Starting phenix.real_space_refine
on Wed Feb 12 00:56:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6s5t_10100/02_2025/6s5t_10100.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6s5t_10100/02_2025/6s5t_10100.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6s5t_10100/02_2025/6s5t_10100.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6s5t_10100/02_2025/6s5t_10100.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6s5t_10100/02_2025/6s5t_10100.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6s5t_10100/02_2025/6s5t_10100.cif"
  }
  resolution = 4.15
  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=   0.000 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      22      5.16       5
     C    4429      2.51       5
     N    1186      2.21       5
     O    1318      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6958
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 752, 5977
          Classifications: {'peptide': 752}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 31, 'TRANS': 720}
          Unresolved non-hydrogen bonds: 160
          Unresolved non-hydrogen angles: 193
          Unresolved non-hydrogen dihedrals: 129
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 104
    Chain: "B"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 950
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 2, 'TRANS': 141}
          Unresolved non-hydrogen bonds: 193
          Unresolved non-hydrogen angles: 243
          Unresolved non-hydrogen dihedrals: 153
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 148
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.39, per 1000 atoms: 0.63
  Number of scatterers: 6958
  At special positions: 0
  Unit cell: (101.76, 106.56, 86.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     P       3     15.00
     O    1318      8.00
     N    1186      7.00
     C    4429      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: 1.81
  Conformation dependent library (CDL) restraints added in 851.7 milliseconds
  

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 8 sheets defined
      58.9% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 135 through 158
    Processing helix  chain 'A' and resid 164 through 182
      removed outlier: 3.586A  pdb=" N   ILE A 168 " --> pdb=" O   PRO A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 206
      Proline residue:  A 197  - end of helix
      removed outlier: 3.794A  pdb=" N   SER A 204 " --> pdb=" O   THR A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 220
      removed outlier: 3.802A  pdb=" N   GLU A 218 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS A 219 " --> pdb=" O   GLU A 215 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 3.724A  pdb=" N   SER A 235 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 246
    Processing helix  chain 'A' and resid 251 through 261
      removed outlier: 3.566A  pdb=" N   LYS A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 269
      removed outlier: 3.556A  pdb=" N   LEU A 268 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE A 269 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 265 through 269'
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 303 through 311
    Processing helix  chain 'A' and resid 342 through 344
      No H-bonds generated for 'chain 'A' and resid 342 through 344'
    Processing helix  chain 'A' and resid 374 through 391
      removed outlier: 4.324A  pdb=" N   LEU A 378 " --> pdb=" O   PRO A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 396
      removed outlier: 3.826A  pdb=" N   LEU A 395 " --> pdb=" O   HIS A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 419
    Processing helix  chain 'A' and resid 420 through 422
      No H-bonds generated for 'chain 'A' and resid 420 through 422'
    Processing helix  chain 'A' and resid 424 through 432
      removed outlier: 3.677A  pdb=" N   ILE A 432 " --> pdb=" O   PHE A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 450
    Processing helix  chain 'A' and resid 459 through 481
      removed outlier: 3.555A  pdb=" N   LEU A 463 " --> pdb=" O   ASP A 459 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLU A 480 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 530
    Processing helix  chain 'A' and resid 550 through 553
    Processing helix  chain 'A' and resid 556 through 563
      removed outlier: 3.532A  pdb=" N   PHE A 563 " --> pdb=" O   THR A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 568
