Starting phenix.real_space_refine
on Thu Feb 13 16:21:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hbu_0190/02_2025/6hbu_0190.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hbu_0190/02_2025/6hbu_0190.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hbu_0190/02_2025/6hbu_0190.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hbu_0190/02_2025/6hbu_0190.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hbu_0190/02_2025/6hbu_0190.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hbu_0190/02_2025/6hbu_0190.cif"
  }
  resolution = 3.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      58      5.16       5
     C    5910      2.51       5
     N    1512      2.21       5
     O    1658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9146
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4541
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 20, 'TRANS': 563}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.19, per 1000 atoms: 0.90
  Number of scatterers: 9146
  At special positions: 0
  Unit cell: (81.81, 89.91, 132.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      58     16.00
     P       6     15.00
     Mg      2     11.99
     O    1658      8.00
     N    1512      7.00
     C    5910      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 592 " - pdb=" SG  CYS A 608 " distance=2.03

  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: 2.21
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2164

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      57.5% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 85 through 94
    Processing helix  chain 'A' and resid 135 through 148
      removed outlier: 3.542A  pdb=" N   LEU A 146 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 169
    Processing helix  chain 'A' and resid 187 through 199
      removed outlier: 3.761A  pdb=" N   GLU A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.694A  pdb=" N   ASN A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 251
    Processing helix  chain 'A' and resid 273 through 278
    Processing helix  chain 'A' and resid 289 through 298
      removed outlier: 3.718A  pdb=" N   LEU A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP A 296 " --> pdb=" O   ASP A 292 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE A 297 " --> pdb=" O   PHE A 293 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE A 298 " --> pdb=" O   PHE A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 308
    Processing helix  chain 'A' and resid 327 through 338
    Processing helix  chain 'A' and resid 339 through 353
      removed outlier: 3.819A  pdb=" N   LYS A 343 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   GLN A 351 " --> pdb=" O   ALA A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
      removed outlier: 3.506A  pdb=" N   ARG A 378 " --> pdb=" O   CYS A 374 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LYS A 382 " --> pdb=" O   ARG A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 413
    Processing helix  chain 'A' and resid 422 through 440
      removed outlier: 4.106A  pdb=" N   PHE A 431 " --> pdb=" O   ALA A 427 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE A 432 " --> pdb=" O   GLY A 428 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN A 437 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 448
      removed outlier: 3.782A  pdb=" N   GLU A 446 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 447 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   PHE A 448 " --> pdb=" O   VAL A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 461
    Processing helix  chain 'A' and resid 465 through 479
      removed outlier: 3.651A  pdb=" N   LEU A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   SER A 476 " --> pdb=" O   GLY A 472 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASP A 477 " --> pdb=" O   LYS A 473 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU A 479 " --> pdb=" O   LEU A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 493
      removed outlier: 3.767A  pdb=" N   PHE A 489 " --> pdb=" O   PRO A 485 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   THR A 490 " --> pdb=" O   SER A 486 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL A 493 " --> pdb=" O   PHE A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 529
      removed outlier: 3.791A  pdb=" N   PHE A 507 " --> pdb=" O   ALA A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 551
      removed outlier: 3.690A  pdb=" N   LEU A 539 " --> pdb=" O   SER A 535 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE A 550 " --> pdb=" O   VAL A 546 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   PHE A 551 " --> pdb=" O   PHE A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 571
