Starting phenix.real_space_refine
on Wed Sep 25 00:08:58 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/09_2024/7pqx_13606.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/09_2024/7pqx_13606.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/09_2024/7pqx_13606.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/09_2024/7pqx_13606.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/09_2024/7pqx_13606.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/09_2024/7pqx_13606.cif"
  }
  resolution = 3.08
  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=   0.105
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    5784      2.51       5
     N    1572      2.21       5
     O    1652      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 9032
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 4516
          Classifications: {'peptide': 580}
          Link IDs: {'PTRANS': 17, 'TRANS': 562}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.80, per 1000 atoms: 0.97
  Number of scatterers: 9032
  At special positions: 0
  Unit cell: (80.704, 118.976, 141.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1652      8.00
     N    1572      7.00
     C    5784      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: 2.32
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 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:
      46 helices and 8 sheets defined
      67.3% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 103
      removed outlier: 4.442A  pdb=" N   GLN A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 144
      Proline residue:  A 134  - end of helix
    Processing helix  chain 'A' and resid 147 through 152
      removed outlier: 3.520A  pdb=" N   GLY A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 205
      removed outlier: 3.757A  pdb=" N   GLN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 213
      removed outlier: 3.729A  pdb=" N   HIS A 211 " --> pdb=" O   ASP A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 239
    Processing helix  chain 'A' and resid 240 through 259
    Processing helix  chain 'A' and resid 260 through 309
      removed outlier: 4.074A  pdb=" N   ALA A 264 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR A 286 " --> pdb=" O   THR A 282 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   LYS A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   PHE A 288 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ASN A 309 " --> pdb=" O   ASP A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 316
      removed outlier: 3.614A  pdb=" N   PHE A 316 " --> pdb=" O   ALA A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 371
      removed outlier: 3.711A  pdb=" N   GLU A 322 " --> pdb=" O   ASN A 318 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER A 336 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LYS A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 392
      removed outlier: 3.605A  pdb=" N   LEU A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   VAL A 381 " --> pdb=" O   VAL A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 398
      removed outlier: 4.021A  pdb=" N   GLY A 398 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 395 through 398'
    Processing helix  chain 'A' and resid 399 through 418
      removed outlier: 3.754A  pdb=" N   ARG A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 488
    Processing helix  chain 'A' and resid 509 through 516
    Processing helix  chain 'A' and resid 531 through 537
    Processing helix  chain 'A' and resid 543 through 554
    Processing helix  chain 'A' and resid 556 through 562
    Processing helix  chain 'A' and resid 565 through 568
      removed outlier: 3.612A  pdb=" N   GLN A 568 " --> pdb=" O   HIS A 565 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 565 through 568'
    Processing helix  chain 'A' and resid 579 through 595
    Processing helix  chain 'A' and resid 609 through 625
    Processing helix  chain 'A' and resid 660 through 666
      removed outlier: 3.957A  pdb=" N   GLU A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 674
      removed outlier: 4.309A  pdb=" N   GLU A 673 " --> pdb=" O   VAL A 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 103
    Processing helix  chain 'B' and resid 109 through 144
      Proline residue:  B 134  - end of helix
    Processing helix  chain 'B' and resid 147 through 152
      removed outlier: 3.521A  pdb=" N   GLY B 152 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 205
      removed outlier: 3.757A  pdb=" N   GLN B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 213
      removed outlier: 3.730A  pdb=" N   HIS B 211 " --> pdb=" O   ASP B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 239
    Processing helix  chain 'B' and resid 240 through 259
    Processing helix  chain 'B' and resid 260 through 309
      removed outlier: 4.074A  pdb=" N   ALA B 264 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR B 286 " --> pdb=" O   THR B 282 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   LYS B 287 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   PHE B 288 " --> pdb=" O   TRP B 284 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASN B 309 " --> pdb=" O   ASP B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 316
      removed outlier: 3.614A  pdb=" N   PHE B 316 " --> pdb=" O   ALA B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 371
