Starting phenix.real_space_refine
on Tue Mar  3 20:25:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xmq_22261/03_2026/6xmq_22261.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xmq_22261/03_2026/6xmq_22261.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xmq_22261/03_2026/6xmq_22261.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xmq_22261/03_2026/6xmq_22261.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xmq_22261/03_2026/6xmq_22261.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xmq_22261/03_2026/6xmq_22261.cif"
  }
  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=  -0.001 sd=   0.055
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      37      5.16       5
     C    5410      2.51       5
     N    1375      2.21       5
     O    1536      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8362
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1085, 8330
          Classifications: {'peptide': 1085}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 48, 'TRANS': 1036}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 197
          Unresolved non-hydrogen angles: 241
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 13, 'TYR:plan': 2, 'ASP:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 142
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ACP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.71, per 1000 atoms: 0.20
  Number of scatterers: 8362
  At special positions: 0
  Unit cell: (84.49, 95.2, 136.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      37     16.00
     P       3     15.00
     Mg      1     11.99
     O    1536      8.00
     N    1375      7.00
     C    5410      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: 0.54
  Conformation dependent library (CDL) restraints added in 320.2 milliseconds
  

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2042

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 9 sheets defined
      48.2% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 44
      removed outlier: 3.595A  pdb=" N   PHE A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      Proline residue:  A  34  - end of helix
    Processing helix  chain 'A' and resid 57 through 74
      removed outlier: 3.701A  pdb=" N   LEU A  61 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 77
      No H-bonds generated for 'chain 'A' and resid 75 through 77'
    Processing helix  chain 'A' and resid 78 through 86
    Processing helix  chain 'A' and resid 149 through 154
      removed outlier: 3.830A  pdb=" N   GLU A 153 " --> pdb=" O   PHE A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 163
      removed outlier: 3.956A  pdb=" N   GLN A 161 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 188 through 198
      removed outlier: 3.880A  pdb=" N   VAL A 198 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 215
    Processing helix  chain 'A' and resid 218 through 247
      removed outlier: 3.524A  pdb=" N   ARG A 247 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 250
      No H-bonds generated for 'chain 'A' and resid 248 through 250'
    Processing helix  chain 'A' and resid 334 through 336
      No H-bonds generated for 'chain 'A' and resid 334 through 336'
    Processing helix  chain 'A' and resid 372 through 375
      removed outlier: 3.791A  pdb=" N   GLU A 375 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 372 through 375'
    Processing helix  chain 'A' and resid 376 through 387
    Processing helix  chain 'A' and resid 396 through 424
      removed outlier: 3.813A  pdb=" N   LEU A 400 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 443
      removed outlier: 4.536A  pdb=" N   LEU A 433 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASP A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   VAL A 443 " --> pdb=" O   ILE A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 463
      removed outlier: 4.096A  pdb=" N   MET A 453 " --> pdb=" O   MET A 449 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA A 454 " --> pdb=" O   GLU A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 473
      No H-bonds generated for 'chain 'A' and resid 471 through 473'
    Processing helix  chain 'A' and resid 474 through 480
      removed outlier: 4.258A  pdb=" N   ARG A 480 " --> pdb=" O   PRO A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 3.717A  pdb=" N   ILE A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLY A 530 " --> pdb=" O   ILE A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 606 through 611
    Processing helix  chain 'A' and resid 620 through 630
      removed outlier: 3.848A  pdb=" N   TYR A 625 " --> pdb=" O   TYR A 621 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LYS A 626 " --> pdb=" O   ASP A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 689
      removed outlier: 3.659A  pdb=" N   THR A 682 " --> pdb=" O   ASP A 678 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ILE A 683 " --> pdb=" O   ALA A 679 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LYS A 684 " --> pdb=" O   ILE A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 712
      removed outlier: 3.512A  pdb=" N   ALA A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 758
    Processing helix  chain 'A' and resid 767 through 773
    Processing helix  chain 'A' and resid 778 through 786
      removed outlier: 3.697A  pdb=" N   ARG A 784 " --> pdb=" O   ARG A 780 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   HIS A 785 " --> pdb=" O   ASP A 781 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR A 786 " --> pdb=" O   LEU A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 808
