Starting phenix.real_space_refine
on Thu Feb 13 14:43:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7psd_13612/02_2025/7psd_13612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7psd_13612/02_2025/7psd_13612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7psd_13612/02_2025/7psd_13612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7psd_13612/02_2025/7psd_13612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7psd_13612/02_2025/7psd_13612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7psd_13612/02_2025/7psd_13612.cif"
  }
  resolution = 3.0
  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=   0.102
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    1574      2.21       5
     O    1650      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-5592/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: 8.33, per 1000 atoms: 0.92
  Number of scatterers: 9032
  At special positions: 0
  Unit cell: (118.976, 75.712, 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    1650      8.00
     N    1574      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: 2.03
  Conformation dependent library (CDL) restraints added in 1.2 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:
      48 helices and 6 sheets defined
      69.2% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'B' and resid 95 through 103
      removed outlier: 3.669A  pdb=" N   GLN B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 145
      Proline residue:  B 134  - end of helix
    Processing helix  chain 'B' and resid 159 through 206
      removed outlier: 3.750A  pdb=" N   GLN B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 213
    Processing helix  chain 'B' and resid 217 through 240
    Processing helix  chain 'B' and resid 240 through 259
    Processing helix  chain 'B' and resid 260 through 309
      removed outlier: 3.824A  pdb=" N   ALA B 264 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   THR B 286 " --> pdb=" O   THR B 282 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   LYS B 287 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE B 288 " --> pdb=" O   TRP B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 316
    Processing helix  chain 'B' and resid 318 through 371
      removed outlier: 3.504A  pdb=" N   GLU B 322 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER B 336 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 391
      removed outlier: 3.662A  pdb=" N   LEU B 380 " --> pdb=" O   SER B 376 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL B 381 " --> pdb=" O   VAL B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 398
      removed outlier: 4.270A  pdb=" N   ASN B 395 " --> pdb=" O   VAL B 392 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   PHE B 396 " --> pdb=" O   PRO B 393 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B 397 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY B 398 " --> pdb=" O   ASN B 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 392 through 398'
    Processing helix  chain 'B' and resid 399 through 418
      removed outlier: 3.742A  pdb=" N   ARG B 405 " --> pdb=" O   TYR B 401 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU B 414 " --> pdb=" O   ASP B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 488
      removed outlier: 4.653A  pdb=" N   ARG B 485 " --> pdb=" O   SER B 481 " (cutoff:3.500A)
    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 563
    Processing helix  chain 'B' and resid 565 through 568
      removed outlier: 4.052A  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 603 through 607
      removed outlier: 3.937A  pdb=" N   ALA B 607 " --> pdb=" O   ALA B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 625
    Processing helix  chain 'B' and resid 637 through 642
      removed outlier: 3.922A  pdb=" N   TYR B 642 " --> pdb=" O   ARG B 639 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 661 through 666
      removed outlier: 3.554A  pdb=" N   GLU B 666 " --> pdb=" O   ARG B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 674
      removed outlier: 4.033A  pdb=" N   GLU B 673 " --> pdb=" O   VAL B 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 110 through 145
      Proline residue:  A 134  - end of helix
    Processing helix  chain 'A' and resid 159 through 206
      removed outlier: 3.749A  pdb=" N   GLN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   SER A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 213
    Processing helix  chain 'A' and resid 217 through 240
    Processing helix  chain 'A' and resid 240 through 259