      removed outlier: 3.710A  pdb=" N   GLU B 322 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER B 336 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LYS B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 392
      removed outlier: 3.605A  pdb=" N   LEU B 380 " --> pdb=" O   SER B 376 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   VAL B 381 " --> pdb=" O   VAL B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 398
      removed outlier: 4.021A  pdb=" N   GLY B 398 " --> pdb=" O   ASN B 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 395 through 398'
    Processing helix  chain 'B' and resid 399 through 418
      removed outlier: 3.754A  pdb=" N   ARG B 405 " --> pdb=" O   TYR B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 488
    Processing helix  chain 'B' and resid 509 through 516
    Processing helix  chain 'B' and resid 531 through 537
    Processing helix  chain 'B' and resid 543 through 554
    Processing helix  chain 'B' and resid 556 through 562
    Processing helix  chain 'B' and resid 565 through 568
      removed outlier: 3.611A  pdb=" N   GLN B 568 " --> pdb=" O   HIS B 565 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 565 through 568'
    Processing helix  chain 'B' and resid 579 through 595
    Processing helix  chain 'B' and resid 609 through 625
    Processing helix  chain 'B' and resid 660 through 666
      removed outlier: 3.958A  pdb=" N   GLU B 666 " --> pdb=" O   ARG B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 674
      removed outlier: 4.309A  pdb=" N   GLU B 673 " --> pdb=" O   VAL B 670 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 457 through 460
      removed outlier: 5.481A  pdb=" N   ARG A 458 " --> pdb=" O   PHE A 448 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE A 448 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460
      removed outlier: 5.481A  pdb=" N   ARG A 458 " --> pdb=" O   PHE A 448 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE A 448 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   VAL A 446 " --> pdb=" O   GLN A 495 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   GLN A 495 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 517 through 518
      removed outlier: 6.398A  pdb=" N   GLY A 518 " --> pdb=" O   PHE A 600 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ASP A 602 " --> pdb=" O   GLY A 518 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   LEU A 599 " --> pdb=" O   LEU A 632 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   VAL A 634 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   PHE A 601 " --> pdb=" O   VAL A 634 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA A 635 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   ALA A 471 " --> pdb=" O   ILE A 648 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   LEU A 650 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   VAL A 473 " --> pdb=" O   LEU A 650 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ILE A 647 " --> pdb=" O   GLN A 658 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   GLN A 658 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   VAL A 649 " --> pdb=" O   VAL A 656 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   VAL A 656 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL A 654 " --> pdb=" O   LYS A 651 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 530
    Processing sheet with id=AA5, first strand: chain 'B' and resid 457 through 460
      removed outlier: 5.481A  pdb=" N   ARG B 458 " --> pdb=" O   PHE B 448 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE B 448 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 457 through 460
      removed outlier: 5.481A  pdb=" N   ARG B 458 " --> pdb=" O   PHE B 448 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE B 448 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   VAL B 446 " --> pdb=" O   GLN B 495 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   GLN B 495 " --> pdb=" O   VAL B 446 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 517 through 518
      removed outlier: 6.398A  pdb=" N   GLY B 518 " --> pdb=" O   PHE B 600 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ASP B 602 " --> pdb=" O   GLY B 518 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   LEU B 599 " --> pdb=" O   LEU B 632 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   VAL B 634 " --> pdb=" O   LEU B 599 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   PHE B 601 " --> pdb=" O   VAL B 634 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA B 635 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   ALA B 471 " --> pdb=" O   ILE B 648 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   LEU B 650 " --> pdb=" O   ALA B 471 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   VAL B 473 " --> pdb=" O   LEU B 650 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ILE B 647 " --> pdb=" O   GLN B 658 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   GLN B 658 " --> pdb=" O   ILE B 647 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   VAL B 649 " --> pdb=" O   VAL B 656 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   VAL B 656 " --> pdb=" O   VAL B 649 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL B 654 " --> pdb=" O   LYS B 651 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 529 through 530

    590 hydrogen bonds defined for protein.