    Processing helix  chain 'A' and resid 572 through 586
      removed outlier: 3.503A  pdb=" N   TYR A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 618
      removed outlier: 3.722A  pdb=" N   TYR A 613 " --> pdb=" O   THR A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 650
      removed outlier: 3.678A  pdb=" N   TRP A 627 " --> pdb=" O   PRO A 623 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   ASN A 629 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   HIS A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE A 640 " --> pdb=" O   MET A 636 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU A 648 " --> pdb=" O   ALA A 644 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 94
    Processing helix  chain 'B' and resid 135 through 148
      removed outlier: 3.542A  pdb=" N   LEU B 146 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 169
    Processing helix  chain 'B' and resid 187 through 199
      removed outlier: 3.762A  pdb=" N   GLU B 199 " --> pdb=" O   SER B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 233
      removed outlier: 3.695A  pdb=" N   ASN B 222 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 251
    Processing helix  chain 'B' and resid 273 through 278
    Processing helix  chain 'B' and resid 289 through 298
      removed outlier: 3.717A  pdb=" N   LEU B 295 " --> pdb=" O   ALA B 291 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP B 296 " --> pdb=" O   ASP B 292 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE B 297 " --> pdb=" O   PHE B 293 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE B 298 " --> pdb=" O   PHE B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 308
    Processing helix  chain 'B' and resid 327 through 338
    Processing helix  chain 'B' and resid 339 through 353
      removed outlier: 3.819A  pdb=" N   LYS B 343 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU B 348 " --> pdb=" O   GLU B 344 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   GLN B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 391
      removed outlier: 3.506A  pdb=" N   ARG B 378 " --> pdb=" O   CYS B 374 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LYS B 382 " --> pdb=" O   ARG B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 413
    Processing helix  chain 'B' and resid 422 through 440
      removed outlier: 4.105A  pdb=" N   PHE B 431 " --> pdb=" O   ALA B 427 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE B 432 " --> pdb=" O   GLY B 428 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN B 437 " --> pdb=" O   LEU B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 448
      removed outlier: 3.782A  pdb=" N   GLU B 446 " --> pdb=" O   SER B 443 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 447 " --> pdb=" O   ALA B 444 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   PHE B 448 " --> pdb=" O   VAL B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 461
    Processing helix  chain 'B' and resid 465 through 479
      removed outlier: 3.652A  pdb=" N   LEU B 475 " --> pdb=" O   LEU B 471 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   SER B 476 " --> pdb=" O   GLY B 472 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASP B 477 " --> pdb=" O   LYS B 473 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU B 479 " --> pdb=" O   LEU B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 493
      removed outlier: 3.768A  pdb=" N   PHE B 489 " --> pdb=" O   PRO B 485 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   THR B 490 " --> pdb=" O   SER B 486 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL B 493 " --> pdb=" O   PHE B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 529
      removed outlier: 3.791A  pdb=" N   PHE B 507 " --> pdb=" O   ALA B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 551
      removed outlier: 3.690A  pdb=" N   LEU B 539 " --> pdb=" O   SER B 535 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE B 550 " --> pdb=" O   VAL B 546 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   PHE B 551 " --> pdb=" O   PHE B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 571
    Processing helix  chain 'B' and resid 572 through 586
      removed outlier: 3.503A  pdb=" N   TYR B 576 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 618
      removed outlier: 3.723A  pdb=" N   TYR B 613 " --> pdb=" O   THR B 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 650