    Processing helix  chain 'A' and resid 260 through 309
      removed outlier: 3.823A  pdb=" N   ALA A 264 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   THR A 286 " --> pdb=" O   THR A 282 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LYS A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE A 288 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 316
    Processing helix  chain 'A' and resid 318 through 371
      removed outlier: 3.504A  pdb=" N   GLU A 322 " --> pdb=" O   ASN A 318 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER A 336 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 391
      removed outlier: 3.661A  pdb=" N   LEU A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 381 " --> pdb=" O   VAL A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 398
      removed outlier: 4.271A  pdb=" N   ASN A 395 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   PHE A 396 " --> pdb=" O   PRO A 393 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU A 397 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A 398 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 392 through 398'
    Processing helix  chain 'A' and resid 399 through 418
      removed outlier: 3.743A  pdb=" N   ARG A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 414 " --> pdb=" O   ASP A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 488
      removed outlier: 4.653A  pdb=" N   ARG A 485 " --> pdb=" O   SER A 481 " (cutoff:3.500A)
    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 563
    Processing helix  chain 'A' and resid 565 through 568
      removed outlier: 4.052A  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 603 through 607
      removed outlier: 3.937A  pdb=" N   ALA A 607 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 625
    Processing helix  chain 'A' and resid 637 through 642
      removed outlier: 3.923A  pdb=" N   TYR A 642 " --> pdb=" O   ARG A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 666
      removed outlier: 3.555A  pdb=" N   GLU A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 674
      removed outlier: 4.034A  pdb=" N   GLU A 673 " --> pdb=" O   VAL A 670 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 457 through 464
      removed outlier: 5.296A  pdb=" N   ARG B 458 " --> pdb=" O   PHE B 448 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   PHE B 448 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LEU B 462 " --> pdb=" O   GLU B 444 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   GLU B 444 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   ILE B 464 " --> pdb=" O   ARG B 442 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   ARG B 442 " --> pdb=" O   ILE B 464 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   VAL B 446 " --> pdb=" O   GLN B 495 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   GLN B 495 " --> pdb=" O   VAL B 446 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 517 through 519
      removed outlier: 3.556A  pdb=" N   ILE B 647 " --> pdb=" O   GLY B 659 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   GLU B 657 " --> pdb=" O   VAL B 649 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 529 through 530
    Processing sheet with id=AA4, first strand: chain 'A' and resid 457 through 464
      removed outlier: 5.296A  pdb=" N   ARG A 458 " --> pdb=" O   PHE A 448 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   PHE A 448 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   LEU A 462 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   GLU A 444 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   ILE A 464 " --> pdb=" O   ARG A 442 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ARG A 442 " --> pdb=" O   ILE A 464 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   VAL A 446 " --> pdb=" O   GLN A 495 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   GLN A 495 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 517 through 519
      removed outlier: 3.556A  pdb=" N   ILE A 647 " --> pdb=" O   GLY A 659 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   GLU A 657 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 530

    612 hydrogen bonds defined for protein.
    1800 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: 2.82

  Time building geometry restraints manager: 2.37 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: 2635
        1.33 -     1.45: 1694
        1.45 -     1.58: 4823
        1.58 -     1.70: 0
        1.70 -     1.82: 44
  Bond restraints: 9196
