Starting phenix.real_space_refine
on Wed Sep 17 14:13:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pro_13609/09_2025/7pro_13609.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pro_13609/09_2025/7pro_13609.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pro_13609/09_2025/7pro_13609.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pro_13609/09_2025/7pro_13609.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pro_13609/09_2025/7pro_13609.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pro_13609/09_2025/7pro_13609.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=  -0.000 sd=   0.152
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.81, per 1000 atoms: 0.42
  Number of scatterers: 9032
  At special positions: 0
  Unit cell: (117.312, 85.696, 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: 0.89
  Conformation dependent library (CDL) restraints added in 348.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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:
      44 helices and 4 sheets defined
      67.3% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 103
      removed outlier: 4.083A  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 159 through 205
      removed outlier: 3.538A  pdb=" N   GLN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 3.765A  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: 3.721A  pdb=" N   ALA A 264 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR A 286 " --> pdb=" O   THR A 282 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LYS A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 3.666A  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: 3.530A  pdb=" N   SER A 336 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LYS A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 392
      removed outlier: 3.752A  pdb=" N   LEU A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A 381 " --> pdb=" O   VAL A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 395
      No H-bonds generated for 'chain 'A' and resid 393 through 395'
    Processing helix  chain 'A' and resid 396 through 417
      removed outlier: 4.723A  pdb=" N   TYR A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   ARG A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ARG A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A 414 " --> pdb=" O   ASP A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 488
      removed outlier: 4.565A  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 530 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 569
      removed outlier: 4.162A  pdb=" N   GLN A 568 " --> pdb=" O   HIS A 565 " (cutoff:3.500A)
    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 665
    Processing helix  chain 'A' and resid 670 through 674
      removed outlier: 4.186A  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 159 through 205
      removed outlier: 3.539A  pdb=" N   GLN B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 3.764A  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: 3.721A  pdb=" N   ALA B 264 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR B 286 " --> pdb=" O   THR B 282 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LYS B 287 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
      removed outlier: 3.666A  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: 3.529A  pdb=" N   SER B 336 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LYS B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 392
      removed outlier: 3.753A  pdb=" N   LEU B 380 " --> pdb=" O   SER B 376 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL B 381 " --> pdb=" O   VAL B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 395
      No H-bonds generated for 'chain 'B' and resid 393 through 395'
    Processing helix  chain 'B' and resid 396 through 417
      removed outlier: 4.724A  pdb=" N   TYR B 401 " --> pdb=" O   LEU B 397 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   ARG B 402 " --> pdb=" O   GLY B 398 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ARG B 405 " --> pdb=" O   TYR B 401 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU B 414 " --> pdb=" O   ASP B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 488
      removed outlier: 4.565A  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 530 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 569
      removed outlier: 4.161A  pdb=" N   GLN B 568 " --> pdb=" O   HIS B 565 " (cutoff:3.500A)
    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 665
    Processing helix  chain 'B' and resid 670 through 674
      removed outlier: 4.187A  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 464
      removed outlier: 4.660A  pdb=" N   VAL A 446 " --> pdb=" O   ASN A 459 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   SER A 461 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   GLU A 444 " --> pdb=" O   SER A 461 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   THR A 463 " --> pdb=" O   ARG A 442 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ARG A 442 " --> pdb=" O   THR A 463 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   VAL A 446 " --> pdb=" O   GLN A 495 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   GLN A 495 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519
      removed outlier: 6.566A  pdb=" N   GLY A 518 " --> pdb=" O   PHE A 600 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   LYS A 469 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   ILE A 648 " --> pdb=" O   LYS A 469 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   ALA A 471 " --> pdb=" O   ILE A 648 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   LEU A 650 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   VAL A 473 " --> pdb=" O   LEU A 650 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   GLU A 657 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 457 through 464
      removed outlier: 4.660A  pdb=" N   VAL B 446 " --> pdb=" O   ASN B 459 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   SER B 461 " --> pdb=" O   GLU B 444 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   GLU B 444 " --> pdb=" O   SER B 461 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   THR B 463 " --> pdb=" O   ARG B 442 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ARG B 442 " --> pdb=" O   THR B 463 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   VAL B 446 " --> pdb=" O   GLN B 495 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   GLN B 495 " --> pdb=" O   VAL B 446 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 517 through 519
      removed outlier: 6.566A  pdb=" N   GLY B 518 " --> pdb=" O   PHE B 600 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LYS B 469 " --> pdb=" O   LEU B 646 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   ILE B 648 " --> pdb=" O   LYS B 469 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   ALA B 471 " --> pdb=" O   ILE B 648 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   LEU B 650 " --> pdb=" O   ALA B 471 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL B 473 " --> pdb=" O   LEU B 650 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   GLU B 657 " --> pdb=" O   VAL B 649 " (cutoff:3.500A)

