Starting phenix.real_space_refine
on Fri Aug 22 20:31:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xos_22278/08_2025/6xos_22278.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xos_22278/08_2025/6xos_22278.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xos_22278/08_2025/6xos_22278.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xos_22278/08_2025/6xos_22278.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xos_22278/08_2025/6xos_22278.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xos_22278/08_2025/6xos_22278.map"
  }
  resolution = 3.7
  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=   0.001
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      39      5.16       5
     C    4901      2.51       5
     N    1305      2.21       5
     O    1459      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7704
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7704
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 966, 7698
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 966, 7698
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7882
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ASER A 723 " occ=0.42
      ... (10 atoms not shown)
      pdb=" OG BSER A 723 " occ=0.58
  Time building chain proxies: 3.22, per 1000 atoms: 0.42
  Number of scatterers: 7704
  At special positions: 0
  Unit cell: (82.176, 88.168, 95.016, 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      39     16.00
     O    1459      8.00
     N    1305      7.00
     C    4901      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: 0.60
  Conformation dependent library (CDL) restraints added in 345.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1826

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 7 sheets defined
      53.8% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 38
      removed outlier: 3.757A  pdb=" N   ARG A  36 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 61
    Processing helix  chain 'A' and resid 101 through 110
    Processing helix  chain 'A' and resid 111 through 113
      No H-bonds generated for 'chain 'A' and resid 111 through 113'
    Processing helix  chain 'A' and resid 121 through 127
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 200 through 210
    Processing helix  chain 'A' and resid 212 through 226
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.694A  pdb=" N   VAL A 233 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 245
      removed outlier: 3.536A  pdb=" N   GLU A 244 " --> pdb=" O   CYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 258
    Processing helix  chain 'A' and resid 259 through 261
      No H-bonds generated for 'chain 'A' and resid 259 through 261'
    Processing helix  chain 'A' and resid 272 through 284
      removed outlier: 3.916A  pdb=" N   HIS A 276 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 288
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 419
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 3.643A  pdb=" N   ILE A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 457
      removed outlier: 4.685A  pdb=" N   SER A 453 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   CYS A 454 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   HIS A 457 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 481
      removed outlier: 3.585A  pdb=" N   ASN A 481 " --> pdb=" O   CYS A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 509 through 527
    Processing helix  chain 'A' and resid 530 through 550
    Processing helix  chain 'A' and resid 561 through 565
    Processing helix  chain 'A' and resid 608 through 613
      removed outlier: 3.669A  pdb=" N   ARG A 612 " --> pdb=" O   GLU A 609 " (cutoff:3.500A)
      Proline residue:  A 613  - end of helix
    Processing helix  chain 'A' and resid 614 through 622
    Processing helix  chain 'A' and resid 631 through 642
    Processing helix  chain 'A' and resid 676 through 690
    Processing helix  chain 'A' and resid 695 through 713
      removed outlier: 3.618A  pdb=" N   PHE A 699 " --> pdb=" O   GLU A 695 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL A 701 " --> pdb=" O   GLU A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 727
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 742 through 755
      removed outlier: 3.743A  pdb=" N   VAL A 746 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 763
    Processing helix  chain 'A' and resid 763 through 773
      removed outlier: 4.229A  pdb=" N   ARG A 767 " --> pdb=" O   ARG A 763 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   HIS A 771 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 802
    Processing helix  chain 'A' and resid 878 through 894