      removed outlier: 3.743A  pdb=" N   GLY A 808 " --> pdb=" O   LEU A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 819
      No H-bonds generated for 'chain 'A' and resid 817 through 819'
    Processing helix  chain 'A' and resid 820 through 827
    Processing helix  chain 'A' and resid 837 through 851
    Processing helix  chain 'A' and resid 972 through 1012
      removed outlier: 4.370A  pdb=" N   ALA A1012 " --> pdb=" O   ILE A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1017 through 1036
      removed outlier: 4.107A  pdb=" N   CYS A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   SER A1036 " --> pdb=" O   PHE A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1055 through 1084
    Processing helix  chain 'A' and resid 1099 through 1121
      removed outlier: 4.139A  pdb=" N   PHE A1117 " --> pdb=" O   GLN A1113 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA A1118 " --> pdb=" O   VAL A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1152
      removed outlier: 3.889A  pdb=" N   TYR A1137 " --> pdb=" O   ASN A1133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1162
      removed outlier: 3.996A  pdb=" N   ASN A1159 " --> pdb=" O   LEU A1155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1168 through 1198
      removed outlier: 4.114A  pdb=" N   ILE A1173 " --> pdb=" O   ASP A1169 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LYS A1174 " --> pdb=" O   ASP A1170 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A1179 " --> pdb=" O   LEU A1175 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET A1198 " --> pdb=" O   LYS A1194 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8
      removed outlier: 3.640A  pdb=" N   VAL A 143 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.801A  pdb=" N   TYR A 102 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   SER A  15 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LEU A 100 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   LEU A  17 " --> pdb=" O   HIS A  98 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   HIS A  98 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A 111 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 120
    Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130
      removed outlier: 3.565A  pdb=" N   PHE A 130 " --> pdb=" O   LYS A 133 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 267
      removed outlier: 4.715A  pdb=" N   ASN A 257 " --> pdb=" O   SER A 279 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER A 279 " --> pdb=" O   ASN A 257 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   LEU A 277 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LEU A 366 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU A 296 " --> pdb=" O   LEU A 366 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ASP A 292 " --> pdb=" O   THR A 370 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 317
      removed outlier: 6.682A  pdb=" N   SER A 299 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   VAL A 348 " --> pdb=" O   SER A 299 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE A 301 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 469
      removed outlier: 6.729A  pdb=" N   GLY A 830 " --> pdb=" O   PHE A 964 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   SER A 966 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ALA A 832 " --> pdb=" O   SER A 966 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A 829 " --> pdb=" O   THR A 811 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP A 487 " --> pdb=" O   CYS A 814 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   CYS A 484 " --> pdb=" O   ILE A 694 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ILE A 696 " --> pdb=" O   CYS A 484 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   PHE A 486 " --> pdb=" O   ILE A 696 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   TYR A 789 " --> pdb=" O   SER A 693 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   MET A 695 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   LEU A 719 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   THR A 766 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   LEU A 721 " --> pdb=" O   THR A 766 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 515 through 516
      removed outlier: 3.642A  pdb=" N   VAL A 498 " --> pdb=" O   HIS A 672 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   ILE A 670 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   LEU A 502 " --> pdb=" O   PHE A 668 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   PHE A 668 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   PHE A 665 " --> pdb=" O   SER A 640 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   SER A 640 " --> pdb=" O   PHE A 665 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLY A 667 " --> pdb=" O   LEU A 638 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A 600 " --> pdb=" O   ALA A 593 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG A 578 " --> pdb=" O   ILE A 592 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER A 594 " --> pdb=" O   ILE A 576 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   ILE A 576 " --> pdb=" O   SER A 594 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 536 through 537
      removed outlier: 3.880A  pdb=" N   VAL A 536 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    403 hydrogen bonds defined for protein.