      removed outlier: 3.913A  pdb=" N   LEU A 567 " --> pdb=" O   PHE A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 576
      removed outlier: 3.690A  pdb=" N   PHE A 576 " --> pdb=" O   PRO A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 592
      removed outlier: 3.644A  pdb=" N   ARG A 592 " --> pdb=" O   GLY A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 623
      removed outlier: 3.918A  pdb=" N   TYR A 597 " --> pdb=" O   LEU A 593 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR A 602 " --> pdb=" O   LEU A 598 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE A 603 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A 608 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 654
      removed outlier: 3.645A  pdb=" N   GLU A 637 " --> pdb=" O   ALA A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 667
      removed outlier: 3.551A  pdb=" N   THR A 663 " --> pdb=" O   SER A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 682
    Processing helix  chain 'A' and resid 685 through 689
    Processing helix  chain 'A' and resid 690 through 702
    Processing helix  chain 'A' and resid 738 through 774
      removed outlier: 3.660A  pdb=" N   GLU A 742 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A 751 " --> pdb=" O   ALA A 747 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU A 758 " --> pdb=" O   GLY A 754 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A 763 " --> pdb=" O   ASP A 759 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS A 764 " --> pdb=" O   LYS A 760 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS A 771 " --> pdb=" O   GLU A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 793
      removed outlier: 3.656A  pdb=" N   ASP A 793 " --> pdb=" O   ALA A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 817
    Processing helix  chain 'A' and resid 826 through 846
      removed outlier: 3.632A  pdb=" N   ARG A 846 " --> pdb=" O   GLN A 842 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 20
    Processing helix  chain 'B' and resid 32 through 40
      removed outlier: 3.793A  pdb=" N   VAL B  36 " --> pdb=" O   GLU B  32 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ARG B  38 " --> pdb=" O   GLY B  34 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER B  39 " --> pdb=" O   THR B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 57
    Processing helix  chain 'B' and resid 65 through 77
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'B' and resid 102 through 113
      removed outlier: 3.502A  pdb=" N   LEU B 106 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 128
    Processing helix  chain 'B' and resid 139 through 146
    Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124
      removed outlier: 3.923A  pdb=" N   SER A 585 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 294
    Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350
      removed outlier: 7.022A  pdb=" N   LEU A 346 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   SER A 357 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ARG A 348 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   VAL A 442 " --> pdb=" O   LEU A 405 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 350
      removed outlier: 7.022A  pdb=" N   LEU A 346 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   SER A 357 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ARG A 348 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 482 through 483
    Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 29
    Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 101

    381 hydrogen bonds defined for protein.
    1080 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: 2.03

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2242
        1.34 -     1.46: 1722
        1.46 -     1.58: 3098
        1.58 -     1.70: 5
        1.70 -     1.82: 41
  Bond restraints: 7108
  Sorted by residual:
  bond pdb=" N3B ANP A 901 "
       pdb=" PG  ANP A 901 "
    ideal  model  delta    sigma   weight residual
    1.795  1.641  0.154 2.00e-02 2.50e+03 5.96e+01
  bond pdb=" O3A ANP A 901 "
       pdb=" PB  ANP A 901 "
    ideal  model  delta    sigma   weight residual
    1.700  1.604  0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" O5' ANP A 901 "
       pdb=" PA  ANP A 901 "
    ideal  model  delta    sigma   weight residual
    1.655  1.602  0.053 2.00e-02 2.50e+03 7.06e+00