    1746 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: 2.78

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2683
        1.34 -     1.45: 1415
        1.45 -     1.57: 5054
        1.57 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 9196
  Sorted by residual:
  bond pdb=" C   TRP A 563 "
       pdb=" N   PRO A 564 "
    ideal  model  delta    sigma   weight residual
    1.335  1.368 -0.033 1.30e-02 5.92e+03 6.42e+00
  bond pdb=" C   TRP B 563 "
       pdb=" N   PRO B 564 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.032 1.30e-02 5.92e+03 6.00e+00
  bond pdb=" CB  ARG B 170 "
       pdb=" CG  ARG B 170 "
    ideal  model  delta    sigma   weight residual
    1.520  1.454  0.066 3.00e-02 1.11e+03 4.81e+00
  bond pdb=" CB  ARG A 170 "
       pdb=" CG  ARG A 170 "
    ideal  model  delta    sigma   weight residual
    1.520  1.455  0.065 3.00e-02 1.11e+03 4.72e+00
  bond pdb=" CB  THR B 281 "
       pdb=" CG2 THR B 281 "
    ideal  model  delta    sigma   weight residual
    1.521  1.450  0.071 3.30e-02 9.18e+02 4.58e+00
  ... (remaining 9191 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 11862
        2.28 -     4.55: 498
        4.55 -     6.83: 66
        6.83 -     9.10: 40
        9.10 -    11.38: 4
  Bond angle restraints: 12470
  Sorted by residual:
  angle pdb=" N   GLU A 622 "
        pdb=" CA  GLU A 622 "
        pdb=" CB  GLU A 622 "
      ideal   model   delta    sigma   weight residual
     110.39  118.50   -8.11 1.66e+00 3.63e-01 2.39e+01
  angle pdb=" N   GLU B 622 "
        pdb=" CA  GLU B 622 "
        pdb=" CB  GLU B 622 "
      ideal   model   delta    sigma   weight residual
     110.39  118.46   -8.07 1.66e+00 3.63e-01 2.36e+01
  angle pdb=" C   GLU A 444 "
        pdb=" N   ASN A 445 "
        pdb=" CA  ASN A 445 "
      ideal   model   delta    sigma   weight residual
     121.54  129.16   -7.62 1.91e+00 2.74e-01 1.59e+01
  angle pdb=" OG1 THR B 482 "
        pdb=" CB  THR B 482 "
        pdb=" CG2 THR B 482 "
      ideal   model   delta    sigma   weight residual
     109.30  101.32    7.98 2.00e+00 2.50e-01 1.59e+01
  angle pdb=" C   GLU B 444 "
        pdb=" N   ASN B 445 "
        pdb=" CA  ASN B 445 "
      ideal   model   delta    sigma   weight residual
     121.54  129.15   -7.61 1.91e+00 2.74e-01 1.59e+01
  ... (remaining 12465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 4884
       16.44 -    32.87: 498
       32.87 -    49.31: 110
       49.31 -    65.74: 14
       65.74 -    82.18: 10
  Dihedral angle restraints: 5516
    sinusoidal: 2156
      harmonic: 3360
  Sorted by residual:
  dihedral pdb=" CA  ASP B 502 "
           pdb=" C   ASP B 502 "
           pdb=" N   GLN B 503 "
           pdb=" CA  GLN B 503 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.22   22.78     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASP A 502 "
           pdb=" C   ASP A 502 "
           pdb=" N   GLN A 503 "
           pdb=" CA  GLN A 503 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.23   22.77     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  TYR B 451 "
           pdb=" C   TYR B 451 "
           pdb=" N   PRO B 452 "
           pdb=" CA  PRO B 452 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.99  -22.01     0      5.00e+00 4.00e-02 1.94e+01
  ... (remaining 5513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 874
       0.048 -    0.095: 402
       0.095 -    0.143: 137
       0.143 -    0.190: 35
       0.190 -    0.238: 16
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CG  LEU B 487 "
            pdb=" CB  LEU B 487 "
            pdb=" CD1 LEU B 487 "
            pdb=" CD2 LEU B 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.83    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  ILE B 641 "
            pdb=" CA  ILE B 641 "
            pdb=" CG1 ILE B 641 "
            pdb=" CG2 ILE B 641 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CG  LEU A 487 "
            pdb=" CB  LEU A 487 "
            pdb=" CD1 LEU A 487 "
            pdb=" CD2 LEU A 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1461 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 388 "    0.030 2.00e-02 2.50e+03   2.21e-02 8.55e+00
        pdb=" CG  PHE A 388 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 388 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 388 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 388 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 388 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 388 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 388 "   -0.030 2.00e-02 2.50e+03   2.21e-02 8.52e+00