    1182 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: 1.33

  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 -     1.35: 2661
        1.35 -     1.48: 2089
        1.48 -     1.60: 3725
        1.60 -     1.73: 4
        1.73 -     1.86: 64
  Bond restraints: 8543
  Sorted by residual:
  bond pdb=" C1' ACP A1301 "
       pdb=" O4' ACP A1301 "
    ideal  model  delta    sigma   weight residual
    1.390  1.615 -0.225 2.00e-02 2.50e+03 1.26e+02
  bond pdb=" C1' ACP A1301 "
       pdb=" C2' ACP A1301 "
    ideal  model  delta    sigma   weight residual
    1.527  1.304  0.223 2.00e-02 2.50e+03 1.24e+02
  bond pdb=" C4' ACP A1301 "
       pdb=" O4' ACP A1301 "
    ideal  model  delta    sigma   weight residual
    1.428  1.301  0.127 2.00e-02 2.50e+03 4.04e+01
  bond pdb=" C6  ACP A1301 "
       pdb=" N6  ACP A1301 "
    ideal  model  delta    sigma   weight residual
    1.335  1.448 -0.113 2.00e-02 2.50e+03 3.21e+01
  bond pdb=" C2' ACP A1301 "
       pdb=" O2' ACP A1301 "
    ideal  model  delta    sigma   weight residual
    1.401  1.490 -0.089 2.00e-02 2.50e+03 1.99e+01
  ... (remaining 8538 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 11500
        2.65 -     5.30: 99
        5.30 -     7.95: 3
        7.95 -    10.60: 7
       10.60 -    13.25: 1
  Bond angle restraints: 11610
  Sorted by residual:
  angle pdb=" O3A ACP A1301 "
        pdb=" PA  ACP A1301 "
        pdb=" O5' ACP A1301 "
      ideal   model   delta    sigma   weight residual
      93.75  107.00  -13.25 3.00e+00 1.11e-01 1.95e+01
  angle pdb=" N1  ACP A1301 "
        pdb=" C6  ACP A1301 "
        pdb=" N6  ACP A1301 "
      ideal   model   delta    sigma   weight residual
     119.32  108.84   10.48 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" C3B ACP A1301 "
        pdb=" PB  ACP A1301 "
        pdb=" O3A ACP A1301 "
      ideal   model   delta    sigma   weight residual
      98.05  108.34  -10.29 3.00e+00 1.11e-01 1.18e+01
  angle pdb=" O1B ACP A1301 "
        pdb=" PB  ACP A1301 "
        pdb=" O2B ACP A1301 "
      ideal   model   delta    sigma   weight residual
     119.60  110.06    9.54 3.00e+00 1.11e-01 1.01e+01
  angle pdb=" O1A ACP A1301 "
        pdb=" PA  ACP A1301 "
        pdb=" O2A ACP A1301 "
      ideal   model   delta    sigma   weight residual
     118.95  110.47    8.48 3.00e+00 1.11e-01 7.99e+00
  ... (remaining 11605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.49: 4751
       18.49 -    36.98: 313
       36.98 -    55.46: 31
       55.46 -    73.95: 13
       73.95 -    92.44: 8
  Dihedral angle restraints: 5116
    sinusoidal: 1964
      harmonic: 3152
  Sorted by residual:
  dihedral pdb=" O1B ACP A1301 "
           pdb=" C3B ACP A1301 "
           pdb=" PB  ACP A1301 "
           pdb=" PG  ACP A1301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -52.82   39.62  -92.44     1      3.00e+01 1.11e-03 1.11e+01
  dihedral pdb=" CB  GLU A 420 "
           pdb=" CG  GLU A 420 "
           pdb=" CD  GLU A 420 "
           pdb=" OE1 GLU A 420 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.81  -89.81     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A 520 "
           pdb=" CG  GLU A 520 "
           pdb=" CD  GLU A 520 "
           pdb=" OE1 GLU A 520 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.40  -89.40     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 5113 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1163
       0.057 -    0.114: 180
       0.114 -    0.171: 18
       0.171 -    0.227: 0
       0.227 -    0.284: 1
  Chirality restraints: 1362
  Sorted by residual:
  chirality pdb=" C2' ACP A1301 "
            pdb=" C1' ACP A1301 "
            pdb=" C3' ACP A1301 "
            pdb=" O2' ACP A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.47   -0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  ILE A 301 "
            pdb=" N   ILE A 301 "
            pdb=" C   ILE A 301 "
            pdb=" CB  ILE A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.26e-01
  chirality pdb=" CA  ILE A 289 "
            pdb=" N   ILE A 289 "
            pdb=" C   ILE A 289 "
            pdb=" CB  ILE A 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  ... (remaining 1359 not shown)

  Planarity restraints: 1460
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A1039 "    0.023 5.00e-02 4.00e+02   3.55e-02 2.02e+00
        pdb=" N   PRO A1040 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A1040 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A1040 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 273 "   -0.022 5.00e-02 4.00e+02   3.28e-02 1.72e+00
        pdb=" N   PRO A 274 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 274 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 274 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 962 "    0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO A 963 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 963 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 963 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1457 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 18
        2.31 -     2.96: 3914
        2.96 -     3.60: 11684
        3.60 -     4.25: 16694
        4.25 -     4.90: 28749
  Nonbonded interactions: 61059
  Sorted by model distance:
  nonbonded pdb=" O3G ACP A1301 "
            pdb="MG    MG A1302 "
     model   vdw
     1.660 2.170
  nonbonded pdb=" OD2 ASP A 816 "
            pdb="MG    MG A1302 "
     model   vdw
     2.005 2.170
  nonbonded pdb=" OD2 ASP A 487 "
            pdb="MG    MG A1302 "