      removed outlier: 3.677A  pdb=" N   TRP B 627 " --> pdb=" O   PRO B 623 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   ASN B 629 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   HIS B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE B 640 " --> pdb=" O   MET B 636 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 648 " --> pdb=" O   ALA B 644 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 71
      removed outlier: 5.560A  pdb=" N   ILE A  67 " --> pdb=" O   ASN A  41 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ASN A  41 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47
    Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 124
      removed outlier: 6.013A  pdb=" N   GLY A 122 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   ASP A 210 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   VAL A 124 " --> pdb=" O   ASP A 210 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   LEU A 256 " --> pdb=" O   HIS A 267 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   HIS A 267 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU A 258 " --> pdb=" O   MET A 265 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 71
      removed outlier: 5.560A  pdb=" N   ILE B  67 " --> pdb=" O   ASN B  41 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ASN B  41 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 47
    Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 124
      removed outlier: 6.014A  pdb=" N   GLY B 122 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   ASP B 210 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   VAL B 124 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LEU B 256 " --> pdb=" O   HIS B 267 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   HIS B 267 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU B 258 " --> pdb=" O   MET B 265 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1332 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.67

  Time building geometry restraints manager: 2.57 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2434
        1.33 -     1.45: 1814
        1.45 -     1.57: 4984
        1.57 -     1.70: 10
        1.70 -     1.82: 94
  Bond restraints: 9336
  Sorted by residual:
  bond pdb=" C4  ATP B1501 "
       pdb=" C5  ATP B1501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.462 -0.074 1.00e-02 1.00e+04 5.52e+01
  bond pdb=" C4  ATP A1501 "
       pdb=" C5  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.462 -0.074 1.00e-02 1.00e+04 5.48e+01
  bond pdb=" C5  ATP B1501 "
       pdb=" C6  ATP B1501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.473 -0.064 1.00e-02 1.00e+04 4.06e+01
  bond pdb=" C5  ATP A1501 "
       pdb=" C6  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.473 -0.064 1.00e-02 1.00e+04 4.05e+01
  bond pdb=" C4  ATP B1501 "
       pdb=" N9  ATP B1501 "
    ideal  model  delta    sigma   weight residual
    1.374  1.324  0.050 1.00e-02 1.00e+04 2.50e+01
  ... (remaining 9331 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.63: 12413
        3.63 -     7.25: 191
        7.25 -    10.88: 38
       10.88 -    14.51: 4
       14.51 -    18.13: 2
  Bond angle restraints: 12648
  Sorted by residual:
  angle pdb=" PB  ATP B1501 "
        pdb=" O3B ATP B1501 "
        pdb=" PG  ATP B1501 "
      ideal   model   delta    sigma   weight residual
     139.87  121.74   18.13 1.00e+00 1.00e+00 3.29e+02
  angle pdb=" PB  ATP A1501 "
        pdb=" O3B ATP A1501 "
        pdb=" PG  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     139.87  121.74   18.13 1.00e+00 1.00e+00 3.29e+02
  angle pdb=" PA  ATP B1501 "
        pdb=" O3A ATP B1501 "
        pdb=" PB  ATP B1501 "
      ideal   model   delta    sigma   weight residual
     136.83  123.39   13.44 1.00e+00 1.00e+00 1.81e+02
  angle pdb=" PA  ATP A1501 "
        pdb=" O3A ATP A1501 "
        pdb=" PB  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     136.83  123.43   13.40 1.00e+00 1.00e+00 1.80e+02
  angle pdb=" C5  ATP B1501 "
        pdb=" C4  ATP B1501 "
        pdb=" N3  ATP B1501 "
      ideal   model   delta    sigma   weight residual
     126.80  119.17    7.63 1.00e+00 1.00e+00 5.82e+01
  ... (remaining 12643 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.33: 5199
       15.33 -    30.67: 269
       30.67 -    46.00: 77
       46.00 -    61.33: 18
       61.33 -    76.67: 10
  Dihedral angle restraints: 5573
    sinusoidal: 2205
      harmonic: 3368
  Sorted by residual:
  dihedral pdb=" CA  ASN B 604 "
           pdb=" C   ASN B 604 "
           pdb=" N   TYR B 605 "
           pdb=" CA  TYR B 605 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  108.75   71.25     0      5.00e+00 4.00e-02 2.03e+02
  dihedral pdb=" CA  ASN A 604 "
           pdb=" C   ASN A 604 "
           pdb=" N   TYR A 605 "