  Sorted by residual:
  bond pdb=" CB  THR A 281 "
       pdb=" CG2 THR A 281 "
    ideal  model  delta    sigma   weight residual
    1.521  1.391  0.130 3.30e-02 9.18e+02 1.54e+01
  bond pdb=" CB  THR B 281 "
       pdb=" CG2 THR B 281 "
    ideal  model  delta    sigma   weight residual
    1.521  1.392  0.129 3.30e-02 9.18e+02 1.53e+01
  bond pdb=" C   SER B 156 "
       pdb=" N   ALA B 157 "
    ideal  model  delta    sigma   weight residual
    1.332  1.287  0.046 1.40e-02 5.10e+03 1.07e+01
  bond pdb=" C   SER A 156 "
       pdb=" N   ALA A 157 "
    ideal  model  delta    sigma   weight residual
    1.332  1.288  0.045 1.40e-02 5.10e+03 1.03e+01
  bond pdb=" CG1 ILE A 192 "
       pdb=" CD1 ILE A 192 "
    ideal  model  delta    sigma   weight residual
    1.513  1.392  0.121 3.90e-02 6.57e+02 9.60e+00
  ... (remaining 9191 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 11973
        2.56 -     5.13: 436
        5.13 -     7.69: 47
        7.69 -    10.25: 10
       10.25 -    12.81: 4
  Bond angle restraints: 12470
  Sorted by residual:
  angle pdb=" CA  TRP A 284 "
        pdb=" CB  TRP A 284 "
        pdb=" CG  TRP A 284 "
      ideal   model   delta    sigma   weight residual
     113.60  121.87   -8.27 1.90e+00 2.77e-01 1.89e+01
  angle pdb=" CA  TRP B 284 "
        pdb=" CB  TRP B 284 "
        pdb=" CG  TRP B 284 "
      ideal   model   delta    sigma   weight residual
     113.60  121.84   -8.24 1.90e+00 2.77e-01 1.88e+01
  angle pdb=" N   VAL B 400 "
        pdb=" CA  VAL B 400 "
        pdb=" C   VAL B 400 "
      ideal   model   delta    sigma   weight residual
     110.36  114.48   -4.12 1.05e+00 9.07e-01 1.54e+01
  angle pdb=" N   VAL A 400 "
        pdb=" CA  VAL A 400 "
        pdb=" C   VAL A 400 "
      ideal   model   delta    sigma   weight residual
     110.36  114.48   -4.12 1.05e+00 9.07e-01 1.54e+01
  angle pdb=" N   VAL B 155 "
        pdb=" CA  VAL B 155 "
        pdb=" C   VAL B 155 "
      ideal   model   delta    sigma   weight residual
     110.21  105.89    4.32 1.13e+00 7.83e-01 1.46e+01
  ... (remaining 12465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 4918
       17.12 -    34.24: 485
       34.24 -    51.36: 89
       51.36 -    68.48: 10
       68.48 -    85.59: 14
  Dihedral angle restraints: 5516
    sinusoidal: 2156
      harmonic: 3360
  Sorted by residual:
  dihedral pdb=" CA  TYR A 451 "
           pdb=" C   TYR A 451 "
           pdb=" N   PRO A 452 "
           pdb=" CA  PRO A 452 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.36  -25.64     0      5.00e+00 4.00e-02 2.63e+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 -154.39  -25.61     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  SER B 399 "
           pdb=" C   SER B 399 "
           pdb=" N   VAL B 400 "
           pdb=" CA  VAL B 400 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.21  -22.79     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 5513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1365
       0.118 -    0.235: 97
       0.235 -    0.353: 0
       0.353 -    0.470: 0
       0.470 -    0.588: 2
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CB  ILE A 192 "
            pdb=" CA  ILE A 192 "
            pdb=" CG1 ILE A 192 "
            pdb=" CG2 ILE A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.06    0.59 2.00e-01 2.50e+01 8.63e+00
  chirality pdb=" CB  ILE B 192 "
            pdb=" CA  ILE B 192 "
            pdb=" CG1 ILE B 192 "
            pdb=" CG2 ILE B 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.06    0.59 2.00e-01 2.50e+01 8.61e+00
  chirality pdb=" CA  PHE A 355 "
            pdb=" N   PHE A 355 "
            pdb=" C   PHE A 355 "
            pdb=" CB  PHE A 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1461 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 137 "    0.015 2.00e-02 2.50e+03   2.54e-02 1.13e+01
        pdb=" CG  PHE A 137 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 137 "    0.032 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 137 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 137 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 137 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 137 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 137 "   -0.015 2.00e-02 2.50e+03   2.52e-02 1.11e+01
        pdb=" CG  PHE B 137 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 137 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 137 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 137 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 137 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 137 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 388 "   -0.031 2.00e-02 2.50e+03   1.97e-02 6.78e+00