      removed outlier: 4.407A  pdb=" N   SER A 882 " --> pdb=" O   PRO A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 901
    Processing helix  chain 'A' and resid 928 through 945
    Processing helix  chain 'A' and resid 948 through 964
    Processing helix  chain 'A' and resid 968 through 972
      removed outlier: 3.834A  pdb=" N   LYS A 972 " --> pdb=" O   PRO A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 979
      removed outlier: 3.987A  pdb=" N   PHE A 977 " --> pdb=" O   GLY A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 996
    Processing helix  chain 'A' and resid 997 through 1008
    Processing helix  chain 'A' and resid 1025 through 1030
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46
      removed outlier: 5.856A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 134 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 5.856A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 186
    Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313
      removed outlier: 3.516A  pdb=" N   CYS A 313 " --> pdb=" O   ARG A 505 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL A 328 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   GLN A 394 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   VAL A 330 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   GLY A 392 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   PHE A 332 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   SER A 390 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   TYR A 388 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP A 336 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   GLU A 386 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASP A 373 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 313
      removed outlier: 3.516A  pdb=" N   CYS A 313 " --> pdb=" O   ARG A 505 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL A 328 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   GLN A 394 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   VAL A 330 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   GLY A 392 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   PHE A 332 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   SER A 390 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   TYR A 388 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP A 336 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   GLU A 386 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 579
      removed outlier: 8.040A  pdb=" N   VAL A 782 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLN A 586 " --> pdb=" O   VAL A 782 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   ALA A 784 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 671 " --> pdb=" O   GLY A 645 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLY A 645 " --> pdb=" O   LEU A 671 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU A 673 " --> pdb=" O   THR A 643 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   THR A 643 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912
      removed outlier: 3.550A  pdb=" N   VAL A 866 " --> pdb=" O   SER A 922 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   ASN A 864 " --> pdb=" O   ARG A 924 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY A1022 " --> pdb=" O   PHE A 857 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LYS A 854 " --> pdb=" O   ILE A1035 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   ARG A1037 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   HIS A 856 " --> pdb=" O   ARG A1037 " (cutoff:3.500A)

    471 hydrogen bonds defined for protein.
    1342 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: 0.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2439
        1.34 -     1.46: 1434
        1.46 -     1.57: 3961
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 7896
  Sorted by residual:
  bond pdb=" CB  ASP A 165 "
       pdb=" CG  ASP A 165 "
    ideal  model  delta    sigma   weight residual
    1.516  1.461  0.055 2.50e-02 1.60e+03 4.81e+00
  bond pdb=" CG1 ILE A 432 "
       pdb=" CD1 ILE A 432 "
    ideal  model  delta    sigma   weight residual
    1.513  1.433  0.080 3.90e-02 6.57e+02 4.24e+00
  bond pdb=" CG  LEU A 736 "
       pdb=" CD2 LEU A 736 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.12e+00
  bond pdb=" CB  PRO A 103 "
       pdb=" CG  PRO A 103 "
    ideal  model  delta    sigma   weight residual
    1.492  1.405  0.087 5.00e-02 4.00e+02 3.03e+00
  bond pdb=" C   ILE A 242 "
       pdb=" N   PRO A 243 "
    ideal  model  delta    sigma   weight residual
    1.337  1.353 -0.017 9.80e-03 1.04e+04 2.94e+00
  ... (remaining 7891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 10074