    600 hydrogen bonds defined for protein.
    1782 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.16 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: 2519
        1.33 -     1.45: 1459
        1.45 -     1.57: 5174
        1.57 -     1.69: 0
        1.69 -     1.80: 44
  Bond restraints: 9196
  Sorted by residual:
  bond pdb=" CG  LEU B 390 "
       pdb=" CD1 LEU B 390 "
    ideal  model  delta    sigma   weight residual
    1.521  1.398  0.123 3.30e-02 9.18e+02 1.39e+01
  bond pdb=" CG  LEU A 390 "
       pdb=" CD1 LEU A 390 "
    ideal  model  delta    sigma   weight residual
    1.521  1.399  0.122 3.30e-02 9.18e+02 1.38e+01
  bond pdb=" C   SER B 156 "
       pdb=" N   ALA B 157 "
    ideal  model  delta    sigma   weight residual
    1.332  1.296  0.036 1.40e-02 5.10e+03 6.63e+00
  bond pdb=" C   SER A 156 "
       pdb=" N   ALA A 157 "
    ideal  model  delta    sigma   weight residual
    1.332  1.297  0.035 1.40e-02 5.10e+03 6.38e+00
  bond pdb=" CB  ARG A 170 "
       pdb=" CG  ARG A 170 "
    ideal  model  delta    sigma   weight residual
    1.520  1.453  0.067 3.00e-02 1.11e+03 5.04e+00
  ... (remaining 9191 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 12222
        3.20 -     6.40: 216
        6.40 -     9.60: 28
        9.60 -    12.80: 2
       12.80 -    16.00: 2
  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  122.96   -9.36 1.90e+00 2.77e-01 2.43e+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  122.95   -9.35 1.90e+00 2.77e-01 2.42e+01
  angle pdb=" C   LYS B 625 "
        pdb=" N   GLU B 626 "
        pdb=" CA  GLU B 626 "
      ideal   model   delta    sigma   weight residual
     122.40  129.10   -6.70 1.45e+00 4.76e-01 2.13e+01
  angle pdb=" C   LYS A 625 "
        pdb=" N   GLU A 626 "
        pdb=" CA  GLU A 626 "
      ideal   model   delta    sigma   weight residual
     122.40  129.10   -6.70 1.45e+00 4.76e-01 2.13e+01
  angle pdb=" CA  LEU A 586 "
        pdb=" CB  LEU A 586 "
        pdb=" CG  LEU A 586 "
      ideal   model   delta    sigma   weight residual
     116.30  132.30  -16.00 3.50e+00 8.16e-02 2.09e+01
  ... (remaining 12465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 5041
       17.79 -    35.58: 383
       35.58 -    53.36: 70
       53.36 -    71.15: 10
       71.15 -    88.94: 12
  Dihedral angle restraints: 5516
    sinusoidal: 2156
      harmonic: 3360
  Sorted by residual:
  dihedral pdb=" CA  MET A 665 "
           pdb=" C   MET A 665 "
           pdb=" N   GLU A 666 "
           pdb=" CA  GLU A 666 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.44   22.56     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  MET B 665 "
           pdb=" C   MET B 665 "
           pdb=" N   GLU B 666 "
           pdb=" CA  GLU B 666 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.45   22.55     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  SER B 156 "
           pdb=" C   SER B 156 "
           pdb=" N   ALA B 157 "
           pdb=" CA  ALA B 157 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.13   19.87     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 887
       0.052 -    0.105: 448
       0.105 -    0.157: 106
       0.157 -    0.209: 20
       0.209 -    0.261: 3
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CB  VAL A 155 "
            pdb=" CA  VAL A 155 "
            pdb=" CG1 VAL A 155 "
            pdb=" CG2 VAL A 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  VAL B 155 "
            pdb=" CA  VAL B 155 "
            pdb=" CG1 VAL B 155 "
            pdb=" CG2 VAL B 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  ASP B 108 "
            pdb=" N   ASP B 108 "
            pdb=" C   ASP B 108 "
            pdb=" CB  ASP B 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1461 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 405 "    0.013 2.00e-02 2.50e+03   2.58e-02 6.67e+00
        pdb=" C   ARG B 405 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ARG B 405 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLN B 406 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 405 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.61e+00
        pdb=" C   ARG A 405 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ARG A 405 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLN A 406 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 138 "    0.091 9.50e-02 1.11e+02   4.60e-02 6.54e+00
        pdb=" NE  ARG B 138 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 138 "   -0.042 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 138 "    0.012 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 138 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1020
        2.73 -     3.28: 9288
        3.28 -     3.82: 15229
        3.82 -     4.36: 18021
        4.36 -     4.90: 31384
  Nonbonded interactions: 74942
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 537 "
            pdb=" OE2 GLU B 322 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OE2 GLU A 322 "
            pdb=" OH  TYR B 537 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   GLY B 566 "
            pdb=" OG1 THR B 569 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   GLY A 566 "
            pdb=" OG1 THR A 569 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   LEU B 586 "
            pdb=" OG  SER B 589 "
     model   vdw
     2.342 3.040
  ... (remaining 74937 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: 0.02
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:             2.670
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.790
  Find NCS groups from input model:        0.070
  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:6.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
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      :  0.012   0.123   9196  Z= 0.488
  Angle     :  1.092  15.996  12470  Z= 0.610
  Chirality :  0.062   0.261   1464
  Planarity :  0.009   0.052   1584
  Dihedral  : 13.800  88.940   3352
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.23), residues: 1156
  helix: -0.49 (0.17), residues: 754
  sheet: -1.95 (0.58), residues: 58
  loop : -2.05 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.041   0.006   ARG B 138 
 TYR   0.044   0.004   TYR B 315 
 PHE   0.040   0.004   PHE B 137 
 TRP   0.042   0.004   TRP A 284 
 HIS   0.010   0.002   HIS B 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.01193 ( 9196)
  covalent geometry    : angle       1.09164 (12470)
  hydrogen bonds       : bond        0.15845 (  600)
  hydrogen bonds       : angle       6.45543 ( 1782)