        pdb=" CG  PHE B 388 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 388 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 388 "    0.015 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 388 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 388 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 388 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 454
        2.70 -     3.25: 9435
        3.25 -     3.80: 14950
        3.80 -     4.35: 18651
        4.35 -     4.90: 31686
  Nonbonded interactions: 75176
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 566 "
            pdb=" OG1 THR A 569 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   GLY B 566 "
            pdb=" OG1 THR B 569 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   LEU A 586 "
            pdb=" OG  SER A 589 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   LEU B 586 "
            pdb=" OG  SER B 589 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   ARG B 637 "
            pdb=" OG1 THR B 640 "
     model   vdw
     2.302 3.040
  ... (remaining 75171 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:             1.580
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.220
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
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      :  0.015   0.130   9196  Z= 0.967
  Angle     :  1.115  12.813  12470  Z= 0.626
  Chirality :  0.069   0.588   1464
  Planarity :  0.006   0.056   1584
  Dihedral  : 14.392  85.594   3352
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  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: -1.38 (0.23), residues: 1156
  helix: -0.59 (0.17), residues: 750
  sheet: -0.63 (0.68), residues: 56
  loop : -1.37 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.005   TRP B 284 
 HIS   0.004   0.001   HIS A 202 
 PHE   0.053   0.005   PHE A 137 
 TYR   0.017   0.003   TYR A 401 
 ARG   0.014   0.001   ARG B 170 

*********************** 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
  123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.012 
Fit side-chains
REVERT: B  468 LYS cc_start: 0.7532 (mmmm) cc_final: 0.7306 (mmpt)
REVERT: B  621 ASN cc_start: 0.9158 (m-40) cc_final: 0.8475 (m110)
REVERT: B  632 LEU cc_start: 0.8247 (mp) cc_final: 0.7948 (mp)
  outliers start: 0
  outliers final: 1
  residues processed: 123
  average time/residue: 0.8536
  time to fit residues: 116.0959
Evaluate side-chains
  103 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 87 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9980
   chunk 105 optimal weight:    9.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 205 ASN
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.204036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.118707 restraints weight = 9525.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 1.85
r_work: 0.3255 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   9196  Z= 0.407
  Angle     :  0.694   7.597  12470  Z= 0.373
  Chirality :  0.047   0.162   1464
  Planarity :  0.005   0.050   1584
  Dihedral  :  5.262  22.239   1268
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.23 %
    Favored  : 87.01 %
  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: -0.24 (0.24), residues: 1156
  helix:  0.38 (0.18), residues: 754
  sheet: -0.52 (0.67), residues: 56
  loop : -1.08 (0.36), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 284 
 HIS   0.004   0.001   HIS B 211 
 PHE   0.035   0.003   PHE B 388 
 TYR   0.012   0.001   TYR B 136 
 ARG   0.006   0.001   ARG B 221 

*********************** 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
  116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 1.030 
Fit side-chains
REVERT: B  154 THR cc_start: 0.8102 (p) cc_final: 0.7899 (t)
REVERT: B  632 LEU cc_start: 0.7898 (mp) cc_final: 0.7601 (mp)
REVERT: A  305 ASP cc_start: 0.7970 (t70) cc_final: 0.7729 (t0)
REVERT: A  595 ASP cc_start: 0.8020 (t0) cc_final: 0.7551 (p0)
  outliers start: 17
  outliers final: 9
  residues processed: 112
  average time/residue: 0.7076
  time to fit residues: 89.0929
Evaluate side-chains
  103 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  556 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 205 ASN
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.207704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.120853 restraints weight = 9755.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.94