        pdb=" CG  PHE B 388 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 388 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 388 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 388 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 388 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 388 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 454 "    0.045 5.00e-02 4.00e+02   6.89e-02 7.60e+00
        pdb=" N   PRO A 455 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 455 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 455 "    0.038 5.00e-02 4.00e+02
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2706
        2.82 -     3.34: 8629
        3.34 -     3.86: 15223
        3.86 -     4.38: 17097
        4.38 -     4.90: 29971
  Nonbonded interactions: 73626
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 206 "
            pdb=" OH  TYR B 310 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   GLU B 558 "
            pdb=" OG  SER B 562 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   GLU A 558 "
            pdb=" OG  SER A 562 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   GLY A 566 "
            pdb=" OG1 THR A 569 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   GLY B 566 "
            pdb=" OG1 THR B 569 "
     model   vdw
     2.312 3.040
  ... (remaining 73621 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
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:             2.640
  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:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.730
  Find NCS groups from input model:        0.220
  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:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
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      :  0.010   0.103   9196  Z= 0.600
  Angle     :  1.108  11.381  12470  Z= 0.605
  Chirality :  0.063   0.238   1464
  Planarity :  0.007   0.069   1584
  Dihedral  : 14.204  82.177   3352
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  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: -2.13 (0.21), residues: 1156
  helix: -1.08 (0.16), residues: 740
  sheet:  0.20 (0.67), residues: 60
  loop : -2.15 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 284 
 HIS   0.007   0.002   HIS B 132 
 PHE   0.038   0.005   PHE A 388 
 TYR   0.028   0.003   TYR A 274 
 ARG   0.016   0.001   ARG B 425 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.029 
Fit side-chains
REVERT: A  532 GLU cc_start: 0.7287 (tp30) cc_final: 0.6662 (tp30)
REVERT: B  401 TYR cc_start: 0.6469 (t80) cc_final: 0.6267 (t80)
REVERT: B  532 GLU cc_start: 0.7289 (tp30) cc_final: 0.6705 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2078
  time to fit residues: 34.7081
Evaluate side-chains
  96 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 48 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0370
   chunk 90 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 67 optimal weight:    0.5980
   chunk 105 optimal weight:    9.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 555 HIS
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 HIS
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9196  Z= 0.196
  Angle     :  0.600   7.793  12470  Z= 0.319
  Chirality :  0.043   0.155   1464
  Planarity :  0.004   0.050   1584
  Dihedral  :  5.094  21.202   1266
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.24), residues: 1156
  helix:  0.58 (0.18), residues: 748
  sheet:  0.07 (0.66), residues: 60
  loop : -1.70 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 284 
 HIS   0.003   0.001   HIS B 132 
 PHE   0.028   0.002   PHE A 355 
 TYR   0.011   0.001   TYR B 274 
 ARG   0.002   0.000   ARG A 536 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8863 (p) cc_final: 0.8446 (m)
REVERT: A  617 MET cc_start: 0.8818 (tpp) cc_final: 0.8470 (tpp)
REVERT: B  617 MET cc_start: 0.8810 (tpp) cc_final: 0.8451 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1651
  time to fit residues: 30.6748
Evaluate side-chains
  107 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 105 optimal weight:    9.9990
   chunk 114 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   chunk 104 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 HIS