           pdb=" CA  TYR A 605 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  108.79   71.21     0      5.00e+00 4.00e-02 2.03e+02
  dihedral pdb=" CA  ALA B 115 "
           pdb=" C   ALA B 115 "
           pdb=" N   ASN B 116 "
           pdb=" CA  ASN B 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  123.00   57.00     0      5.00e+00 4.00e-02 1.30e+02
  ... (remaining 5570 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1213
       0.075 -    0.150: 230
       0.150 -    0.226: 14
       0.226 -    0.301: 7
       0.301 -    0.376: 2
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" CA  GLN B 589 "
            pdb=" N   GLN B 589 "
            pdb=" C   GLN B 589 "
            pdb=" CB  GLN B 589 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.89   -0.38 2.00e-01 2.50e+01 3.53e+00
  chirality pdb=" CA  GLN A 589 "
            pdb=" N   GLN A 589 "
            pdb=" C   GLN A 589 "
            pdb=" CB  GLN A 589 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.48e+00
  chirality pdb=" CG  LEU A 225 "
            pdb=" CB  LEU A 225 "
            pdb=" CD1 LEU A 225 "
            pdb=" CD2 LEU A 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 2.00e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 601 "    0.068 5.00e-02 4.00e+02   1.02e-01 1.67e+01
        pdb=" N   PRO A 602 "   -0.177 5.00e-02 4.00e+02
        pdb=" CA  PRO A 602 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 602 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 601 "   -0.068 5.00e-02 4.00e+02   1.02e-01 1.67e+01
        pdb=" N   PRO B 602 "    0.177 5.00e-02 4.00e+02
        pdb=" CA  PRO B 602 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO B 602 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 588 "   -0.013 2.00e-02 2.50e+03   2.77e-02 7.68e+00
        pdb=" C   GLY A 588 "    0.048 2.00e-02 2.50e+03
        pdb=" O   GLY A 588 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLN A 589 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 52
        2.55 -     3.14: 6600
        3.14 -     3.73: 13922
        3.73 -     4.31: 21187
        4.31 -     4.90: 34775
  Nonbonded interactions: 76536
  Sorted by model distance:
  nonbonded pdb=" CE  LYS B 500 "
            pdb=" OE1 GLN B 589 "
     model   vdw
     1.965 3.440
  nonbonded pdb=" CE  LYS A 500 "
            pdb=" OE1 GLN A 589 "
     model   vdw
     1.977 3.440
  nonbonded pdb=" SG  CYS A 603 "
            pdb=" SG  CYS B 603 "
     model   vdw
     2.012 3.760
  nonbonded pdb=" SG  CYS B 592 "
            pdb=" SG  CYS B 608 "
     model   vdw
     2.034 3.760
  nonbonded pdb=" NH2 ARG B 184 "
            pdb=" O1A ATP A1501 "
     model   vdw
     2.315 3.120
  ... (remaining 76531 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.400
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
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      :  0.009   0.074   9336  Z= 0.561
  Angle     :  1.177  18.132  12648  Z= 0.683
  Chirality :  0.060   0.376   1466
  Planarity :  0.008   0.102   1566
  Dihedral  : 11.560  76.667   3406
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  4.86 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.71 %

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: -5.40 (0.17), residues: 1152
  helix: -4.20 (0.10), residues: 648
  sheet: -1.86 (0.42), residues: 76
  loop : -2.49 (0.26), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP B 624 
 HIS   0.013   0.003   HIS A 583 
 PHE   0.032   0.003   PHE A 578 
 TYR   0.039   0.003   TYR A 463 
 ARG   0.010   0.001   ARG B  96 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A  251 LYS cc_start: 0.8156 (ttpm) cc_final: 0.7946 (mtpt)
REVERT: A  451 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7597 (tt0)
REVERT: B  451 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7475 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.2464
  time to fit residues: 60.8855
Evaluate side-chains
  112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 87 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
A 211 GLN
A 387 ASN
A 437 GLN
A 557 ASN
A 583 HIS
B 154 ASN
B 211 GLN
B 387 ASN
B 437 GLN
B 531 GLN
B 557 ASN
B 583 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.137240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.120041 restraints weight = 9866.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 0.87
r_work: 0.2973 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9336  Z= 0.218
  Angle     :  0.707   8.167  12648  Z= 0.368
  Chirality :  0.044   0.176   1466
  Planarity :  0.006   0.093   1566
  Dihedral  :  9.806  84.653   1314
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.17 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  6.43 %