*********************** 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
  119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 SER cc_start: 0.7648 (m) cc_final: 0.7418 (m)
REVERT: A  568 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8127 (mp10)
REVERT: A  585 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.6480 (tpp80)
REVERT: A  617 MET cc_start: 0.7925 (tpt) cc_final: 0.7575 (tpp)
REVERT: B  400 VAL cc_start: 0.8584 (t) cc_final: 0.8348 (p)
REVERT: B  516 SER cc_start: 0.7892 (m) cc_final: 0.7328 (p)
REVERT: B  645 ASP cc_start: 0.7077 (t0) cc_final: 0.6851 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.5408
  time to fit residues: 69.3365
Evaluate side-chains
  93 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:   20.0000
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
A 317 ASN
A 384 ASN
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 ASN
B 317 ASN
B 384 ASN
B 495 GLN
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.216759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.143420 restraints weight = 9591.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.85
r_work: 0.3204 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.1287

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= 0.154
  Angle     :  0.637   7.147  12470  Z= 0.337
  Chirality :  0.044   0.147   1464
  Planarity :  0.004   0.034   1584
  Dihedral  :  4.948  20.185   1266
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  8.73 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.24), residues: 1156
  helix:  0.81 (0.18), residues: 744
  sheet: -1.57 (0.59), residues: 58
  loop : -1.64 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 536 
 TYR   0.023   0.002   TYR B 315 
 PHE   0.020   0.002   PHE A 388 
 TRP   0.026   0.002   TRP A 284 
 HIS   0.007   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9196)
  covalent geometry    : angle       0.63718 (12470)
  hydrogen bonds       : bond        0.05230 (  600)
  hydrogen bonds       : angle       4.50826 ( 1782)