  bond pdb=" C   TYR A 222 "
       pdb=" N   PRO A 223 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 8.40e-03 1.42e+04 6.44e+00
  bond pdb=" C   LEU A 117 "
       pdb=" N   PRO A 118 "
    ideal  model  delta    sigma   weight residual
    1.329  1.357 -0.028 1.18e-02 7.18e+03 5.65e+00
  ... (remaining 7103 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 8400
        2.14 -     4.28: 1144
        4.28 -     6.42: 91
        6.42 -     8.56: 10
        8.56 -    10.70: 1
  Bond angle restraints: 9646
  Sorted by residual:
  angle pdb=" CA  PHE A 269 "
        pdb=" CB  PHE A 269 "
        pdb=" CG  PHE A 269 "
      ideal   model   delta    sigma   weight residual
     113.80  118.84   -5.04 1.00e+00 1.00e+00 2.54e+01
  angle pdb=" C   THR A 654 "
        pdb=" CA  THR A 654 "
        pdb=" CB  THR A 654 "
      ideal   model   delta    sigma   weight residual
     109.02  116.89   -7.87 1.68e+00 3.54e-01 2.19e+01
  angle pdb=" CA  ASP A 542 "
        pdb=" CB  ASP A 542 "
        pdb=" CG  ASP A 542 "
      ideal   model   delta    sigma   weight residual
     112.60  117.26   -4.66 1.00e+00 1.00e+00 2.17e+01
  angle pdb=" C   THR A 451 "
        pdb=" CA  THR A 451 "
        pdb=" CB  THR A 451 "
      ideal   model   delta    sigma   weight residual
     110.19  116.95   -6.76 1.62e+00 3.81e-01 1.74e+01
  angle pdb=" C   ASP A 542 "
        pdb=" CA  ASP A 542 "
        pdb=" CB  ASP A 542 "
      ideal   model   delta    sigma   weight residual
     110.42  118.64   -8.22 1.99e+00 2.53e-01 1.71e+01
  ... (remaining 9641 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.54: 4124
       35.54 -    71.08: 154
       71.08 -   106.63: 5
      106.63 -   142.17: 0
      142.17 -   177.71: 1
  Dihedral angle restraints: 4284
    sinusoidal: 1649
      harmonic: 2635
  Sorted by residual:
  dihedral pdb=" O1B ANP A 901 "
           pdb=" N3B ANP A 901 "
           pdb=" PB  ANP A 901 "
           pdb=" PG  ANP A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15 -142.56  177.71     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CA  TYR A 222 "
           pdb=" C   TYR A 222 "
           pdb=" N   PRO A 223 "
           pdb=" CA  PRO A 223 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.03  -22.97     0      5.00e+00 4.00e-02 2.11e+01
  dihedral pdb=" C   THR A 654 "
           pdb=" N   THR A 654 "
           pdb=" CA  THR A 654 "
           pdb=" CB  THR A 654 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.28   11.28     0      2.50e+00 1.60e-01 2.03e+01
  ... (remaining 4281 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 681
       0.081 -    0.162: 307
       0.162 -    0.242: 90
       0.242 -    0.323: 11
       0.323 -    0.404: 2
  Chirality restraints: 1091
  Sorted by residual:
  chirality pdb=" CA  ASN A 271 "
            pdb=" N   ASN A 271 "
            pdb=" C   ASN A 271 "
            pdb=" CB  ASN A 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.08e+00
  chirality pdb=" CA  THR A 654 "
            pdb=" N   THR A 654 "
            pdb=" C   THR A 654 "
            pdb=" CB  THR A 654 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.15    0.37 2.00e-01 2.50e+01 3.50e+00
  chirality pdb=" CA  ASP A 542 "
            pdb=" N   ASP A 542 "
            pdb=" C   ASP A 542 "
            pdb=" CB  ASP A 542 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.31 2.00e-01 2.50e+01 2.33e+00
  ... (remaining 1088 not shown)

  Planarity restraints: 1236
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 606 "   -0.013 2.00e-02 2.50e+03   7.66e-03 1.17e+00
        pdb=" CG  TYR A 606 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 606 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 606 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 606 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 606 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 606 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 606 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 393 "    0.068 9.50e-02 1.11e+02   3.13e-02 1.07e+00
        pdb=" NE  ARG A 393 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 393 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 393 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 393 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 242 "    0.005 2.00e-02 2.50e+03   1.02e-02 1.04e+00
        pdb=" C   ILE A 242 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   ILE A 242 "    0.007 2.00e-02 2.50e+03