        2.09 -     4.17: 542
        4.17 -     6.26: 69
        6.26 -     8.34: 18
        8.34 -    10.43: 5
  Bond angle restraints: 10708
  Sorted by residual:
  angle pdb=" C   ALA A 580 "
        pdb=" N   GLY A 581 "
        pdb=" CA  GLY A 581 "
      ideal   model   delta    sigma   weight residual
     121.70  128.48   -6.78 1.80e+00 3.09e-01 1.42e+01
  angle pdb=" CA  PRO A 243 "
        pdb=" N   PRO A 243 "
        pdb=" CD  PRO A 243 "
      ideal   model   delta    sigma   weight residual
     112.00  106.95    5.05 1.40e+00 5.10e-01 1.30e+01
  angle pdb=" N   GLY A 581 "
        pdb=" CA  GLY A 581 "
        pdb=" C   GLY A 581 "
      ideal   model   delta    sigma   weight residual
     113.30  103.20   10.10 2.90e+00 1.19e-01 1.21e+01
  angle pdb=" C   HIS A 229 "
        pdb=" N   THR A 230 "
        pdb=" CA  THR A 230 "
      ideal   model   delta    sigma   weight residual
     120.63  126.16   -5.53 1.61e+00 3.86e-01 1.18e+01
  angle pdb=" C   ASP A 339 "
        pdb=" N   THR A 340 "
        pdb=" CA  THR A 340 "
      ideal   model   delta    sigma   weight residual
     120.54  124.96   -4.42 1.35e+00 5.49e-01 1.07e+01
  ... (remaining 10703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 4425
       17.76 -    35.52: 263
       35.52 -    53.28: 61
       53.28 -    71.04: 17
       71.04 -    88.80: 9
  Dihedral angle restraints: 4775
    sinusoidal: 1953
      harmonic: 2822
  Sorted by residual:
  dihedral pdb=" CA  PRO A 170 "
           pdb=" C   PRO A 170 "
           pdb=" N   CYS A 171 "
           pdb=" CA  CYS A 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.88   25.12     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  PHE A 210 "
           pdb=" C   PHE A 210 "
           pdb=" N   THR A 211 "
           pdb=" CA  THR A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.36   21.64     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" C   ILE A 242 "
           pdb=" N   ILE A 242 "
           pdb=" CA  ILE A 242 "
           pdb=" CB  ILE A 242 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.59    9.59     0      2.50e+00 1.60e-01 1.47e+01
  ... (remaining 4772 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 731
       0.053 -    0.106: 330
       0.106 -    0.159: 85
       0.159 -    0.212: 21
       0.212 -    0.265: 7
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CB  ILE A 242 "
            pdb=" CA  ILE A 242 "
            pdb=" CG1 ILE A 242 "
            pdb=" CG2 ILE A 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CG  LEU A 895 "
            pdb=" CB  LEU A 895 "
            pdb=" CD1 LEU A 895 "
            pdb=" CD2 LEU A 895 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CB  VAL A1004 "
            pdb=" CA  VAL A1004 "
            pdb=" CG1 VAL A1004 "
            pdb=" CG2 VAL A1004 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.66e+00
  ... (remaining 1171 not shown)

  Planarity restraints: 1398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 899 "    0.018 2.00e-02 2.50e+03   3.50e-02 1.23e+01
        pdb=" C   ILE A 899 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   ILE A 899 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ARG A 900 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A  34 "    0.014 2.00e-02 2.50e+03   2.78e-02 7.71e+00
        pdb=" C   CYS A  34 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   CYS A  34 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLU A  35 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 896 "    0.013 2.00e-02 2.50e+03   2.70e-02 7.27e+00
        pdb=" C   HIS A 896 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   HIS A 896 "    0.017 2.00e-02 2.50e+03
        pdb=" N   THR A 897 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1395 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1339
        2.76 -     3.30: 7122
        3.30 -     3.83: 12843
        3.83 -     4.37: 14940
        4.37 -     4.90: 26004
  Nonbonded interactions: 62248
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A  98 "
            pdb=" OG1 THR A 100 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OE1 GLN A 737 "
            pdb=" OG  SER A 741 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   SER A 190 "
            pdb=" OH  TYR A 538 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   SER A 351 "
            pdb=" OG  SER A 355 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" NH2 ARG A  36 "
            pdb=" O   ASN A 270 "
     model   vdw
     2.374 3.120
  ... (remaining 62243 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.42 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:             1.510
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.300