r_work: 0.3311 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9196  Z= 0.206
  Angle     :  0.591   7.506  12470  Z= 0.315
  Chirality :  0.043   0.163   1464
  Planarity :  0.004   0.038   1584
  Dihedral  :  4.850  21.031   1268
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.83 %
    Favored  : 84.10 %
  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:  0.60 (0.25), residues: 1156
  helix:  1.09 (0.18), residues: 756
  sheet:  0.06 (0.86), residues: 36
  loop : -0.95 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 284 
 HIS   0.002   0.001   HIS B 211 
 PHE   0.030   0.002   PHE B 388 
 TYR   0.009   0.001   TYR A 136 
 ARG   0.003   0.000   ARG B 536 

*********************** 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 to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: B  305 ASP cc_start: 0.7794 (t70) cc_final: 0.7572 (t0)
REVERT: B  632 LEU cc_start: 0.7969 (mp) cc_final: 0.7726 (mp)
REVERT: B  657 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7066 (pm20)
REVERT: A  441 ILE cc_start: 0.8881 (mt) cc_final: 0.8487 (mm)
REVERT: A  595 ASP cc_start: 0.8109 (t0) cc_final: 0.7610 (p0)
REVERT: A  657 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7346 (pm20)
  outliers start: 20
  outliers final: 11
  residues processed: 111
  average time/residue: 0.8027
  time to fit residues: 98.7918
Evaluate side-chains
  105 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 86 optimal weight:    0.0670
   chunk 79 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 503 GLN ** 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 = 0.4379 r_free = 0.4379 target = 0.208762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.121470 restraints weight = 9530.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.99
r_work: 0.3305 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9196  Z= 0.189
  Angle     :  0.558   7.545  12470  Z= 0.295
  Chirality :  0.042   0.155   1464
  Planarity :  0.003   0.032   1584
  Dihedral  :  4.538  19.444   1268
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.80 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.25), residues: 1156
  helix:  1.43 (0.19), residues: 754
  sheet:  0.37 (0.87), residues: 36
  loop : -0.79 (0.35), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 284 
 HIS   0.003   0.001   HIS A 555 
 PHE   0.026   0.002   PHE B 388 
 TYR   0.009   0.001   TYR A 232 
 ARG   0.002   0.000   ARG B 536 

*********************** 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
  125 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
REVERT: B  225 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7665 (mtt90)
REVERT: B  515 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8096 (ttmm)
REVERT: B  632 LEU cc_start: 0.7885 (mp) cc_final: 0.7601 (mp)
REVERT: A  225 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7548 (mtt90)
REVERT: A  441 ILE cc_start: 0.8836 (mt) cc_final: 0.8436 (mm)
REVERT: A  595 ASP cc_start: 0.8156 (t0) cc_final: 0.7812 (p0)
REVERT: A  657 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7271 (pm20)
  outliers start: 21
  outliers final: 10
  residues processed: 119
  average time/residue: 0.7600
  time to fit residues: 101.1854
Evaluate side-chains
  103 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 115 optimal weight:    0.3980
   chunk 20 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 29 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 621 ASN
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.207193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.121841 restraints weight = 9416.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.91
r_work: 0.3300 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9196  Z= 0.204
  Angle     :  0.551   7.098  12470  Z= 0.292
  Chirality :  0.042   0.151   1464
  Planarity :  0.003   0.031   1584
  Dihedral  :  4.404  18.450   1268
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.94 %
    Favored  : 80.46 %
  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:  1.37 (0.25), residues: 1156
  helix:  1.71 (0.19), residues: 742
  sheet:  0.38 (0.87), residues: 36
  loop : -0.63 (0.35), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 284 
 HIS   0.003   0.000   HIS A 211 
 PHE   0.025   0.002   PHE B 388 
 TYR   0.008   0.001   TYR B 232 
 ARG   0.002   0.000   ARG A 536 

*********************** 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
  124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