        pdb=" N   HIS A 243 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1233 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 2628
        2.94 -     3.43: 6963
        3.43 -     3.92: 11094
        3.92 -     4.41: 12009
        4.41 -     4.90: 19812
  Nonbonded interactions: 52506
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 350 "
            pdb=" OG1 THR A 353 "
     model   vdw
     2.450 3.040
  nonbonded pdb=" ND2 ASN A 470 "
            pdb=" O   ARG A 536 "
     model   vdw
     2.525 3.120
  nonbonded pdb=" NE2 GLN A 842 "
            pdb=" O   GLU B 115 "
     model   vdw
     2.525 3.120
  nonbonded pdb=" O   TRP A 845 "
            pdb=" N   GLU A 847 "
     model   vdw
     2.525 3.120
  nonbonded pdb=" O   GLU A 294 "
            pdb=" OG  SER A 297 "
     model   vdw
     2.526 3.040
  ... (remaining 52501 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  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:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     19.720
  Find NCS groups from input model:        0.060
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
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      :  0.007   0.154   7108  Z= 0.449
  Angle     :  1.477  10.703   9646  Z= 0.994
  Chirality :  0.094   0.404   1091
  Planarity :  0.003   0.031   1236
  Dihedral  : 17.703 177.709   2580
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  7.06 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 13.90 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.35 %
  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: -4.05 (0.22), residues: 892
  helix: -2.73 (0.17), residues: 498
  sheet: -0.64 (0.92), residues: 32
  loop : -2.63 (0.26), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 845 
 HIS   0.006   0.001   HIS A 800 
 PHE   0.017   0.002   PHE A 269 
 TYR   0.015   0.003   TYR A 606 
 ARG   0.012   0.001   ARG A 393 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A  117 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8357 (mp)
REVERT: A  218 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8752 (tp30)
REVERT: A  239 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8249 (mp)
REVERT: A  245 TYR cc_start: 0.8840 (m-80) cc_final: 0.8597 (m-10)
REVERT: A  282 TYR cc_start: 0.9150 (m-80) cc_final: 0.8789 (m-10)
REVERT: A  339 TYR cc_start: 0.7710 (t80) cc_final: 0.7463 (t80)
REVERT: A  345 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7677 (mtp85)
REVERT: A  381 GLU cc_start: 0.8667 (tp30) cc_final: 0.8349 (tp30)
REVERT: A  461 GLU cc_start: 0.8142 (tt0) cc_final: 0.7532 (tm-30)
REVERT: A  480 GLU cc_start: 0.8583 (tp30) cc_final: 0.8093 (tm-30)
REVERT: A  490 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8698 (pt)
REVERT: A  640 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8217 (t0)
REVERT: A  682 MET cc_start: 0.9016 (mtt) cc_final: 0.8715 (mtm)
REVERT: A  732 TYR cc_start: 0.8997 (t80) cc_final: 0.8729 (t80)
REVERT: A  735 GLU cc_start: 0.9302 (pm20) cc_final: 0.8928 (pm20)
REVERT: A  771 LYS cc_start: 0.8429 (mttt) cc_final: 0.8006 (mtpp)
REVERT: A  817 TYR cc_start: 0.8676 (m-80) cc_final: 0.8471 (m-10)
REVERT: A  834 ARG cc_start: 0.8956 (mtp180) cc_final: 0.8747 (ttp-170)
REVERT: B   22 LYS cc_start: 0.8635 (mttt) cc_final: 0.7919 (mtmt)
REVERT: B   32 GLU cc_start: 0.8675 (pp20) cc_final: 0.7897 (mp0)
REVERT: B   68 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7938 (tm-30)
REVERT: B  115 GLU cc_start: 0.5243 (mt-10) cc_final: 0.4820 (mt-10)
  outliers start: 28
  outliers final: 8
  residues processed: 196
  average time/residue: 0.2097
  time to fit residues: 53.6195
Evaluate side-chains
  140 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 67 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
A 189 ASN
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 308 ASN
A 517 GLN
A 800 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.144380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.110128 restraints weight = 10347.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.110514 restraints weight = 10773.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.111742 restraints weight = 8901.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7108  Z= 0.310
  Angle     :  0.654   6.470   9646  Z= 0.345
  Chirality :  0.042   0.144   1091
  Planarity :  0.005   0.046   1236