    Favored  : 91.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.80 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.22), residues: 1152
  helix: -1.45 (0.18), residues: 640
  sheet: -1.37 (0.48), residues: 76
  loop : -2.08 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 627 
 HIS   0.005   0.001   HIS B 243 
 PHE   0.013   0.001   PHE A 578 
 TYR   0.015   0.002   TYR A 605 
 ARG   0.004   0.001   ARG A 113 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.096 
Fit side-chains
REVERT: A   71 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7591 (mtt)
REVERT: A  105 ASP cc_start: 0.8198 (p0) cc_final: 0.7948 (p0)
REVERT: A  206 ILE cc_start: 0.9044 (mt) cc_final: 0.8667 (mt)
REVERT: A  251 LYS cc_start: 0.8410 (ttpm) cc_final: 0.8209 (mtpt)
REVERT: A  451 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7592 (tt0)
REVERT: A  590 ASN cc_start: 0.7979 (t0) cc_final: 0.7770 (t0)
REVERT: B  237 THR cc_start: 0.8910 (t) cc_final: 0.8706 (m)
REVERT: B  451 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7453 (tt0)
REVERT: B  590 ASN cc_start: 0.7868 (t0) cc_final: 0.7660 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 138
  average time/residue: 0.1938
  time to fit residues: 38.9886
Evaluate side-chains
  120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  478 LEU
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 111 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 99 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 531 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.134192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.115297 restraints weight = 9921.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.07
r_work: 0.2955 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9336  Z= 0.328
  Angle     :  0.718   8.281  12648  Z= 0.363
  Chirality :  0.046   0.161   1466
  Planarity :  0.005   0.093   1566
  Dihedral  :  9.419  78.053   1314
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.21 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  :  7.63 %
    Favored  : 89.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.71 %

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: -1.16 (0.24), residues: 1152
  helix: -0.05 (0.20), residues: 642
  sheet: -1.14 (0.47), residues: 78
  loop : -1.70 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 627 
 HIS   0.004   0.001   HIS B 243 
 PHE   0.016   0.002   PHE B 489 
 TYR   0.012   0.002   TYR B 605 
 ARG   0.003   0.000   ARG B 113 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 1.988 
Fit side-chains
REVERT: A   71 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8077 (mtp)
REVERT: A  105 ASP cc_start: 0.8306 (p0) cc_final: 0.8089 (p0)
REVERT: A  251 LYS cc_start: 0.8488 (ttpm) cc_final: 0.8243 (mtpt)
REVERT: A  299 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.8832 (t0)
REVERT: A  451 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7578 (tt0)
REVERT: A  590 ASN cc_start: 0.8111 (t0) cc_final: 0.7827 (t0)
REVERT: B  172 LYS cc_start: 0.8383 (ptmt) cc_final: 0.8083 (pttt)
REVERT: B  237 THR cc_start: 0.9025 (t) cc_final: 0.8715 (m)
REVERT: B  378 ARG cc_start: 0.8082 (mtm180) cc_final: 0.7756 (ptm160)
REVERT: B  451 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7425 (tt0)
REVERT: B  590 ASN cc_start: 0.8004 (t0) cc_final: 0.7658 (t0)
  outliers start: 28
  outliers final: 18
  residues processed: 129
  average time/residue: 0.2054
  time to fit residues: 38.4322
Evaluate side-chains
  125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  616 LYS
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  374 CYS
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  609 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0050
   chunk 72 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0010
   chunk 7 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.7202

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.137219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.118514 restraints weight = 9722.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 0.91
r_work: 0.2925 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9336  Z= 0.177
  Angle     :  0.626   8.020  12648  Z= 0.320
  Chirality :  0.042   0.144   1466
  Planarity :  0.005   0.086   1566
  Dihedral  :  9.007  74.707   1314
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.03 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  :  9.04 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.71 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.25), residues: 1152
  helix:  0.89 (0.21), residues: 628
  sheet: -1.01 (0.48), residues: 78