*********************** 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 to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A  311 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7350 (mp0)
REVERT: A  568 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7719 (mp10)
REVERT: A  585 ARG cc_start: 0.6504 (mtt-85) cc_final: 0.6208 (tpp80)
REVERT: A  617 MET cc_start: 0.8231 (tpt) cc_final: 0.7816 (tpp)
REVERT: B  147 ASP cc_start: 0.7244 (t0) cc_final: 0.6800 (p0)
REVERT: B  301 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7572 (m)
REVERT: B  424 ILE cc_start: 0.7895 (mm) cc_final: 0.7604 (mp)
REVERT: B  516 SER cc_start: 0.7837 (m) cc_final: 0.7384 (p)
REVERT: B  617 MET cc_start: 0.7952 (tpt) cc_final: 0.7636 (tpp)
REVERT: B  645 ASP cc_start: 0.6830 (t0) cc_final: 0.6517 (t0)
  outliers start: 16
  outliers final: 7
  residues processed: 116
  average time/residue: 0.4035
  time to fit residues: 51.7264
Evaluate side-chains
  105 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  519 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 56 optimal weight:   20.0000
   chunk 8 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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**
** B 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 = 0.4427 r_free = 0.4427 target = 0.213674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.139038 restraints weight = 9555.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.83
r_work: 0.3546 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3410 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9196  Z= 0.207
  Angle     :  0.634   6.766  12470  Z= 0.335
  Chirality :  0.045   0.147   1464
  Planarity :  0.004   0.035   1584
  Dihedral  :  4.788  20.810   1266
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.03 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.25), residues: 1156
  helix:  1.15 (0.18), residues: 746
  sheet: -1.71 (0.55), residues: 58
  loop : -1.39 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 138 
 TYR   0.020   0.002   TYR A 315 
 PHE   0.021   0.002   PHE A 388 
 TRP   0.020   0.002   TRP A 284 
 HIS   0.003   0.001   HIS B 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 9196)
  covalent geometry    : angle       0.63437 (12470)
  hydrogen bonds       : bond        0.05326 (  600)
  hydrogen bonds       : angle       4.39952 ( 1782)

*********************** 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
  114 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 ASP cc_start: 0.7258 (t0) cc_final: 0.6858 (p0)
REVERT: A  311 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7505 (mp0)
REVERT: A  492 ASP cc_start: 0.7512 (m-30) cc_final: 0.7242 (m-30)
REVERT: A  516 SER cc_start: 0.7709 (m) cc_final: 0.7317 (p)
REVERT: A  568 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7955 (mp10)
REVERT: A  600 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.6587 (m-80)
REVERT: A  617 MET cc_start: 0.8201 (tpt) cc_final: 0.7802 (tpp)
REVERT: B  147 ASP cc_start: 0.7273 (t0) cc_final: 0.6891 (p0)
REVERT: B  516 SER cc_start: 0.7928 (m) cc_final: 0.7472 (p)
REVERT: B  568 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7795 (mp10)
REVERT: B  600 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6772 (m-80)
REVERT: B  645 ASP cc_start: 0.6877 (t0) cc_final: 0.6568 (t0)
  outliers start: 19
  outliers final: 11
  residues processed: 106
  average time/residue: 0.4537
  time to fit residues: 52.5786
Evaluate side-chains
  106 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  205 ASN
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  205 ASN
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  600 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 94 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 113 optimal weight:   10.0000
   chunk 90 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0270
   chunk 65 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9242

-------------------------------------------------------------------------------
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**
B 495 GLN
** B 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 = 0.4454 r_free = 0.4454 target = 0.216744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.142650 restraints weight = 9673.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 1.86
r_work: 0.3648 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9196  Z= 0.141
  Angle     :  0.568   6.805  12470  Z= 0.298
  Chirality :  0.042   0.143   1464
  Planarity :  0.003   0.035   1584
  Dihedral  :  4.505  21.033   1266
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.28 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.25), residues: 1156
  helix:  1.56 (0.19), residues: 746
  sheet: -1.65 (0.54), residues: 58
  loop : -1.24 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 585 
 TYR   0.014   0.001   TYR A 315 
 PHE   0.021   0.002   PHE B 388 
 TRP   0.018   0.002   TRP A 284 
 HIS   0.004   0.001   HIS B 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9196)
  covalent geometry    : angle       0.56788 (12470)
  hydrogen bonds       : bond        0.04629 (  600)
  hydrogen bonds       : angle       4.18061 ( 1782)

