089570 restraints weight = 19300.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.092477 restraints weight = 10856.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.094429 restraints weight = 7419.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9274  Z= 0.124
  Angle     :  0.666  14.005  12628  Z= 0.314
  Chirality :  0.043   0.334   1520
  Planarity :  0.004   0.043   1617
  Dihedral  :  7.669 157.891   1348
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.36 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 26.33 %
    Favored  : 68.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.58 (0.25), residues: 1189
  helix:  1.72 (0.19), residues: 784
  sheet:  0.25 (0.73), residues: 58
  loop : -0.26 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 475 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.023   0.001   PHE B 509 
 TYR   0.030   0.001   TYR A 419 
 ARG   0.004   0.000   ARG B  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03851 (  638)
  hydrogen bonds       : angle       4.42595 ( 1884)
  covalent geometry    : bond        0.00269 ( 9274)
  covalent geometry    : angle       0.66626 (12628)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 156
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8797 (mp)
REVERT: A    9 TYR cc_start: 0.8410 (m-80) cc_final: 0.7988 (m-80)
REVERT: A   56 GLU cc_start: 0.8155 (tt0) cc_final: 0.7878 (tm-30)
REVERT: A  135 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7528 (mpt)
REVERT: A  195 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7642 (tmm160)
REVERT: A  294 MET cc_start: 0.8206 (mmt) cc_final: 0.7970 (mtt)
REVERT: A  298 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7427 (m-80)
REVERT: B   15 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7443 (ptm160)
REVERT: B  172 GLU cc_start: 0.6953 (tp30) cc_final: 0.6443 (tp30)
REVERT: B  248 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8228 (t0)
REVERT: B  281 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6965 (mp0)
REVERT: B  344 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8735 (t0)
REVERT: B  353 MET cc_start: 0.8257 (ppp) cc_final: 0.7614 (ptt)
REVERT: B  472 GLN cc_start: 0.8398 (tp40) cc_final: 0.7940 (tp40)
REVERT: B  599 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7186 (m-30)
REVERT: B  630 ILE cc_start: 0.5585 (OUTLIER) cc_final: 0.5191 (mm)
  outliers start: 53
  outliers final: 40
  residues processed: 198
  average time/residue: 0.2130
  time to fit residues: 62.3752
Evaluate side-chains
  192 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 143
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   44 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  298 PHE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  344 ASN
Chi-restraints excluded: chain B residue  387 ARG
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  528 ILE
Chi-restraints excluded: chain B residue  542 VAL
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  599 ASP
Chi-restraints excluded: chain B residue  630 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0670
   chunk 4 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
A 124 HIS
** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 334 GLN
B 344 ASN
** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.116028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.090156 restraints weight = 19045.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.092855 restraints weight = 11189.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.094663 restraints weight = 7842.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9274  Z= 0.131
  Angle     :  0.684  13.621  12628  Z= 0.321
  Chirality :  0.043   0.328   1520
  Planarity :  0.004   0.047   1617
  Dihedral  :  7.663 157.475   1348
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.36 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 25.91 %
    Favored  : 68.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.25), residues: 1189
  helix:  1.67 (0.18), residues: 787
  sheet:  0.30 (0.74), residues: 58
  loop : -0.30 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 475 
 HIS   0.004   0.001   HIS A 505 
 PHE   0.020   0.001   PHE B 509 
 TYR   0.026   0.001   TYR A 419 
 ARG   0.004   0.000   ARG B  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03870 (  638)
  hydrogen bonds       : angle       4.43737 ( 1884)
  covalent geometry    : bond        0.00291 ( 9274)
  covalent geometry    : angle       0.68374 (12628)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 154
  time to evaluate  : 2.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8819 (mp)
REVERT: A    9 TYR cc_start: 0.8288 (m-80) cc_final: 0.7859 (m-80)
REVERT: A  135 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7553 (mpt)
REVERT: A  298 PHE cc_start: 0.7581 (m-80) cc_final: 0.7301 (m-80)
REVERT: B   15 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7368 (ptm160)
REVERT: B  172 GLU cc_start: 0.6759 (tp30) cc_final: 0.6323 (tp30)
REVERT: B  248 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8181 (t0)
REVERT: B  281 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6962 (mp0)
REVERT: B  472 GLN cc_start: 0.8441 (tp40) cc_final: 0.7958 (tp40)
REVERT: B  599 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7098 (m-30)
REVERT: B  630 ILE cc_start: 0.5518 (OUTLIER) cc_final: 0.5133 (mm)