  loop : -1.48 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.012   0.001   PHE B 489 
 TYR   0.013   0.001   TYR A 605 
 ARG   0.003   0.000   ARG A 113 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 1.079 
Fit side-chains
REVERT: A   71 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8515 (mmt)
REVERT: A  150 THR cc_start: 0.8683 (p) cc_final: 0.8423 (p)
REVERT: A  251 LYS cc_start: 0.8517 (ttpm) cc_final: 0.8308 (mtpt)
REVERT: A  451 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7603 (tt0)
REVERT: A  590 ASN cc_start: 0.7845 (t0) cc_final: 0.7523 (t0)
REVERT: B  378 ARG cc_start: 0.8020 (mtm180) cc_final: 0.7790 (ptm160)
REVERT: B  451 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7473 (tt0)
REVERT: B  590 ASN cc_start: 0.7739 (t0) cc_final: 0.7394 (t0)
  outliers start: 28
  outliers final: 21
  residues processed: 129
  average time/residue: 0.1994
  time to fit residues: 37.1132
Evaluate side-chains
  118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  374 CYS
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0870
   chunk 98 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0010
   chunk 32 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.0168

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
B 436 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.136249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.118477 restraints weight = 9873.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 0.86
r_work: 0.2927 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9336  Z= 0.206
  Angle     :  0.624   7.911  12648  Z= 0.317
  Chirality :  0.043   0.143   1466
  Planarity :  0.005   0.087   1566
  Dihedral  :  8.737  71.052   1314
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.12 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  9.54 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.53 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.26), residues: 1152
  helix:  1.09 (0.21), residues: 652
  sheet: -0.86 (0.51), residues: 78
  loop : -1.31 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 379 
 HIS   0.003   0.001   HIS B 243 
 PHE   0.013   0.001   PHE B 489 
 TYR   0.012   0.001   TYR B 605 
 ARG   0.003   0.000   ARG A 113 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 1.079 
Fit side-chains
REVERT: A  150 THR cc_start: 0.8603 (p) cc_final: 0.8375 (p)
REVERT: A  251 LYS cc_start: 0.8553 (ttpm) cc_final: 0.8349 (mtpt)
REVERT: A  299 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8635 (t0)
REVERT: A  378 ARG cc_start: 0.8089 (mtm180) cc_final: 0.7548 (mmt-90)
REVERT: A  451 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7622 (tt0)
REVERT: A  590 ASN cc_start: 0.7757 (t0) cc_final: 0.7434 (t0)
REVERT: B  451 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7477 (tt0)
REVERT: B  590 ASN cc_start: 0.7673 (t0) cc_final: 0.7339 (t0)
  outliers start: 26
  outliers final: 23
  residues processed: 124
  average time/residue: 0.2079
  time to fit residues: 36.5622
Evaluate side-chains
  120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  374 CYS
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  609 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 26 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 29 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 375 HIS
B 375 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.132584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.115216 restraints weight = 9911.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 0.85
r_work: 0.2904 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   9336  Z= 0.373
  Angle     :  0.704   9.191  12648  Z= 0.354
  Chirality :  0.047   0.156   1466
  Planarity :  0.005   0.085   1566
  Dihedral  :  9.084  79.714   1314
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.03 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  :  9.84 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.53 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.25), residues: 1152
  helix:  0.99 (0.21), residues: 652
  sheet: -0.63 (0.52), residues: 78
  loop : -1.28 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 379 
 HIS   0.004   0.001   HIS A 243 
 PHE   0.016   0.002   PHE A  39 
 TYR   0.016   0.002   TYR B 123 
 ARG   0.003   0.000   ARG B 184 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 1.047 
Fit side-chains
REVERT: A  150 THR cc_start: 0.8687 (p) cc_final: 0.8459 (p)
REVERT: A  378 ARG cc_start: 0.8053 (mtm180) cc_final: 0.7571 (mmt-90)
REVERT: A  451 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7647 (tt0)
REVERT: A  590 ASN cc_start: 0.7732 (t0) cc_final: 0.7479 (t0)
REVERT: B   64 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8324 (mp)