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.087   7896  Z= 0.377
  Angle     :  1.086  10.429  10708  Z= 0.593
  Chirality :  0.065   0.265   1174
  Planarity :  0.007   0.053   1398
  Dihedral  : 13.213  88.800   2949
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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: -1.45 (0.24), residues: 965
  helix: -1.12 (0.20), residues: 462
  sheet:  0.49 (0.36), residues: 174
  loop : -1.27 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  81 
 TYR   0.026   0.004   TYR A 258 
 PHE   0.026   0.003   PHE A 389 
 TRP   0.021   0.003   TRP A 303 
 HIS   0.011   0.003   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00877 ( 7896)
  covalent geometry    : angle       1.08593 (10708)
  hydrogen bonds       : bond        0.16655 (  429)
  hydrogen bonds       : angle       6.87265 ( 1342)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 ARG cc_start: 0.8588 (mmp-170) cc_final: 0.8376 (mmm160)
REVERT: A  504 MET cc_start: 0.8109 (ttp) cc_final: 0.7886 (ttm)
REVERT: A  721 TYR cc_start: 0.8657 (m-80) cc_final: 0.8085 (m-80)
REVERT: A  923 TYR cc_start: 0.7822 (t80) cc_final: 0.7255 (t80)
REVERT: A  928 THR cc_start: 0.8506 (p) cc_final: 0.8236 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0886
  time to fit residues: 15.0094
Evaluate side-chains
  79 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
A 151 GLN
A 204 ASN
A 430 HIS
A 712 ASN
A 852 GLN
A 989 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.066555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.052493 restraints weight = 28453.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.054726 restraints weight = 14421.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.056266 restraints weight = 9138.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.057340 restraints weight = 6597.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.058046 restraints weight = 5225.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7896  Z= 0.149
  Angle     :  0.676  12.628  10708  Z= 0.344
  Chirality :  0.044   0.237   1174
  Planarity :  0.005   0.045   1398
  Dihedral  :  4.312  20.249   1037
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 10.02 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.37 (0.27), residues: 965
  helix:  0.87 (0.24), residues: 469
  sheet:  0.44 (0.37), residues: 177
  loop : -0.68 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 924 
 TYR   0.018   0.001   TYR A 450 
 PHE   0.013   0.001   PHE A 341 
 TRP   0.010   0.002   TRP A 178 
 HIS   0.003   0.001   HIS A 998 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7896)
  covalent geometry    : angle       0.67646 (10708)
  hydrogen bonds       : bond        0.04026 (  429)
  hydrogen bonds       : angle       4.90320 ( 1342)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.9049 (m-30) cc_final: 0.8567 (p0)
REVERT: A  178 TRP cc_start: 0.8560 (m-10) cc_final: 0.8261 (m-10)
REVERT: A  215 ARG cc_start: 0.9119 (mmp-170) cc_final: 0.8748 (mmm160)
REVERT: A  721 TYR cc_start: 0.9309 (m-80) cc_final: 0.8802 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 93
  average time/residue: 0.0768
  time to fit residues: 10.2099
Evaluate side-chains
  70 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 67 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 1 optimal weight:    0.2980
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 698 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.067470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.053612 restraints weight = 27912.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.055879 restraints weight = 14017.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.057456 restraints weight = 8736.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.058548 restraints weight = 6237.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.059281 restraints weight = 4885.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7896  Z= 0.119
  Angle     :  0.658  10.728  10708  Z= 0.321
  Chirality :  0.043   0.144   1174
  Planarity :  0.004   0.043   1398
  Dihedral  :  4.073  17.483   1037
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.66 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.84 (0.27), residues: 965
  helix:  1.31 (0.25), residues: 468
  sheet:  0.66 (0.38), residues: 180
  loop : -0.55 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 924 
 TYR   0.010   0.001   TYR A 632 
 PHE   0.012   0.001   PHE A 699 
 TRP   0.022   0.001   TRP A 851 
 HIS   0.006   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7896)
  covalent geometry    : angle       0.65809 (10708)
  hydrogen bonds       : bond        0.03283 (  429)