REVERT: B  221 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7422 (ttm110)
REVERT: B  225 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7677 (mtt90)
REVERT: B  355 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8047 (t80)
REVERT: B  468 LYS cc_start: 0.7402 (mmmm) cc_final: 0.7048 (mmmm)
REVERT: B  515 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8106 (ttmm)
REVERT: B  632 LEU cc_start: 0.7974 (mp) cc_final: 0.7706 (mp)
REVERT: A  221 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7258 (ttm110)
REVERT: A  225 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7559 (mtt90)
REVERT: A  355 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8020 (t80)
REVERT: A  441 ILE cc_start: 0.8870 (mt) cc_final: 0.8385 (mm)
REVERT: A  595 ASP cc_start: 0.8164 (t0) cc_final: 0.7877 (p0)
REVERT: A  657 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7285 (pm20)
  outliers start: 25
  outliers final: 17
  residues processed: 113
  average time/residue: 0.9122
  time to fit residues: 114.3119
Evaluate side-chains
  115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  602 ASP
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 16 optimal weight:    0.0270
   chunk 13 optimal weight:    1.9990
   chunk 106 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 48 optimal weight:    9.9990
   chunk 2 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0670
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0170
   chunk 86 optimal weight:    0.3980
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.2414

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

Flipped N/Q/H residues before XYZ refinement:
B  99 GLN
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 503 GLN
A 552 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.210378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.127234 restraints weight = 9334.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.90
r_work: 0.3363 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9196  Z= 0.149
  Angle     :  0.528   7.587  12470  Z= 0.278
  Chirality :  0.040   0.155   1464
  Planarity :  0.003   0.027   1584
  Dihedral  :  4.219  17.780   1268
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.40 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.26), residues: 1156
  helix:  1.99 (0.19), residues: 742
  sheet:  0.47 (0.86), residues: 36
  loop : -0.53 (0.36), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 284 
 HIS   0.003   0.000   HIS B 211 
 PHE   0.027   0.002   PHE A 210 
 TYR   0.008   0.001   TYR A 232 
 ARG   0.003   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
  127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.915 
Fit side-chains
REVERT: B  221 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7459 (ttm110)
REVERT: B  225 ARG cc_start: 0.7927 (mtt90) cc_final: 0.7653 (mtt90)
REVERT: B  250 MET cc_start: 0.8774 (mtt) cc_final: 0.8571 (mtm)
REVERT: B  468 LYS cc_start: 0.7394 (mmmm) cc_final: 0.7029 (mmmm)
REVERT: B  515 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8159 (ttmm)
REVERT: B  632 LEU cc_start: 0.8019 (mp) cc_final: 0.7757 (mp)
REVERT: A  221 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7251 (ttm110)
REVERT: A  225 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7572 (mtt90)
REVERT: A  595 ASP cc_start: 0.8138 (t0) cc_final: 0.7875 (p0)
REVERT: A  657 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7389 (pm20)
  outliers start: 22
  outliers final: 11
  residues processed: 119
  average time/residue: 0.8750
  time to fit residues: 114.5867
Evaluate side-chains
  105 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  602 ASP
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 552 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.208494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.121010 restraints weight = 9661.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.01
r_work: 0.3251 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9196  Z= 0.240
  Angle     :  0.569   7.847  12470  Z= 0.299
  Chirality :  0.043   0.194   1464
  Planarity :  0.003   0.035   1584
  Dihedral  :  4.227  17.113   1268
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 19.96 %
    Favored  : 78.07 %
  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:  1.70 (0.26), residues: 1156
  helix:  1.97 (0.19), residues: 740
  sheet:  0.50 (0.87), residues: 36
  loop : -0.47 (0.36), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 284 
 HIS   0.003   0.001   HIS A 211 
 PHE   0.024   0.002   PHE A 388 
 TYR   0.010   0.001   TYR B 274 
 ARG   0.002   0.000   ARG A 138 