  Dihedral  :  9.483 178.018   1001
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.53 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.26), residues: 892
  helix: -0.49 (0.22), residues: 497
  sheet: -0.29 (0.84), residues: 38
  loop : -1.91 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 845 
 HIS   0.003   0.001   HIS A 171 
 PHE   0.017   0.002   PHE A 292 
 TYR   0.018   0.002   TYR A 274 
 ARG   0.006   0.001   ARG A 394 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 ASP cc_start: 0.7714 (t0) cc_final: 0.7180 (t0)
REVERT: A  218 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8011 (tp30)
REVERT: A  245 TYR cc_start: 0.8326 (m-80) cc_final: 0.8096 (m-10)
REVERT: A  308 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8576 (m-40)
REVERT: A  414 GLU cc_start: 0.8575 (mp0) cc_final: 0.8358 (mp0)
REVERT: A  642 MET cc_start: 0.8940 (tpp) cc_final: 0.8656 (tpp)
REVERT: A  735 GLU cc_start: 0.8959 (pm20) cc_final: 0.8704 (pm20)
REVERT: A  771 LYS cc_start: 0.8814 (mttt) cc_final: 0.8297 (mtpt)
REVERT: B   22 LYS cc_start: 0.8601 (mttt) cc_final: 0.7906 (mtmt)
REVERT: B   25 ASP cc_start: 0.8477 (p0) cc_final: 0.8152 (p0)
REVERT: B   32 GLU cc_start: 0.8352 (pp20) cc_final: 0.7952 (mp0)
REVERT: B   73 MET cc_start: 0.9014 (tpp) cc_final: 0.8779 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2046
  time to fit residues: 43.4672
Evaluate side-chains
  114 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 21 optimal weight:    0.0870
   chunk 77 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 60 optimal weight:    0.6980
   chunk 88 optimal weight:   50.0000
   chunk 59 optimal weight:    4.9990
   overall best weight:    1.5362

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 472 HIS ** 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 = 0.3609 r_free = 0.3609 target = 0.148056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.116402 restraints weight = 10264.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.115722 restraints weight = 11186.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.117247 restraints weight = 10130.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7108  Z= 0.187
  Angle     :  0.540   6.619   9646  Z= 0.279
  Chirality :  0.040   0.149   1091
  Planarity :  0.004   0.048   1236
  Dihedral  :  8.786 175.718   1001
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.11 %
    Favored  : 97.75 %
  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: -0.63 (0.27), residues: 892
  helix:  0.44 (0.23), residues: 497
  sheet: -0.63 (0.85), residues: 33
  loop : -1.59 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 635 
 HIS   0.003   0.001   HIS A 472 
 PHE   0.016   0.002   PHE A 475 
 TYR   0.016   0.001   TYR A 147 
 ARG   0.003   0.000   ARG A 394 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 ASP cc_start: 0.7624 (t0) cc_final: 0.7105 (t0)
REVERT: A  218 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8101 (tp30)
REVERT: A  771 LYS cc_start: 0.8823 (mttt) cc_final: 0.8310 (mtpt)
REVERT: A  825 TYR cc_start: 0.8789 (m-80) cc_final: 0.8279 (m-10)
REVERT: B   22 LYS cc_start: 0.8547 (mttt) cc_final: 0.7898 (mtmt)
REVERT: B   25 ASP cc_start: 0.8208 (p0) cc_final: 0.7960 (p0)
REVERT: B   32 GLU cc_start: 0.8201 (pp20) cc_final: 0.7983 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1764
  time to fit residues: 37.9278
Evaluate side-chains
  123 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 84 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0030
   chunk 15 optimal weight:    0.9980
   chunk 24 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    3.9996

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

Flipped N/Q/H residues before XYZ refinement:
A 208 HIS
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 308 ASN
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 800 HIS
B 108 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.160441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.125515 restraints weight = 10890.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.124117 restraints weight = 9538.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.125811 restraints weight = 8231.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   7108  Z= 0.365
  Angle     :  0.659   8.949   9646  Z= 0.342
  Chirality :  0.044   0.142   1091
  Planarity :  0.005   0.053   1236
  Dihedral  :  9.136 175.634   1001