     model   vdw
     2.042 2.170
  nonbonded pdb=" OD2 ASP A 487 "
            pdb=" O3G ACP A1301 "
     model   vdw
     2.080 3.040
  nonbonded pdb=" OD1 ASP A 816 "
            pdb="MG    MG A1302 "
     model   vdw
     2.102 2.170
  ... (remaining 61054 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     8.610
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
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      :  0.006   0.225   8543  Z= 0.287
  Angle     :  0.662  13.253  11610  Z= 0.343
  Chirality :  0.042   0.284   1362
  Planarity :  0.004   0.036   1460
  Dihedral  : 13.161  92.440   3074
  Min Nonbonded Distance : 1.660

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.23), residues: 1077
  helix: -0.19 (0.21), residues: 489
  sheet: -1.75 (0.40), residues: 132
  loop : -1.80 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 613 
 TYR   0.013   0.001   TYR A 625 
 PHE   0.016   0.002   PHE A 237 
 TRP   0.006   0.001   TRP A 137 
 HIS   0.004   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 8543)
  covalent geometry    : angle       0.66219 (11610)
  hydrogen bonds       : bond        0.17257 (  403)
  hydrogen bonds       : angle       6.23827 ( 1182)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.311 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0891
  time to fit residues: 8.7435
Evaluate side-chains
  36 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.0010
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
A 166 HIS
A 514 HIS
** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 776 HIS
A 785 HIS
A 826 GLN
A 987 ASN
A1065 GLN
A1069 HIS
A1122 GLN
A1209 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.071930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.059989 restraints weight = 31217.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.061914 restraints weight = 16418.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.063202 restraints weight = 10883.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.064041 restraints weight = 8249.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.064651 restraints weight = 6827.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8543  Z= 0.119
  Angle     :  0.522   8.174  11610  Z= 0.271
  Chirality :  0.039   0.143   1362
  Planarity :  0.004   0.032   1460
  Dihedral  :  6.853  83.448   1178
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  9.11 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.25), residues: 1077
  helix:  1.49 (0.24), residues: 485
  sheet: -1.59 (0.38), residues: 150
  loop : -1.19 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 239 
 TYR   0.010   0.001   TYR A  28 
 PHE   0.015   0.001   PHE A1016 
 TRP   0.006   0.001   TRP A 212 
 HIS   0.005   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8543)
  covalent geometry    : angle       0.52180 (11610)
  hydrogen bonds       : bond        0.05097 (  403)
  hydrogen bonds       : angle       4.23601 ( 1182)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  239 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8804 (tpt170)
REVERT: A  246 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8056 (t80)
  outliers start: 11
  outliers final: 4
  residues processed: 52
  average time/residue: 0.0735
  time to fit residues: 5.8781
Evaluate side-chains
  41 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 106 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 63 optimal weight:    0.1980
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 533 HIS ** 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 = 0.3381 r_free = 0.3381 target = 0.069233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.057306 restraints weight = 31310.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.059169 restraints weight = 16680.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.060419 restraints weight = 11151.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.061192 restraints weight = 8485.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.061831 restraints weight = 7092.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8543  Z= 0.203
  Angle     :  0.574   6.674  11610  Z= 0.296
  Chirality :  0.040   0.143   1362
  Planarity :  0.004   0.031   1460
  Dihedral  :  6.664  84.667   1178
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.49 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.26), residues: 1077
  helix:  1.83 (0.24), residues: 485
  sheet: -1.25 (0.42), residues: 142
  loop : -1.03 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 634 
 TYR   0.013   0.001   TYR A 625 
 PHE   0.014   0.001   PHE A 499 
 TRP   0.006   0.001   TRP A 787 
 HIS   0.004   0.001   HIS A 691 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 8543)
  covalent geometry    : angle       0.57380 (11610)
  hydrogen bonds       : bond        0.05690 (  403)
  hydrogen bonds       : angle       4.23218 ( 1182)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  246 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8441 (t80)
REVERT: A  807 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8534 (mtm)
REVERT: A 1162 MET cc_start: 0.9073 (mmm) cc_final: 0.8782 (tpt)
  outliers start: 16
  outliers final: 11
  residues processed: 50
  average time/residue: 0.0719
  time to fit residues: 5.6455
Evaluate side-chains
  49 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  584 SER
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  807 MET
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.0980