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9196  Z= 0.273
  Angle     :  0.609   8.237  12470  Z= 0.318
  Chirality :  0.044   0.176   1464
  Planarity :  0.004   0.041   1584
  Dihedral  :  4.823  19.232   1266
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.81 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.25), residues: 1156
  helix:  1.13 (0.19), residues: 748
  sheet:  0.24 (0.67), residues: 60
  loop : -1.47 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 284 
 HIS   0.005   0.001   HIS A 555 
 PHE   0.025   0.002   PHE B 355 
 TYR   0.016   0.001   TYR A 274 
 ARG   0.003   0.000   ARG B 170 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7282 (t80)
REVERT: A  617 MET cc_start: 0.8825 (tpp) cc_final: 0.8475 (tpp)
REVERT: B  355 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7301 (t80)
REVERT: B  617 MET cc_start: 0.8818 (tpp) cc_final: 0.8488 (tpp)
  outliers start: 12
  outliers final: 4
  residues processed: 119
  average time/residue: 0.1602
  time to fit residues: 29.3152
Evaluate side-chains
  111 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 54 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0060
   chunk 55 optimal weight:    9.9990
   chunk 100 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
A 555 HIS
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 HIS
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9196  Z= 0.184
  Angle     :  0.546   6.586  12470  Z= 0.288
  Chirality :  0.042   0.148   1464
  Planarity :  0.003   0.034   1584
  Dihedral  :  4.638  18.934   1266
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 12.99 %
    Favored  : 85.65 %
  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:  0.81 (0.25), residues: 1156
  helix:  1.40 (0.19), residues: 760
  sheet:  0.37 (0.69), residues: 60
  loop : -1.44 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 284 
 HIS   0.006   0.001   HIS A 555 
 PHE   0.020   0.002   PHE B 355 
 TYR   0.011   0.001   TYR B 274 
 ARG   0.001   0.000   ARG B 585 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8546 (m)
REVERT: A  355 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7257 (t80)
REVERT: A  617 MET cc_start: 0.8851 (tpp) cc_final: 0.8529 (tpp)
REVERT: B  355 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7265 (t80)
REVERT: B  522 GLN cc_start: 0.8342 (tp40) cc_final: 0.8021 (tp40)
REVERT: B  617 MET cc_start: 0.8842 (tpp) cc_final: 0.8504 (tpp)
  outliers start: 13
  outliers final: 6
  residues processed: 109
  average time/residue: 0.1572
  time to fit residues: 26.6056
Evaluate side-chains
  110 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0060
   chunk 1 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 95 optimal weight:    0.4980
   chunk 77 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 555 HIS
A 557 HIS
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 HIS
B 557 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9196  Z= 0.174
  Angle     :  0.527   6.864  12470  Z= 0.276
  Chirality :  0.041   0.149   1464
  Planarity :  0.003   0.032   1584
  Dihedral  :  4.417  17.964   1266
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.89 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.26), residues: 1156
  helix:  1.75 (0.19), residues: 748
  sheet:  0.35 (0.68), residues: 60
  loop : -1.29 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 284 
 HIS   0.006   0.001   HIS B 555 
 PHE   0.019   0.001   PHE B 355 
 TYR   0.010   0.001   TYR B 274 
 ARG   0.001   0.000   ARG A 325 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8471 (m)
REVERT: A  355 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7259 (t80)
REVERT: A  617 MET cc_start: 0.8862 (tpp) cc_final: 0.8544 (tpp)
REVERT: B  355 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7285 (t80)
REVERT: B  617 MET cc_start: 0.8856 (tpp) cc_final: 0.8533 (tpp)
  outliers start: 20
  outliers final: 10
  residues processed: 123
  average time/residue: 0.1490
  time to fit residues: 29.0979
Evaluate side-chains
  113 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 37 optimal weight:    0.0980
   chunk 100 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 317 ASN
A 352 ASN
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 HIS
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 352 ASN
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 HIS