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  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: -0.55 (0.28), residues: 892
  helix:  0.59 (0.24), residues: 491
  sheet: -0.58 (0.88), residues: 33
  loop : -1.65 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 845 
 HIS   0.005   0.001   HIS A 280 
 PHE   0.020   0.002   PHE A 292 
 TYR   0.022   0.002   TYR A 274 
 ARG   0.005   0.000   ARG A 394 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.844 
Fit side-chains
REVERT: A  114 ASP cc_start: 0.7798 (t0) cc_final: 0.7220 (t0)
REVERT: A  682 MET cc_start: 0.8104 (mtm) cc_final: 0.7800 (ttm)
REVERT: A  771 LYS cc_start: 0.8917 (mttt) cc_final: 0.8416 (mtpt)
REVERT: A  825 TYR cc_start: 0.9040 (m-80) cc_final: 0.8576 (m-10)
REVERT: B   32 GLU cc_start: 0.8450 (pp20) cc_final: 0.8035 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1846
  time to fit residues: 37.0352
Evaluate side-chains
  110 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 88 optimal weight:   50.0000
   chunk 41 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 350 GLN
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 842 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.165143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.129217 restraints weight = 10656.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.129323 restraints weight = 8641.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.130814 restraints weight = 7449.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7108  Z= 0.267
  Angle     :  0.589   9.116   9646  Z= 0.303
  Chirality :  0.042   0.141   1091
  Planarity :  0.004   0.051   1236
  Dihedral  :  8.850 173.221   1001
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.28), residues: 892
  helix:  0.71 (0.24), residues: 493
  sheet: -0.14 (0.95), residues: 31
  loop : -1.53 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 845 
 HIS   0.003   0.001   HIS A 280 
 PHE   0.014   0.002   PHE A 292 
 TYR   0.022   0.002   TYR A 147 
 ARG   0.004   0.000   ARG A 262 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 ASP cc_start: 0.7756 (t0) cc_final: 0.7365 (t0)
REVERT: A  339 TYR cc_start: 0.7102 (t80) cc_final: 0.6836 (t80)
REVERT: A  549 ILE cc_start: 0.8489 (tp) cc_final: 0.8179 (tt)
REVERT: A  682 MET cc_start: 0.8012 (mtm) cc_final: 0.7723 (ttm)
REVERT: A  771 LYS cc_start: 0.8839 (mttt) cc_final: 0.8409 (mtpt)
REVERT: A  825 TYR cc_start: 0.8987 (m-80) cc_final: 0.8653 (m-10)
REVERT: B   25 ASP cc_start: 0.8329 (p0) cc_final: 0.8000 (p0)
REVERT: B  110 MET cc_start: 0.7988 (mmm) cc_final: 0.7588 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1799
  time to fit residues: 36.0291
Evaluate side-chains
  115 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 88 optimal weight:   40.0000
   chunk 38 optimal weight:    0.0980
   chunk 79 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0770
   chunk 80 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.4342

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

Flipped N/Q/H residues before XYZ refinement:
A 208 HIS
A 253 ASN
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.154883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.116970 restraints weight = 11280.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.116339 restraints weight = 11599.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.118900 restraints weight = 10317.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7108  Z= 0.186
  Angle     :  0.543   8.802   9646  Z= 0.278
  Chirality :  0.040   0.138   1091
  Planarity :  0.004   0.054   1236
  Dihedral  :  8.432 171.493   1001
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.97 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.28), residues: 892
  helix:  0.87 (0.24), residues: 499
  sheet: -0.26 (0.90), residues: 33
  loop : -1.34 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 635 
 HIS   0.002   0.000   HIS A 171 
 PHE   0.012   0.001   PHE A 475 
 TYR   0.029   0.001   TYR A 147 
 ARG   0.003   0.000   ARG A 262 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7747 (m-40)
REVERT: A  422 SER cc_start: 0.8384 (t) cc_final: 0.8068 (p)
REVERT: A  549 ILE cc_start: 0.8350 (tp) cc_final: 0.7979 (tt)
REVERT: A  590 LYS cc_start: 0.9067 (mttt) cc_final: 0.8662 (mttt)
REVERT: A  650 ILE cc_start: 0.8865 (mm) cc_final: 0.8577 (tt)
REVERT: A  682 MET cc_start: 0.7949 (mtm) cc_final: 0.7704 (ttm)
REVERT: A  771 LYS cc_start: 0.8719 (mttt) cc_final: 0.8290 (mtpt)