  outliers start: 52
  outliers final: 41
  residues processed: 195
  average time/residue: 0.2044
  time to fit residues: 59.5334
Evaluate side-chains
  194 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 146
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   44 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  344 ASN
Chi-restraints excluded: chain B residue  387 ARG
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  528 ILE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  599 ASP
Chi-restraints excluded: chain B residue  630 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 94 optimal weight:    0.4980
   chunk 65 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 100 optimal weight:    5.9990
   chunk 117 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 334 GLN
B 344 ASN
** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.116361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.090421 restraints weight = 19354.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.093143 restraints weight = 11208.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.094972 restraints weight = 7798.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9274  Z= 0.134
  Angle     :  0.695  14.856  12628  Z= 0.324
  Chirality :  0.043   0.321   1520
  Planarity :  0.004   0.048   1617
  Dihedral  :  7.683 158.049   1348
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.36 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 26.96 %
    Favored  : 68.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.25), residues: 1189
  helix:  1.66 (0.18), residues: 785
  sheet:  0.24 (0.73), residues: 58
  loop : -0.30 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 233 
 HIS   0.004   0.001   HIS A 124 
 PHE   0.019   0.001   PHE B 509 
 TYR   0.023   0.001   TYR A 419 
 ARG   0.003   0.000   ARG B  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03849 (  638)
  hydrogen bonds       : angle       4.42528 ( 1884)
  covalent geometry    : bond        0.00301 ( 9274)
  covalent geometry    : angle       0.69529 (12628)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 148
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.8291 (m-80) cc_final: 0.7857 (m-80)
REVERT: A  135 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7556 (mpt)
REVERT: A  298 PHE cc_start: 0.7588 (m-80) cc_final: 0.7307 (m-80)
REVERT: B   15 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7384 (ptm160)
REVERT: B  172 GLU cc_start: 0.6779 (tp30) cc_final: 0.6351 (tp30)
REVERT: B  248 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8172 (t0)
REVERT: B  281 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6956 (mp0)
REVERT: B  339 TYR cc_start: 0.8412 (m-80) cc_final: 0.8158 (m-80)
REVERT: B  472 GLN cc_start: 0.8468 (tp40) cc_final: 0.7989 (tp40)
REVERT: B  599 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7034 (m-30)
REVERT: B  630 ILE cc_start: 0.5515 (OUTLIER) cc_final: 0.5130 (mm)
  outliers start: 47
  outliers final: 38
  residues processed: 187
  average time/residue: 0.1680
  time to fit residues: 46.7127
Evaluate side-chains
  190 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 146
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   44 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   15 ARG
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  344 ASN
Chi-restraints excluded: chain B residue  387 ARG
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  528 ILE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  599 ASP
Chi-restraints excluded: chain B residue  630 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 115 optimal weight:   20.0000
   chunk 81 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 87 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 79 optimal weight:    0.3980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 124 HIS
** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 334 GLN
B 344 ASN
** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.116531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.090725 restraints weight = 19178.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.093459 restraints weight = 11009.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.095312 restraints weight = 7682.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9274  Z= 0.132
  Angle     :  0.695  15.232  12628  Z= 0.324
  Chirality :  0.043   0.314   1520
  Planarity :  0.004   0.048   1617
  Dihedral  :  7.663 159.126   1347
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.45 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 26.65 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.25), residues: 1189
  helix:  1.65 (0.18), residues: 789
  sheet:  0.09 (0.72), residues: 58
  loop : -0.31 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 233 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.018   0.001   PHE B 509 
 TYR   0.024   0.001   TYR A 419 
 ARG   0.003   0.000   ARG B  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03857 (  638)
  hydrogen bonds       : angle       4.43204 ( 1884)
  covalent geometry    : bond        0.00296 ( 9274)
  covalent geometry    : angle       0.69452 (12628)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3005.34 seconds
wall clock time: 54 minutes 12.80 seconds (3252.80 seconds total)