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9196  Z= 0.322
  Angle     :  0.603   7.317  12470  Z= 0.314
  Chirality :  0.045   0.147   1464
  Planarity :  0.003   0.030   1584
  Dihedral  :  4.522  16.584   1266
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.86 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.25), residues: 1156
  helix:  1.50 (0.19), residues: 748
  sheet:  0.32 (0.68), residues: 60
  loop : -1.33 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 284 
 HIS   0.006   0.001   HIS B 555 
 PHE   0.030   0.002   PHE B 448 
 TYR   0.017   0.001   TYR B 274 
 ARG   0.004   0.000   ARG A 170 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7360 (t80)
REVERT: A  617 MET cc_start: 0.8868 (tpp) cc_final: 0.8562 (tpp)
REVERT: B  355 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7357 (t80)
REVERT: B  603 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7889 (pt0)
REVERT: B  617 MET cc_start: 0.8860 (tpp) cc_final: 0.8558 (tpp)
  outliers start: 21
  outliers final: 13
  residues processed: 118
  average time/residue: 0.1526
  time to fit residues: 28.1789
Evaluate side-chains
  118 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 12 optimal weight:    0.0670
   chunk 63 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 111 optimal weight:   10.0000
   chunk 69 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 522 GLN
** B 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9196  Z= 0.187
  Angle     :  0.561   7.221  12470  Z= 0.293
  Chirality :  0.042   0.140   1464
  Planarity :  0.003   0.027   1584
  Dihedral  :  4.431  16.733   1266
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.38 %
    Favored  : 82.64 %
  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:  1.20 (0.25), residues: 1156
  helix:  1.76 (0.19), residues: 748
  sheet:  0.40 (0.69), residues: 60
  loop : -1.28 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 284 
 HIS   0.005   0.001   HIS B 555 
 PHE   0.019   0.001   PHE B 355 
 TYR   0.009   0.001   TYR B 274 
 ARG   0.001   0.000   ARG A 170 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 1.009 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8044 (mp0)
REVERT: A  349 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8506 (m)
REVERT: A  355 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7308 (t80)
REVERT: A  617 MET cc_start: 0.8857 (tpp) cc_final: 0.8550 (tpp)
REVERT: B  355 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7309 (t80)
REVERT: B  617 MET cc_start: 0.8850 (tpp) cc_final: 0.8534 (tpp)
  outliers start: 19
  outliers final: 13
  residues processed: 113
  average time/residue: 0.1858
  time to fit residues: 33.3665
Evaluate side-chains
  115 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  522 GLN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 101 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9196  Z= 0.189
  Angle     :  0.558   7.324  12470  Z= 0.291
  Chirality :  0.042   0.142   1464
  Planarity :  0.003   0.025   1584
  Dihedral  :  4.404  16.311   1266
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.49 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1156
  helix:  1.83 (0.19), residues: 748
  sheet:  0.52 (0.70), residues: 60
  loop : -1.25 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 284 
 HIS   0.006   0.001   HIS B 555 
 PHE   0.027   0.002   PHE B 210 
 TYR   0.010   0.001   TYR B 274 
 ARG   0.001   0.000   ARG B 170 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8500 (m)
REVERT: A  355 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7298 (t80)
REVERT: A  617 MET cc_start: 0.8852 (tpp) cc_final: 0.8555 (tpp)
REVERT: B  319 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8081 (mp0)
REVERT: B  355 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7307 (t80)
REVERT: B  617 MET cc_start: 0.8847 (tpp) cc_final: 0.8540 (tpp)
  outliers start: 20
  outliers final: 12
  residues processed: 113
  average time/residue: 0.1511
  time to fit residues: 26.8801
Evaluate side-chains
  114 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  319 GLU
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 98 optimal weight:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 522 GLN
B 555 HIS
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9196  Z= 0.227
  Angle     :  0.585   7.534  12470  Z= 0.306
  Chirality :  0.043   0.170   1464
  Planarity :  0.003   0.025   1584