*********************** 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
  117 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 1.051 
Fit side-chains
REVERT: B  221 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7309 (ttm110)
REVERT: B  225 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7620 (mtt90)
REVERT: B  468 LYS cc_start: 0.7354 (mmmm) cc_final: 0.6995 (mmmm)
REVERT: B  515 LYS cc_start: 0.8318 (ttpt) cc_final: 0.8052 (ttmm)
REVERT: B  632 LEU cc_start: 0.7890 (mp) cc_final: 0.7640 (mp)
REVERT: A  221 ARG cc_start: 0.7551 (ttm110) cc_final: 0.7247 (ttm110)
REVERT: A  416 ASP cc_start: 0.7718 (m-30) cc_final: 0.7234 (p0)
REVERT: A  441 ILE cc_start: 0.8794 (mt) cc_final: 0.8188 (mm)
REVERT: A  595 ASP cc_start: 0.8188 (t0) cc_final: 0.7903 (p0)
REVERT: A  657 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7317 (pm20)
  outliers start: 19
  outliers final: 14
  residues processed: 110
  average time/residue: 0.8733
  time to fit residues: 105.8429
Evaluate side-chains
  112 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  602 ASP
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 40 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0670
   chunk 23 optimal weight:    1.9990
   chunk 97 optimal weight:    0.1980
   chunk 24 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 103 optimal weight:    4.9990
   chunk 108 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
B 503 GLN
A 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.210872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.124568 restraints weight = 9729.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.02
r_work: 0.3298 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9196  Z= 0.169
  Angle     :  0.558   7.544  12470  Z= 0.289
  Chirality :  0.042   0.174   1464
  Planarity :  0.003   0.031   1584
  Dihedral  :  4.138  16.884   1268
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 20.06 %
    Favored  : 77.75 %
  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:  1.90 (0.26), residues: 1156
  helix:  2.12 (0.19), residues: 740
  sheet:  0.52 (0.87), residues: 36
  loop : -0.40 (0.36), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 284 
 HIS   0.004   0.000   HIS A 211 
 PHE   0.027   0.002   PHE A 210 
 TYR   0.010   0.001   TYR A 537 
 ARG   0.002   0.000   ARG A 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
  122 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: B  221 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7316 (ttm110)
REVERT: B  225 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7545 (mtt90)
REVERT: B  331 GLN cc_start: 0.7894 (tt0) cc_final: 0.7152 (mt0)
REVERT: B  355 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7981 (t80)
REVERT: B  468 LYS cc_start: 0.7352 (mmmm) cc_final: 0.6993 (mmmm)
REVERT: B  515 LYS cc_start: 0.8352 (ttpt) cc_final: 0.8088 (ttmm)
REVERT: B  632 LEU cc_start: 0.7892 (mp) cc_final: 0.7616 (mp)
REVERT: A  355 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.7965 (t80)
REVERT: A  416 ASP cc_start: 0.7674 (m-30) cc_final: 0.7156 (p0)
REVERT: A  595 ASP cc_start: 0.8169 (t0) cc_final: 0.7906 (p0)
REVERT: A  657 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7344 (pm20)
  outliers start: 21
  outliers final: 14
  residues processed: 117
  average time/residue: 0.8833
  time to fit residues: 113.6267
Evaluate side-chains
  114 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  602 ASP
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0670
   chunk 72 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 58 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9990
   chunk 97 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A 552 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.209919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.124785 restraints weight = 9473.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.95
r_work: 0.3329 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9196  Z= 0.187
  Angle     :  0.564  10.731  12470  Z= 0.296
  Chirality :  0.042   0.200   1464
  Planarity :  0.003   0.031   1584
  Dihedral  :  4.127  16.700   1268
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.89 %
    Favored  : 76.72 %
  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:  1.87 (0.26), residues: 1156
  helix:  2.08 (0.19), residues: 742
  sheet:  0.58 (0.88), residues: 36
  loop : -0.39 (0.36), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 284 
 HIS   0.003   0.000   HIS A 211 
 PHE   0.022   0.002   PHE B 388 
 TYR   0.018   0.001   TYR A 537 