  hydrogen bonds       : angle       4.63661 ( 1342)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.9131 (m-30) cc_final: 0.8657 (p0)
REVERT: A  178 TRP cc_start: 0.8512 (m-10) cc_final: 0.8212 (m-10)
REVERT: A  215 ARG cc_start: 0.9135 (mmp-170) cc_final: 0.8739 (mmm160)
REVERT: A  721 TYR cc_start: 0.9340 (m-80) cc_final: 0.8859 (m-80)
REVERT: A  925 ASP cc_start: 0.8488 (t0) cc_final: 0.8188 (t0)
  outliers start: 10
  outliers final: 3
  residues processed: 85
  average time/residue: 0.0692
  time to fit residues: 8.5762
Evaluate side-chains
  69 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  778 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    0.0040
   chunk 92 optimal weight:   10.0000
   chunk 83 optimal weight:    9.9990
   chunk 86 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0980
   chunk 52 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9990
   chunk 84 optimal weight:   10.0000
   chunk 53 optimal weight:    0.2980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.2994

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN
A 486 GLN
** A 664 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 = 0.3355 r_free = 0.3355 target = 0.068102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.054279 restraints weight = 28353.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.056599 restraints weight = 13867.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.058165 restraints weight = 8612.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.059206 restraints weight = 6162.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.059942 restraints weight = 4867.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7896  Z= 0.107
  Angle     :  0.627   9.953  10708  Z= 0.304
  Chirality :  0.043   0.263   1174
  Planarity :  0.004   0.042   1398
  Dihedral  :  3.964  17.852   1037
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.59 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.05 (0.28), residues: 965
  helix:  1.50 (0.25), residues: 468
  sheet:  0.66 (0.37), residues: 181
  loop : -0.41 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 924 
 TYR   0.018   0.001   TYR A 450 
 PHE   0.024   0.001   PHE A 123 
 TRP   0.052   0.002   TRP A 851 
 HIS   0.004   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 7896)
  covalent geometry    : angle       0.62741 (10708)
  hydrogen bonds       : bond        0.02959 (  429)
  hydrogen bonds       : angle       4.49677 ( 1342)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.9130 (m-30) cc_final: 0.8687 (p0)
REVERT: A  178 TRP cc_start: 0.8565 (m-10) cc_final: 0.8206 (m-10)
REVERT: A  215 ARG cc_start: 0.9156 (mmp-170) cc_final: 0.8700 (mmm160)
REVERT: A  721 TYR cc_start: 0.9344 (m-80) cc_final: 0.8821 (m-80)
REVERT: A  925 ASP cc_start: 0.8467 (t0) cc_final: 0.8149 (t0)
  outliers start: 8
  outliers final: 3
  residues processed: 79
  average time/residue: 0.0714
  time to fit residues: 8.1743
Evaluate side-chains
  70 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  184 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 70 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 40 optimal weight:    6.9990
   chunk 43 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1016 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.065791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.051737 restraints weight = 29427.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.053928 restraints weight = 15122.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.055415 restraints weight = 9620.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.056425 restraints weight = 7029.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.057140 restraints weight = 5625.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3113
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7896  Z= 0.202
  Angle     :  0.682   8.493  10708  Z= 0.337
  Chirality :  0.044   0.138   1174
  Planarity :  0.004   0.042   1398
  Dihedral  :  4.100  18.837   1037
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 13.87 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.08 (0.27), residues: 965
  helix:  1.53 (0.25), residues: 469
  sheet:  0.74 (0.37), residues: 182
  loop : -0.46 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 924 
 TYR   0.016   0.002   TYR A 450 
 PHE   0.012   0.002   PHE A 361 
 TRP   0.032   0.002   TRP A 851 
 HIS   0.004   0.001   HIS A 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 7896)
  covalent geometry    : angle       0.68202 (10708)
  hydrogen bonds       : bond        0.03399 (  429)
  hydrogen bonds       : angle       4.57209 ( 1342)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.9099 (m-30) cc_final: 0.8725 (p0)