  Dihedral  :  4.430  16.071   1266
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.97 %
    Favored  : 82.85 %
  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:  1.23 (0.25), residues: 1156
  helix:  1.73 (0.19), residues: 758
  sheet:  0.54 (0.71), residues: 60
  loop : -1.27 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 284 
 HIS   0.006   0.001   HIS B 555 
 PHE   0.029   0.002   PHE A 448 
 TYR   0.012   0.001   TYR A 274 
 ARG   0.002   0.000   ARG A 170 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8059 (mp0)
REVERT: A  349 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8545 (m)
REVERT: A  355 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7333 (t80)
REVERT: A  617 MET cc_start: 0.8846 (tpp) cc_final: 0.8561 (tpp)
REVERT: B  319 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8096 (mp0)
REVERT: B  355 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7336 (t80)
REVERT: B  617 MET cc_start: 0.8842 (tpp) cc_final: 0.8551 (tpp)
  outliers start: 21
  outliers final: 15
  residues processed: 114
  average time/residue: 0.1716
  time to fit residues: 29.5252
Evaluate side-chains
  116 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  319 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  262 GLU
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  319 GLU
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  522 GLN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 115 optimal weight:    0.9980
   chunk 106 optimal weight:    0.5980
   chunk 92 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 503 GLN
B 522 GLN
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9196  Z= 0.210
  Angle     :  0.584   9.204  12470  Z= 0.303
  Chirality :  0.042   0.140   1464
  Planarity :  0.003   0.029   1584
  Dihedral  :  4.405  17.446   1266
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.38 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.25), residues: 1156
  helix:  1.79 (0.19), residues: 758
  sheet:  0.54 (0.71), residues: 60
  loop : -1.21 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 284 
 HIS   0.007   0.001   HIS A 555 
 PHE   0.021   0.002   PHE B 448 
 TYR   0.011   0.001   TYR A 274 
 ARG   0.007   0.000   ARG A 458 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8056 (mp0)
REVERT: A  349 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8511 (m)
REVERT: A  355 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7340 (t80)
REVERT: A  617 MET cc_start: 0.8844 (tpp) cc_final: 0.8546 (tpp)
REVERT: B  319 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8097 (mp0)
REVERT: B  355 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7342 (t80)
REVERT: B  617 MET cc_start: 0.8839 (tpp) cc_final: 0.8550 (tpp)
  outliers start: 21
  outliers final: 15
  residues processed: 116
  average time/residue: 0.1507
  time to fit residues: 27.3463
Evaluate side-chains
  120 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  319 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  262 GLU
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  319 GLU
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  522 GLN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 92 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 80 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 HIS
B 503 GLN
B 522 GLN
** B 557 HIS ** 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 = 0.4305 r_free = 0.4305 target = 0.196349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.120810 restraints weight = 10497.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.08
r_work: 0.3256 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9196  Z= 0.208
  Angle     :  0.586   8.950  12470  Z= 0.305
  Chirality :  0.042   0.164   1464
  Planarity :  0.003   0.041   1584
  Dihedral  :  4.408  16.023   1266
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.38 %
    Favored  : 82.33 %
  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:  1.36 (0.25), residues: 1156
  helix:  1.83 (0.19), residues: 758
  sheet:  0.55 (0.71), residues: 60
  loop : -1.21 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 284 
 HIS   0.007   0.001   HIS A 555 
 PHE   0.024   0.002   PHE A 448 
 TYR   0.011   0.001   TYR B 274 
 ARG   0.007   0.000   ARG B 458 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2177.06 seconds
wall clock time: 39 minutes 28.20 seconds (2368.20 seconds total)