REVERT: B   25 ASP cc_start: 0.8158 (p0) cc_final: 0.7846 (p0)
REVERT: B   37 MET cc_start: 0.8730 (mmm) cc_final: 0.8522 (mmp)
REVERT: B  110 MET cc_start: 0.7891 (mmm) cc_final: 0.7611 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1744
  time to fit residues: 37.4344
Evaluate side-chains
  121 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 63 optimal weight:    9.9990
   chunk 87 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 88 optimal weight:   50.0000
   chunk 3 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 208 HIS
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.147008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.110258 restraints weight = 11037.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.109649 restraints weight = 11137.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.111425 restraints weight = 10586.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7108  Z= 0.419
  Angle     :  0.721  11.743   9646  Z= 0.368
  Chirality :  0.046   0.157   1091
  Planarity :  0.005   0.059   1236
  Dihedral  :  9.227 173.010   1001
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  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: -0.33 (0.28), residues: 892
  helix:  0.64 (0.23), residues: 494
  sheet: -0.32 (0.96), residues: 33
  loop : -1.38 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 845 
 HIS   0.005   0.001   HIS A 280 
 PHE   0.030   0.002   PHE A 261 
 TYR   0.030   0.003   TYR A 147 
 ARG   0.006   0.001   ARG A 232 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.783 
Fit side-chains
REVERT: A  682 MET cc_start: 0.8180 (mtm) cc_final: 0.7863 (ttm)
REVERT: A  771 LYS cc_start: 0.8882 (mttt) cc_final: 0.8373 (mtpt)
REVERT: B   25 ASP cc_start: 0.8411 (p0) cc_final: 0.8163 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1728
  time to fit residues: 32.0757
Evaluate side-chains
  106 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 2 optimal weight:    0.0980
   chunk 4 optimal weight:    4.9990
   chunk 63 optimal weight:    0.2980
   chunk 37 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0020
   chunk 76 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
A 534 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.159586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.124596 restraints weight = 11183.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.121933 restraints weight = 12488.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.123128 restraints weight = 11697.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.4107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7108  Z= 0.154
  Angle     :  0.567   9.718   9646  Z= 0.282
  Chirality :  0.039   0.165   1091
  Planarity :  0.004   0.053   1236
  Dihedral  :  8.193 170.171   1001
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.56 %
    Favored  : 99.30 %
  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:  0.03 (0.29), residues: 892
  helix:  0.84 (0.24), residues: 502
  sheet: -0.19 (0.91), residues: 33
  loop : -1.09 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 635 
 HIS   0.005   0.001   HIS A 302 
 PHE   0.014   0.001   PHE A 475 
 TYR   0.020   0.001   TYR A 387 
 ARG   0.004   0.000   ARG A 262 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 GLU cc_start: 0.8652 (tt0) cc_final: 0.8406 (tt0)
REVERT: A  245 TYR cc_start: 0.8312 (m-80) cc_final: 0.7299 (m-10)
REVERT: A  422 SER cc_start: 0.8367 (t) cc_final: 0.7817 (p)
REVERT: A  517 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7738 (mm-40)
REVERT: A  534 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8254 (t0)
REVERT: A  590 LYS cc_start: 0.9016 (mttt) cc_final: 0.8662 (mttt)
REVERT: A  771 LYS cc_start: 0.8692 (mttt) cc_final: 0.8212 (mtpt)
REVERT: B   25 ASP cc_start: 0.8073 (p0) cc_final: 0.7837 (p0)
REVERT: B   37 MET cc_start: 0.8551 (mmm) cc_final: 0.8328 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1665
  time to fit residues: 36.5241
Evaluate side-chains
  123 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 86 optimal weight:    9.9990
   chunk 22 optimal weight:    8.9990
   chunk 87 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 56 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 208 HIS
A 472 HIS