REVERT: B  451 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7470 (tt0)
REVERT: B  590 ASN cc_start: 0.7681 (t0) cc_final: 0.7429 (t0)
  outliers start: 27
  outliers final: 21
  residues processed: 122
  average time/residue: 0.2060
  time to fit residues: 36.0819
Evaluate side-chains
  117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  374 CYS
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  609 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.136059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.118335 restraints weight = 10007.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 0.85
r_work: 0.2927 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9336  Z= 0.192
  Angle     :  0.609   7.902  12648  Z= 0.309
  Chirality :  0.042   0.142   1466
  Planarity :  0.004   0.085   1566
  Dihedral  :  8.643  74.803   1314
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.12 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 10.14 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.53 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1152
  helix:  1.31 (0.21), residues: 658
  sheet: -0.62 (0.54), residues: 78
  loop : -1.17 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.010   0.001   PHE A 489 
 TYR   0.012   0.001   TYR B 605 
 ARG   0.002   0.000   ARG B 113 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.999 
Fit side-chains
REVERT: A   64 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8309 (mp)
REVERT: A  150 THR cc_start: 0.8583 (p) cc_final: 0.8374 (p)
REVERT: A  299 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8608 (t0)
REVERT: A  378 ARG cc_start: 0.8054 (mtm180) cc_final: 0.7555 (mmt-90)
REVERT: A  451 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7612 (tt0)
REVERT: A  590 ASN cc_start: 0.7654 (t0) cc_final: 0.7310 (t0)
REVERT: B  451 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7444 (tt0)
REVERT: B  590 ASN cc_start: 0.7567 (t0) cc_final: 0.7315 (t0)
  outliers start: 25
  outliers final: 19
  residues processed: 117
  average time/residue: 0.2093
  time to fit residues: 35.0977
Evaluate side-chains
  114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  554 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 109 optimal weight:    6.9990
   chunk 21 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 103 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.136226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.118206 restraints weight = 10064.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 0.90
r_work: 0.2908 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9336  Z= 0.186
  Angle     :  0.605   7.840  12648  Z= 0.307
  Chirality :  0.042   0.147   1466
  Planarity :  0.004   0.083   1566
  Dihedral  :  8.477  70.838   1314
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.12 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 10.44 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.53 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1152
  helix:  1.49 (0.21), residues: 658
  sheet: -0.59 (0.54), residues: 78
  loop : -1.08 (0.33), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.010   0.001   PHE A 489 
 TYR   0.011   0.001   TYR B 605 
 ARG   0.002   0.000   ARG B 113 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.938 
Fit side-chains
REVERT: A   64 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8339 (mp)
REVERT: A  451 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7616 (tt0)
REVERT: A  590 ASN cc_start: 0.7726 (t0) cc_final: 0.7351 (t0)
REVERT: B   64 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8252 (mp)
REVERT: B  451 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7428 (tt0)
REVERT: B  590 ASN cc_start: 0.7608 (t0) cc_final: 0.7327 (t0)
  outliers start: 26
  outliers final: 22
  residues processed: 118
  average time/residue: 0.1918
  time to fit residues: 33.0576
Evaluate side-chains
  116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  374 CYS
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 52 optimal weight:    8.9990
   chunk 69 optimal weight:    0.5980
   chunk 112 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.137588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.120540 restraints weight = 9898.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 0.78
r_work: 0.2958 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9336  Z= 0.169
  Angle     :  0.590   7.793  12648  Z= 0.300
  Chirality :  0.042   0.139   1466
  Planarity :  0.004   0.084   1566
  Dihedral  :  8.179  63.815   1314