 ARG   0.007   0.000   ARG A 221 

*********************** 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
  124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 1.043 
Fit side-chains
REVERT: B  221 ARG cc_start: 0.7712 (ttm110) cc_final: 0.7369 (ttm110)
REVERT: B  225 ARG cc_start: 0.7861 (mtt90) cc_final: 0.7592 (mtt90)
REVERT: B  331 GLN cc_start: 0.7970 (tt0) cc_final: 0.7236 (mt0)
REVERT: B  355 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8011 (t80)
REVERT: B  468 LYS cc_start: 0.7443 (mmmm) cc_final: 0.7085 (mmmm)
REVERT: B  515 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8123 (ttmm)
REVERT: B  632 LEU cc_start: 0.7956 (mp) cc_final: 0.7716 (mp)
REVERT: A  355 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8003 (t80)
REVERT: A  416 ASP cc_start: 0.7695 (m-30) cc_final: 0.7177 (p0)
REVERT: A  595 ASP cc_start: 0.8187 (t0) cc_final: 0.7939 (p0)
REVERT: A  657 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7363 (pm20)
  outliers start: 23
  outliers final: 15
  residues processed: 118
  average time/residue: 0.8299
  time to fit residues: 108.4792
Evaluate side-chains
  114 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  602 ASP
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 109 optimal weight:    0.0980
   chunk 85 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0670
   chunk 51 optimal weight:    8.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN
A 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.210259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.125081 restraints weight = 9601.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.97
r_work: 0.3290 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9196  Z= 0.190
  Angle     :  0.577  12.389  12470  Z= 0.303
  Chirality :  0.042   0.199   1464
  Planarity :  0.003   0.033   1584
  Dihedral  :  4.113  18.296   1268
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.62 %
    Favored  : 76.61 %
  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:  1.92 (0.26), residues: 1156
  helix:  2.12 (0.19), residues: 742
  sheet:  0.60 (0.89), residues: 36
  loop : -0.36 (0.36), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 284 
 HIS   0.003   0.000   HIS A 211 
 PHE   0.027   0.002   PHE A 210 
 TYR   0.017   0.001   TYR A 537 
 ARG   0.007   0.000   ARG A 221 

********************** 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
  112 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: B  221 ARG cc_start: 0.7662 (ttm110) cc_final: 0.7315 (ttm110)
REVERT: B  225 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7527 (mtt90)
REVERT: B  331 GLN cc_start: 0.7910 (tt0) cc_final: 0.7189 (mt0)
REVERT: B  355 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7993 (t80)
REVERT: B  468 LYS cc_start: 0.7417 (mmmm) cc_final: 0.7067 (mmmm)
REVERT: B  515 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8092 (ttmm)
REVERT: B  632 LEU cc_start: 0.7898 (mp) cc_final: 0.7641 (mp)
REVERT: A  355 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7970 (t80)
REVERT: A  416 ASP cc_start: 0.7692 (m-30) cc_final: 0.7137 (p0)
REVERT: A  657 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7404 (pm20)
  outliers start: 17
  outliers final: 14
  residues processed: 109
  average time/residue: 0.8755
  time to fit residues: 105.8362
Evaluate side-chains
  110 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 105 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 110 optimal weight:   10.0000
   chunk 102 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.4371 r_free = 0.4371 target = 0.208284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.120177 restraints weight = 9711.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.03
r_work: 0.3271 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9196  Z= 0.272
  Angle     :  0.606  11.458  12470  Z= 0.315
  Chirality :  0.044   0.206   1464
  Planarity :  0.004   0.045   1584
  Dihedral  :  4.197  20.979   1268
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 22.25 %
    Favored  : 76.20 %
  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:  1.62 (0.25), residues: 1156
  helix:  1.84 (0.18), residues: 752
  sheet:  0.51 (0.88), residues: 36
  loop : -0.43 (0.36), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 284 
 HIS   0.003   0.001   HIS A 211 
 PHE   0.026   0.002   PHE B 210 
 TYR   0.020   0.001   TYR B 537 
 ARG   0.006   0.000   ARG A 221 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6948.35 seconds
wall clock time: 123 minutes 30.56 seconds (7410.56 seconds total)