REVERT: A  178 TRP cc_start: 0.8586 (m-10) cc_final: 0.8297 (m-10)
REVERT: A  206 MET cc_start: 0.7428 (mmt) cc_final: 0.6958 (mmt)
REVERT: A  215 ARG cc_start: 0.9124 (mmp-170) cc_final: 0.8673 (mmm160)
REVERT: A  721 TYR cc_start: 0.9346 (m-80) cc_final: 0.8770 (m-80)
  outliers start: 7
  outliers final: 6
  residues processed: 73
  average time/residue: 0.0761
  time to fit residues: 8.0333
Evaluate side-chains
  70 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  400 ASP
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  778 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 64 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 ASN
** A 325 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 = 0.3311 r_free = 0.3311 target = 0.067704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.053953 restraints weight = 30167.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.056132 restraints weight = 15167.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.057581 restraints weight = 9512.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.058598 restraints weight = 6898.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.059265 restraints weight = 5453.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3106
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3106
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7896  Z= 0.198
  Angle     :  0.684   8.896  10708  Z= 0.339
  Chirality :  0.045   0.261   1174
  Planarity :  0.004   0.040   1398
  Dihedral  :  4.162  17.343   1037
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 14.10 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.96 (0.27), residues: 965
  helix:  1.39 (0.24), residues: 471
  sheet:  0.58 (0.37), residues: 183
  loop : -0.38 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  81 
 TYR   0.015   0.002   TYR A 450 
 PHE   0.026   0.002   PHE A 123 
 TRP   0.032   0.002   TRP A 851 
 HIS   0.015   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 7896)
  covalent geometry    : angle       0.68409 (10708)
  hydrogen bonds       : bond        0.03286 (  429)
  hydrogen bonds       : angle       4.63070 ( 1342)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.9092 (m-30) cc_final: 0.8762 (p0)
REVERT: A  178 TRP cc_start: 0.8575 (m-10) cc_final: 0.8321 (m-10)
REVERT: A  206 MET cc_start: 0.7297 (mmt) cc_final: 0.6896 (mmm)
REVERT: A  215 ARG cc_start: 0.9128 (mmp-170) cc_final: 0.8677 (mmm160)
REVERT: A  721 TYR cc_start: 0.9295 (m-80) cc_final: 0.8704 (m-80)
REVERT: A  869 CYS cc_start: 0.8247 (m) cc_final: 0.7852 (m)
REVERT: A  888 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8214 (tpt170)
  outliers start: 10
  outliers final: 6
  residues processed: 73
  average time/residue: 0.0701
  time to fit residues: 7.4101
Evaluate side-chains
  71 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  400 ASP
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  778 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    0.3980
   chunk 62 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 27 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 48 optimal weight:   20.0000
   chunk 55 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.068344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.054571 restraints weight = 30177.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.056753 restraints weight = 15153.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.058265 restraints weight = 9492.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.059286 restraints weight = 6816.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.059962 restraints weight = 5399.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7896  Z= 0.147
  Angle     :  0.670  10.254  10708  Z= 0.324
  Chirality :  0.045   0.233   1174
  Planarity :  0.004   0.040   1398
  Dihedral  :  4.059  16.886   1037
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 13.99 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.14 (0.27), residues: 965
  helix:  1.54 (0.24), residues: 470
  sheet:  0.66 (0.37), residues: 182
  loop : -0.29 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 924 
 TYR   0.015   0.001   TYR A 450 
 PHE   0.010   0.001   PHE A 857 
 TRP   0.032   0.002   TRP A 851 
 HIS   0.012   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7896)
  covalent geometry    : angle       0.67049 (10708)
  hydrogen bonds       : bond        0.03123 (  429)
  hydrogen bonds       : angle       4.55264 ( 1342)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.9128 (m-30) cc_final: 0.8759 (p0)
REVERT: A  178 TRP cc_start: 0.8604 (m-10) cc_final: 0.8320 (m-10)
REVERT: A  206 MET cc_start: 0.7283 (mmt) cc_final: 0.6894 (mmm)
REVERT: A  215 ARG cc_start: 0.9161 (mmp-170) cc_final: 0.8709 (mmm160)