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.21 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 10.14 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.53 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1152
  helix:  1.74 (0.21), residues: 658
  sheet: -0.40 (0.55), residues: 78
  loop : -0.96 (0.33), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.009   0.001   PHE B  39 
 TYR   0.011   0.001   TYR B 605 
 ARG   0.002   0.000   ARG B 113 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A   64 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8285 (mp)
REVERT: A  288 ASN cc_start: 0.7518 (m-40) cc_final: 0.6937 (t0)
REVERT: A  451 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7609 (tt0)
REVERT: A  590 ASN cc_start: 0.7548 (t0) cc_final: 0.7324 (t0)
REVERT: B   64 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8224 (mp)
REVERT: B  102 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.7832 (mp)
REVERT: B  150 THR cc_start: 0.8572 (p) cc_final: 0.8330 (p)
REVERT: B  288 ASN cc_start: 0.7542 (m110) cc_final: 0.6882 (t0)
REVERT: B  451 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7427 (tt0)
REVERT: B  590 ASN cc_start: 0.7429 (t0) cc_final: 0.7189 (t0)
  outliers start: 26
  outliers final: 21
  residues processed: 124
  average time/residue: 0.1973
  time to fit residues: 35.4610
Evaluate side-chains
  120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  374 CYS
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   chunk 113 optimal weight:    0.0170
   chunk 80 optimal weight:    0.8980
   chunk 48 optimal weight:    0.2980
   overall best weight:    0.9820

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

Flipped N/Q/H residues before XYZ refinement:
B 589 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.136297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.119764 restraints weight = 9983.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 0.78
r_work: 0.2964 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9336  Z= 0.200
  Angle     :  0.616  10.621  12648  Z= 0.309
  Chirality :  0.042   0.143   1466
  Planarity :  0.004   0.082   1566
  Dihedral  :  8.183  63.831   1314
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.03 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 10.84 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.53 %

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:  1.04 (0.26), residues: 1152
  helix:  1.80 (0.21), residues: 652
  sheet: -0.19 (0.57), residues: 78
  loop : -0.91 (0.33), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.010   0.001   PHE B  39 
 TYR   0.010   0.001   TYR A 605 
 ARG   0.002   0.000   ARG A 113 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.991 
Fit side-chains
REVERT: A   64 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8321 (mp)
REVERT: A  288 ASN cc_start: 0.7487 (m-40) cc_final: 0.6955 (t0)
REVERT: A  451 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7639 (tt0)
REVERT: B   64 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8243 (mp)
REVERT: B  150 THR cc_start: 0.8592 (p) cc_final: 0.8352 (p)
REVERT: B  288 ASN cc_start: 0.7514 (m110) cc_final: 0.6921 (t0)
REVERT: B  451 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7416 (tt0)
  outliers start: 23
  outliers final: 19
  residues processed: 114
  average time/residue: 0.1948
  time to fit residues: 32.3197
Evaluate side-chains
  115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 104 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0770
   chunk 73 optimal weight:    0.3980
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 590 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.137472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.120211 restraints weight = 9914.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 0.79
r_work: 0.2941 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9336  Z= 0.173
  Angle     :  0.598   8.000  12648  Z= 0.303
  Chirality :  0.042   0.161   1466
  Planarity :  0.005   0.083   1566
  Dihedral  :  8.073  61.479   1314
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.30 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 11.35 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.26 %
    Twisted General : 0.53 %

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:  1.17 (0.26), residues: 1152
  helix:  1.92 (0.21), residues: 652
  sheet: -0.16 (0.58), residues: 78
  loop : -0.86 (0.33), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 379 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.009   0.001   PHE B  39 
 TYR   0.010   0.001   TYR A 605 
 ARG   0.002   0.000   ARG B 113 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3796.36 seconds
wall clock time: 68 minutes 29.10 seconds (4109.10 seconds total)