*********************** 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
  119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 ASP cc_start: 0.7302 (t0) cc_final: 0.6920 (p0)
REVERT: A  215 GLN cc_start: 0.7256 (tp-100) cc_final: 0.6297 (mp-120)
REVERT: A  301 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7831 (m)
REVERT: A  311 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7586 (mp0)
REVERT: A  516 SER cc_start: 0.7839 (m) cc_final: 0.7435 (p)
REVERT: A  568 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7936 (mp10)
REVERT: A  600 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6725 (m-80)
REVERT: A  617 MET cc_start: 0.8126 (tpt) cc_final: 0.7739 (tpp)
REVERT: B  147 ASP cc_start: 0.7293 (t0) cc_final: 0.6928 (p0)
REVERT: B  301 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7743 (m)
REVERT: B  516 SER cc_start: 0.8083 (m) cc_final: 0.7617 (p)
REVERT: B  568 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7869 (mp10)
REVERT: B  577 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6252 (mmt)
REVERT: B  632 LEU cc_start: 0.7196 (mt) cc_final: 0.6866 (tp)
REVERT: B  645 ASP cc_start: 0.6710 (t0) cc_final: 0.6395 (t0)
  outliers start: 23
  outliers final: 11
  residues processed: 109
  average time/residue: 0.4791
  time to fit residues: 56.8208
Evaluate side-chains
  108 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  424 ILE
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  577 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 55 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 58 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 108 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.8586

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.217605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.144001 restraints weight = 9617.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 1.85
r_work: 0.3603 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9196  Z= 0.136
  Angle     :  0.555   7.528  12470  Z= 0.290
  Chirality :  0.041   0.147   1464
  Planarity :  0.003   0.031   1584
  Dihedral  :  4.302  20.534   1266
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.22 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.25), residues: 1156
  helix:  1.80 (0.19), residues: 746
  sheet: -1.51 (0.54), residues: 58
  loop : -1.08 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 585 
 TYR   0.013   0.001   TYR A 232 
 PHE   0.021   0.002   PHE A 388 
 TRP   0.017   0.002   TRP A 284 
 HIS   0.003   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9196)
  covalent geometry    : angle       0.55495 (12470)
  hydrogen bonds       : bond        0.04517 (  600)
  hydrogen bonds       : angle       4.09219 ( 1782)

*********************** 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
  121 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 ASP cc_start: 0.7335 (t0) cc_final: 0.6949 (p0)
REVERT: A  301 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7648 (m)
REVERT: A  311 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7477 (mp0)
REVERT: A  516 SER cc_start: 0.7699 (m) cc_final: 0.7294 (p)
REVERT: A  568 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7863 (mp10)
REVERT: A  600 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6532 (m-80)
REVERT: A  617 MET cc_start: 0.8127 (tpt) cc_final: 0.7714 (tpp)
REVERT: B  147 ASP cc_start: 0.7329 (t0) cc_final: 0.6992 (p0)
REVERT: B  301 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7576 (m)
REVERT: B  516 SER cc_start: 0.7941 (m) cc_final: 0.7449 (p)
REVERT: B  568 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7791 (mp10)
REVERT: B  577 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6249 (mmt)
REVERT: B  617 MET cc_start: 0.7970 (tpt) cc_final: 0.7551 (tpp)
REVERT: B  645 ASP cc_start: 0.6610 (t0) cc_final: 0.6329 (t0)
  outliers start: 27
  outliers final: 14
  residues processed: 113
  average time/residue: 0.4471
  time to fit residues: 55.4553
Evaluate side-chains
  109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  205 ASN
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  205 ASN
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  424 ILE
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  577 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0270
   chunk 2 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 92 optimal weight:    8.9990
   chunk 30 optimal weight:    0.5980
   chunk 66 optimal weight:    0.7980
   chunk 96 optimal weight:    9.9990
   overall best weight:    0.8842

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.217403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.143922 restraints weight = 9616.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 1.85
r_work: 0.3604 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3471 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9196  Z= 0.137
  Angle     :  0.558   8.914  12470  Z= 0.290
  Chirality :  0.041   0.139   1464
  Planarity :  0.003   0.031   1584
  Dihedral  :  4.244  20.091   1266
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.11 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.25), residues: 1156
  helix:  1.91 (0.19), residues: 746
  sheet: -1.43 (0.55), residues: 58
  loop : -1.01 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 585 
 TYR   0.014   0.001   TYR B 232 
 PHE   0.018   0.001   PHE A 388 
 TRP   0.016   0.002   TRP A 284 
 HIS   0.003   0.001   HIS B 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9196)
  covalent geometry    : angle       0.55847 (12470)
  hydrogen bonds       : bond        0.04422 (  600)
  hydrogen bonds       : angle       4.04234 ( 1782)