REVERT: A  446 MET cc_start: 0.8971 (mmm) cc_final: 0.8764 (mmp)
REVERT: A  721 TYR cc_start: 0.9334 (m-80) cc_final: 0.8695 (m-80)
REVERT: A  755 MET cc_start: 0.8452 (ptp) cc_final: 0.8121 (ptp)
REVERT: A  869 CYS cc_start: 0.8296 (m) cc_final: 0.7852 (m)
REVERT: A  888 ARG cc_start: 0.8669 (tpp-160) cc_final: 0.8292 (tpt170)
  outliers start: 7
  outliers final: 6
  residues processed: 73
  average time/residue: 0.0773
  time to fit residues: 8.1809
Evaluate side-chains
  70 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 HIS
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  778 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 85 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 90 optimal weight:    0.2980
   chunk 80 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
A 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.066872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.052684 restraints weight = 29518.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.054970 restraints weight = 14846.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.056525 restraints weight = 9347.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.057562 restraints weight = 6790.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.058300 restraints weight = 5399.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7896  Z= 0.110
  Angle     :  0.666  11.965  10708  Z= 0.315
  Chirality :  0.044   0.315   1174
  Planarity :  0.004   0.038   1398
  Dihedral  :  3.961  16.831   1037
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 13.87 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.24 (0.28), residues: 965
  helix:  1.65 (0.25), residues: 470
  sheet:  0.64 (0.37), residues: 179
  loop : -0.21 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 924 
 TYR   0.016   0.001   TYR A 450 
 PHE   0.024   0.001   PHE A 123 
 TRP   0.035   0.002   TRP A 851 
 HIS   0.018   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7896)
  covalent geometry    : angle       0.66617 (10708)
  hydrogen bonds       : bond        0.02944 (  429)
  hydrogen bonds       : angle       4.46960 ( 1342)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.9133 (m-30) cc_final: 0.8743 (p0)
REVERT: A  178 TRP cc_start: 0.8579 (m-10) cc_final: 0.8301 (m-10)
REVERT: A  215 ARG cc_start: 0.9176 (mmp-170) cc_final: 0.8725 (mmm160)
REVERT: A  446 MET cc_start: 0.8953 (mmm) cc_final: 0.8733 (mmp)
REVERT: A  721 TYR cc_start: 0.9334 (m-80) cc_final: 0.8646 (m-80)
REVERT: A  755 MET cc_start: 0.8399 (ptp) cc_final: 0.8060 (ptp)
REVERT: A  869 CYS cc_start: 0.8141 (m) cc_final: 0.7745 (m)
REVERT: A  888 ARG cc_start: 0.8666 (tpp-160) cc_final: 0.8316 (tpt170)
  outliers start: 7
  outliers final: 4
  residues processed: 67
  average time/residue: 0.0637
  time to fit residues: 6.3016
Evaluate side-chains
  69 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  772 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    8.9990
   chunk 41 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 664 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 = 0.3333 r_free = 0.3333 target = 0.066971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.052799 restraints weight = 29422.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.055061 restraints weight = 14839.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.056604 restraints weight = 9390.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.057676 restraints weight = 6832.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.058430 restraints weight = 5419.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7896  Z= 0.113
  Angle     :  0.653  11.980  10708  Z= 0.309
  Chirality :  0.044   0.305   1174
  Planarity :  0.004   0.037   1398
  Dihedral  :  3.898  17.497   1037
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 14.34 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.39 (0.28), residues: 965
  helix:  1.72 (0.24), residues: 470
  sheet:  0.78 (0.37), residues: 182
  loop : -0.13 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 924 
 TYR   0.016   0.001   TYR A 450 
 PHE   0.010   0.001   PHE A 389 
 TRP   0.036   0.002   TRP A 851 
 HIS   0.012   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7896)
  covalent geometry    : angle       0.65252 (10708)
  hydrogen bonds       : bond        0.02840 (  429)
  hydrogen bonds       : angle       4.41594 ( 1342)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.9127 (m-30) cc_final: 0.8759 (p0)
REVERT: A  178 TRP cc_start: 0.8542 (m-10) cc_final: 0.8261 (m-10)
REVERT: A  215 ARG cc_start: 0.9190 (mmp-170) cc_final: 0.8733 (mmm160)
REVERT: A  446 MET cc_start: 0.8952 (mmm) cc_final: 0.8734 (mmp)