** A 842 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 = 0.3682 r_free = 0.3682 target = 0.154599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.119713 restraints weight = 11027.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.117560 restraints weight = 11596.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.118653 restraints weight = 12157.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.4072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7108  Z= 0.223
  Angle     :  0.591  10.917   9646  Z= 0.299
  Chirality :  0.041   0.166   1091
  Planarity :  0.004   0.056   1236
  Dihedral  :  8.331 171.720   1001
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  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:  0.01 (0.28), residues: 892
  helix:  0.92 (0.23), residues: 500
  sheet: -0.11 (0.93), residues: 33
  loop : -1.27 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 526 
 HIS   0.002   0.001   HIS A 243 
 PHE   0.022   0.002   PHE A 675 
 TYR   0.016   0.001   TYR A 147 
 ARG   0.004   0.000   ARG A 262 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 TYR cc_start: 0.8390 (m-80) cc_final: 0.7289 (m-10)
REVERT: A  422 SER cc_start: 0.8273 (t) cc_final: 0.7953 (p)
REVERT: A  549 ILE cc_start: 0.8414 (tp) cc_final: 0.8078 (tt)
REVERT: A  650 ILE cc_start: 0.8780 (mm) cc_final: 0.8489 (tt)
REVERT: A  682 MET cc_start: 0.7825 (mtm) cc_final: 0.7601 (ttm)
REVERT: A  771 LYS cc_start: 0.8840 (mttt) cc_final: 0.8365 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1932
  time to fit residues: 39.3102
Evaluate side-chains
  122 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0370
   chunk 3 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    2.8064

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

Flipped N/Q/H residues before XYZ refinement:
A 208 HIS
A 842 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.155375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.120192 restraints weight = 11154.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.117586 restraints weight = 11112.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.118870 restraints weight = 12012.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.4055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7108  Z= 0.286
  Angle     :  0.649  11.429   9646  Z= 0.328
  Chirality :  0.043   0.150   1091
  Planarity :  0.004   0.054   1236
  Dihedral  :  8.556 172.290   1001
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.28 %
    Favored  : 99.58 %
  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: -0.08 (0.28), residues: 892
  helix:  0.87 (0.23), residues: 499
  sheet: -0.10 (0.95), residues: 33
  loop : -1.34 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 845 
 HIS   0.002   0.001   HIS A 472 
 PHE   0.020   0.002   PHE A 261 
 TYR   0.022   0.002   TYR A 147 
 ARG   0.004   0.000   ARG A 262 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 TYR cc_start: 0.8528 (m-80) cc_final: 0.7589 (m-10)
REVERT: A  549 ILE cc_start: 0.8494 (tp) cc_final: 0.8010 (tt)
REVERT: A  650 ILE cc_start: 0.8994 (mm) cc_final: 0.8597 (tt)
REVERT: A  682 MET cc_start: 0.7854 (mtm) cc_final: 0.7621 (ttm)
REVERT: A  771 LYS cc_start: 0.8911 (mttt) cc_final: 0.8381 (mtpt)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1733
  time to fit residues: 33.5812
Evaluate side-chains
  118 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 82 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 75 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 208 HIS
A 842 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.158807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.122856 restraints weight = 10992.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.120779 restraints weight = 10748.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.122322 restraints weight = 11402.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7108  Z= 0.162
  Angle     :  0.571  10.733   9646  Z= 0.283
  Chirality :  0.039   0.145   1091
  Planarity :  0.004   0.055   1236
  Dihedral  :  8.058 170.452   1001
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.42 %
    Favored  : 99.44 %
  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:  0.36 (0.29), residues: 892
  helix:  1.22 (0.24), residues: 495
  sheet:  0.11 (0.93), residues: 33
  loop : -1.12 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 845 
 HIS   0.004   0.001   HIS A 302 
 PHE   0.012   0.001   PHE A 428 
 TYR   0.018   0.001   TYR A 387 
 ARG   0.004   0.000   ARG A 262 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1997.20 seconds
wall clock time: 36 minutes 58.01 seconds (2218.01 seconds total)