*********************** 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
  117 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 ASP cc_start: 0.7420 (t0) cc_final: 0.7022 (p0)
REVERT: A  215 GLN cc_start: 0.7052 (tp40) cc_final: 0.6690 (tp40)
REVERT: A  301 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7623 (m)
REVERT: A  311 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7223 (mm-30)
REVERT: A  516 SER cc_start: 0.7771 (m) cc_final: 0.7347 (p)
REVERT: A  568 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7862 (mp10)
REVERT: A  600 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6552 (m-80)
REVERT: A  617 MET cc_start: 0.8091 (tpt) cc_final: 0.7666 (tpp)
REVERT: B  147 ASP cc_start: 0.7414 (t0) cc_final: 0.7039 (p0)
REVERT: B  301 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7561 (m)
REVERT: B  516 SER cc_start: 0.7953 (m) cc_final: 0.7448 (p)
REVERT: B  568 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7788 (mp10)
REVERT: B  577 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6250 (mmt)
REVERT: B  617 MET cc_start: 0.7935 (tpt) cc_final: 0.7580 (tpp)
REVERT: B  645 ASP cc_start: 0.6610 (t0) cc_final: 0.6366 (t0)
  outliers start: 26
  outliers final: 16
  residues processed: 110
  average time/residue: 0.4554
  time to fit residues: 54.8562
Evaluate side-chains
  112 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  205 ASN
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  205 ASN
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  424 ILE
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  577 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.217697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.143840 restraints weight = 9629.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 1.86
r_work: 0.3661 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3529 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2325

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= 0.137
  Angle     :  0.546   7.074  12470  Z= 0.286
  Chirality :  0.041   0.139   1464
  Planarity :  0.003   0.030   1584
  Dihedral  :  4.204  19.461   1266
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.22 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.25), residues: 1156
  helix:  1.98 (0.19), residues: 746
  sheet: -1.26 (0.56), residues: 58
  loop : -0.94 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 570 
 TYR   0.013   0.001   TYR B 232 
 PHE   0.017   0.001   PHE A 388 
 TRP   0.016   0.001   TRP A 284 
 HIS   0.004   0.001   HIS B 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9196)
  covalent geometry    : angle       0.54558 (12470)
  hydrogen bonds       : bond        0.04395 (  600)
  hydrogen bonds       : angle       4.01850 ( 1782)

*********************** 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
  119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  147 ASP cc_start: 0.7511 (t0) cc_final: 0.7097 (p0)
REVERT: A  215 GLN cc_start: 0.6991 (tp-100) cc_final: 0.6671 (tp40)
REVERT: A  301 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7659 (m)
REVERT: A  311 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7276 (mm-30)
REVERT: A  458 ARG cc_start: 0.7336 (ptp90) cc_final: 0.7136 (ptp90)
REVERT: A  516 SER cc_start: 0.7794 (m) cc_final: 0.7373 (p)
REVERT: A  568 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7877 (mp10)
REVERT: A  600 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6588 (m-80)
REVERT: A  617 MET cc_start: 0.8025 (tpt) cc_final: 0.7588 (tpp)
REVERT: B  147 ASP cc_start: 0.7510 (t0) cc_final: 0.7109 (p0)
REVERT: B  301 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7599 (m)
REVERT: B  516 SER cc_start: 0.7963 (m) cc_final: 0.7455 (p)
REVERT: B  568 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7819 (mp10)
REVERT: B  617 MET cc_start: 0.7928 (tpt) cc_final: 0.7550 (tpp)
REVERT: B  645 ASP cc_start: 0.6589 (t0) cc_final: 0.6309 (t0)
  outliers start: 26
  outliers final: 13
  residues processed: 113
  average time/residue: 0.4660
  time to fit residues: 57.4082
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  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  424 ILE
Chi-restraints excluded: chain B residue  519 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0670
   chunk 83 optimal weight:    0.9980
   chunk 114 optimal weight:   20.0000
   chunk 47 optimal weight:    0.8980
   chunk 91 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0000
   overall best weight:    0.4522