REVERT: A  721 TYR cc_start: 0.9335 (m-80) cc_final: 0.8652 (m-80)
REVERT: A  755 MET cc_start: 0.8451 (ptp) cc_final: 0.8142 (ptp)
REVERT: A  789 MET cc_start: 0.9183 (mmm) cc_final: 0.8961 (mmm)
REVERT: A  869 CYS cc_start: 0.8212 (m) cc_final: 0.7773 (m)
REVERT: A  888 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8322 (tpt170)
  outliers start: 5
  outliers final: 5
  residues processed: 72
  average time/residue: 0.0686
  time to fit residues: 7.2802
Evaluate side-chains
  72 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  772 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0980
   chunk 68 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 664 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 = 0.3369 r_free = 0.3369 target = 0.070041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.056310 restraints weight = 29322.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.058564 restraints weight = 14677.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.060114 restraints weight = 9204.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.061174 restraints weight = 6605.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.061894 restraints weight = 5193.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7896  Z= 0.108
  Angle     :  0.658  12.302  10708  Z= 0.311
  Chirality :  0.044   0.311   1174
  Planarity :  0.004   0.037   1398
  Dihedral  :  3.839  17.973   1037
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 14.45 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.45 (0.28), residues: 965
  helix:  1.76 (0.25), residues: 470
  sheet:  0.76 (0.38), residues: 183
  loop : -0.05 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 924 
 TYR   0.016   0.001   TYR A 923 
 PHE   0.024   0.001   PHE A 123 
 TRP   0.041   0.002   TRP A 851 
 HIS   0.012   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 7896)
  covalent geometry    : angle       0.65829 (10708)
  hydrogen bonds       : bond        0.02784 (  429)
  hydrogen bonds       : angle       4.37911 ( 1342)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.9119 (m-30) cc_final: 0.8763 (p0)
REVERT: A  178 TRP cc_start: 0.8487 (m-10) cc_final: 0.8214 (m-10)
REVERT: A  215 ARG cc_start: 0.9212 (mmp-170) cc_final: 0.8859 (mmp80)
REVERT: A  446 MET cc_start: 0.8952 (mmm) cc_final: 0.8726 (mmp)
REVERT: A  709 GLU cc_start: 0.9166 (tp30) cc_final: 0.8918 (tp30)
REVERT: A  721 TYR cc_start: 0.9323 (m-80) cc_final: 0.8579 (m-80)
REVERT: A  755 MET cc_start: 0.8436 (ptp) cc_final: 0.8146 (ptp)
REVERT: A  789 MET cc_start: 0.9153 (mmm) cc_final: 0.8953 (mmm)
REVERT: A  869 CYS cc_start: 0.8205 (m) cc_final: 0.7749 (m)
REVERT: A  888 ARG cc_start: 0.8670 (tpp-160) cc_final: 0.8351 (tpt170)
  outliers start: 4
  outliers final: 4
  residues processed: 72
  average time/residue: 0.0661
  time to fit residues: 7.0082
Evaluate side-chains
  70 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 87 optimal weight:    7.9990
   chunk 49 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0980
   chunk 95 optimal weight:    0.3980
   overall best weight:    1.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
A 856 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.068969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.055258 restraints weight = 29869.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.057512 restraints weight = 15003.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.059035 restraints weight = 9373.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.060075 restraints weight = 6747.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.060730 restraints weight = 5313.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3147
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3147
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7896  Z= 0.136
  Angle     :  0.667  12.319  10708  Z= 0.318
  Chirality :  0.044   0.297   1174
  Planarity :  0.004   0.037   1398
  Dihedral  :  3.880  18.325   1037
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 14.80 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.47 (0.28), residues: 965
  helix:  1.79 (0.25), residues: 470
  sheet:  0.83 (0.38), residues: 182
  loop : -0.09 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 924 
 TYR   0.016   0.001   TYR A 450 
 PHE   0.010   0.001   PHE A 389 
 TRP   0.039   0.002   TRP A 851 
 HIS   0.011   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7896)
  covalent geometry    : angle       0.66679 (10708)
  hydrogen bonds       : bond        0.02891 (  429)
  hydrogen bonds       : angle       4.42407 ( 1342)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1229.75 seconds
wall clock time: 22 minutes 8.63 seconds (1328.63 seconds total)