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
A 395 ASN
A 503 GLN
B 205 ASN
B 395 ASN
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.220345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.147440 restraints weight = 9526.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 1.83
r_work: 0.3651 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9196  Z= 0.115
  Angle     :  0.538  11.410  12470  Z= 0.277
  Chirality :  0.039   0.138   1464
  Planarity :  0.003   0.032   1584
  Dihedral  :  4.053  18.382   1266
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.36 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.25), residues: 1156
  helix:  2.18 (0.19), residues: 746
  sheet: -0.98 (0.60), residues: 58
  loop : -0.86 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 570 
 TYR   0.012   0.001   TYR A 232 
 PHE   0.018   0.001   PHE A 388 
 TRP   0.017   0.001   TRP A 284 
 HIS   0.004   0.001   HIS B 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9196)
  covalent geometry    : angle       0.53763 (12470)
  hydrogen bonds       : bond        0.04076 (  600)
  hydrogen bonds       : angle       3.91171 ( 1782)

*********************** 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
  115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  147 ASP cc_start: 0.7501 (t0) cc_final: 0.6986 (p0)
REVERT: A  215 GLN cc_start: 0.7013 (tp-100) cc_final: 0.6703 (tp40)
REVERT: A  301 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7422 (p)
REVERT: A  311 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7221 (mm-30)
REVERT: A  516 SER cc_start: 0.7742 (m) cc_final: 0.7339 (p)
REVERT: A  568 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7814 (mp10)
REVERT: A  600 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.6432 (m-80)
REVERT: A  617 MET cc_start: 0.7981 (tpt) cc_final: 0.7509 (tpp)
REVERT: B  147 ASP cc_start: 0.7504 (t0) cc_final: 0.7002 (p0)
REVERT: B  301 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7489 (m)
REVERT: B  516 SER cc_start: 0.7917 (m) cc_final: 0.7406 (p)
REVERT: B  568 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7763 (mp10)
REVERT: B  617 MET cc_start: 0.7879 (tpt) cc_final: 0.7493 (tpp)
REVERT: B  645 ASP cc_start: 0.6239 (t0) cc_final: 0.6012 (t0)
  outliers start: 20
  outliers final: 8
  residues processed: 110
  average time/residue: 0.4276
  time to fit residues: 51.8794
Evaluate side-chains
  107 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  424 ILE
Chi-restraints excluded: chain B residue  519 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 113 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0270
   chunk 87 optimal weight:    0.0980
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
A 552 GLN
B 205 ASN
B 503 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.219158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.145794 restraints weight = 9530.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 1.85
r_work: 0.3676 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2659

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= 0.126
  Angle     :  0.548   8.513  12470  Z= 0.283
  Chirality :  0.040   0.138   1464
  Planarity :  0.003   0.028   1584
  Dihedral  :  4.031  16.753   1266
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 18.09 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.25), residues: 1156
  helix:  2.19 (0.19), residues: 746
  sheet: -0.71 (0.63), residues: 58
  loop : -0.80 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 570 
 TYR   0.013   0.001   TYR B 232 
 PHE   0.016   0.001   PHE A 388 
 TRP   0.015   0.001   TRP A 284 
 HIS   0.004   0.001   HIS B 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9196)
  covalent geometry    : angle       0.54805 (12470)
  hydrogen bonds       : bond        0.04200 (  600)
  hydrogen bonds       : angle       3.93736 ( 1782)

*********************** 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
  112 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  147 ASP cc_start: 0.7531 (t0) cc_final: 0.6985 (p0)
REVERT: A  215 GLN cc_start: 0.7051 (tp-100) cc_final: 0.6754 (tp40)
REVERT: A  271 MET cc_start: 0.8603 (mmm) cc_final: 0.8267 (mmm)
REVERT: A  301 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7643 (m)
REVERT: A  311 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7304 (mm-30)
REVERT: A  516 SER cc_start: 0.7788 (m) cc_final: 0.7383 (p)
REVERT: A  568 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7925 (mp10)
REVERT: A  600 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6675 (m-80)
REVERT: A  617 MET cc_start: 0.7946 (tpt) cc_final: 0.7386 (tpp)
REVERT: B  147 ASP cc_start: 0.7534 (t0) cc_final: 0.6962 (p0)
REVERT: B  215 GLN cc_start: 0.7434 (tp-100) cc_final: 0.7178 (tp40)
REVERT: B  301 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7598 (m)
REVERT: B  516 SER cc_start: 0.8023 (m) cc_final: 0.7521 (p)
REVERT: B  568 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7844 (mp10)
REVERT: B  617 MET cc_start: 0.7820 (tpt) cc_final: 0.7438 (tpp)
  outliers start: 15
  outliers final: 9
  residues processed: 108
  average time/residue: 0.4453
  time to fit residues: 52.7519
Evaluate side-chains
  107 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  424 ILE
Chi-restraints excluded: chain B residue  519 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.4980
   chunk 106 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0170
   chunk 78 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 93 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7022

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
B 205 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.219184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.145786 restraints weight = 9534.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 1.86
r_work: 0.3675 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3542 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2715

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= 0.125
  Angle     :  0.544   7.419  12470  Z= 0.284
  Chirality :  0.040   0.138   1464
  Planarity :  0.003   0.029   1584
  Dihedral  :  4.029  15.739   1266
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 18.09 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.25), residues: 1156
  helix:  2.22 (0.19), residues: 746
  sheet: -0.48 (0.64), residues: 58
  loop : -0.69 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 570 
 TYR   0.013   0.001   TYR A 232 
 PHE   0.015   0.001   PHE A 388 
 TRP   0.016   0.001   TRP A 284 
 HIS   0.004   0.001   HIS B 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9196)
  covalent geometry    : angle       0.54383 (12470)
  hydrogen bonds       : bond        0.04159 (  600)
  hydrogen bonds       : angle       3.93069 ( 1782)

********************** 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
  104 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A  147 ASP cc_start: 0.7504 (t0) cc_final: 0.6929 (p0)
REVERT: A  215 GLN cc_start: 0.7018 (tp-100) cc_final: 0.6728 (tp40)
REVERT: A  301 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7628 (m)
REVERT: A  311 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7300 (mm-30)
REVERT: A  516 SER cc_start: 0.7772 (m) cc_final: 0.7372 (p)
REVERT: A  568 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7899 (mp10)
REVERT: A  600 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.6628 (m-80)
REVERT: A  617 MET cc_start: 0.7974 (tpt) cc_final: 0.7392 (tpp)
REVERT: B  147 ASP cc_start: 0.7503 (t0) cc_final: 0.6923 (p0)
REVERT: B  215 GLN cc_start: 0.7401 (tp-100) cc_final: 0.7146 (tp40)
REVERT: B  301 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7578 (m)
REVERT: B  516 SER cc_start: 0.8006 (m) cc_final: 0.7503 (p)
REVERT: B  568 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7805 (mp10)
REVERT: B  617 MET cc_start: 0.7876 (tpt) cc_final: 0.7471 (tpp)
  outliers start: 15
  outliers final: 10
  residues processed: 100
  average time/residue: 0.4448
  time to fit residues: 48.8897
Evaluate side-chains
  107 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  424 ILE
Chi-restraints excluded: chain B residue  519 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0270
   chunk 110 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 108 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7842

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
B 205 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.218997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.145528 restraints weight = 9472.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 1.85
r_work: 0.3688 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3557 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2768

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= 0.130
  Angle     :  0.548   9.566  12470  Z= 0.286
  Chirality :  0.040   0.137   1464
  Planarity :  0.003   0.028   1584
  Dihedral  :  4.020  15.467   1266
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.46 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.25), residues: 1156
  helix:  2.21 (0.19), residues: 744
  sheet: -0.35 (0.65), residues: 58
  loop : -0.67 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 570 
 TYR   0.013   0.001   TYR B 232 
 PHE   0.015   0.001   PHE A 388 
 TRP   0.015   0.001   TRP A 284 
 HIS   0.004   0.001   HIS B 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9196)
  covalent geometry    : angle       0.54845 (12470)
  hydrogen bonds       : bond        0.04220 (  600)
  hydrogen bonds       : angle       3.94648 ( 1782)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3646.50 seconds
wall clock time: 62 minutes 57.56 seconds (3777.56 seconds total)