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0370
   chunk 107 optimal weight:    0.0050
   chunk 3 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.8276

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

Flipped N/Q/H residues before XYZ refinement:
** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1065 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.071610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.059716 restraints weight = 31703.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.061662 restraints weight = 16576.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.062951 restraints weight = 10921.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.063858 restraints weight = 8249.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.064474 restraints weight = 6740.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8543  Z= 0.100
  Angle     :  0.480   8.031  11610  Z= 0.248
  Chirality :  0.038   0.143   1362
  Planarity :  0.003   0.033   1460
  Dihedral  :  6.364  85.314   1178
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 15.19 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.26), residues: 1077
  helix:  2.25 (0.24), residues: 480
  sheet: -1.03 (0.42), residues: 141
  loop : -0.93 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 239 
 TYR   0.009   0.001   TYR A  28 
 PHE   0.011   0.001   PHE A 405 
 TRP   0.007   0.001   TRP A 137 
 HIS   0.005   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 8543)
  covalent geometry    : angle       0.48012 (11610)
  hydrogen bonds       : bond        0.04526 (  403)
  hydrogen bonds       : angle       3.78298 ( 1182)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A 1162 MET cc_start: 0.9072 (mmm) cc_final: 0.8637 (tpt)
  outliers start: 9
  outliers final: 4
  residues processed: 44
  average time/residue: 0.0647
  time to fit residues: 4.7369
Evaluate side-chains
  42 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   chunk 101 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 71 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
A 327 ASN
A 533 HIS
A 666 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.064927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.053364 restraints weight = 30747.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.054987 restraints weight = 17137.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.056122 restraints weight = 11729.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.056919 restraints weight = 9040.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.057417 restraints weight = 7523.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.048   8543  Z= 0.366
  Angle     :  0.738   6.991  11610  Z= 0.378
  Chirality :  0.045   0.156   1362
  Planarity :  0.004   0.051   1460
  Dihedral  :  6.823  89.149   1178
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.44 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.26), residues: 1077
  helix:  1.64 (0.24), residues: 492
  sheet: -1.24 (0.43), residues: 141
  loop : -1.04 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 260 
 TYR   0.020   0.002   TYR A 625 
 PHE   0.023   0.002   PHE A 499 
 TRP   0.008   0.002   TRP A  77 
 HIS   0.006   0.001   HIS A 691 

Details of bonding type rmsd
  covalent geometry    : bond        0.00852 ( 8543)
  covalent geometry    : angle       0.73760 (11610)
  hydrogen bonds       : bond        0.06863 (  403)
  hydrogen bonds       : angle       4.69769 ( 1182)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 35
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  246 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8368 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 52
  average time/residue: 0.0585
  time to fit residues: 5.0981
Evaluate side-chains
  51 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 35
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  584 SER
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 666 ASN
A 706 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.067640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.055451 restraints weight = 29773.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.057257 restraints weight = 16152.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.058531 restraints weight = 10889.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.059337 restraints weight = 8298.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.059995 restraints weight = 6899.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8543  Z= 0.149
  Angle     :  0.525   6.801  11610  Z= 0.272
  Chirality :  0.039   0.144   1362
  Planarity :  0.003   0.038   1460
  Dihedral  :  6.332  78.891   1178
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.22 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.26), residues: 1077
  helix:  2.14 (0.24), residues: 485
  sheet: -1.27 (0.43), residues: 146
  loop : -0.88 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 634 
 TYR   0.011   0.001   TYR A 625 
 PHE   0.013   0.001   PHE A 499 
 TRP   0.007   0.001   TRP A 137 
 HIS   0.004   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8543)
  covalent geometry    : angle       0.52481 (11610)
  hydrogen bonds       : bond        0.05351 (  403)
  hydrogen bonds       : angle       4.05251 ( 1182)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 39
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  246 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8346 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 55
  average time/residue: 0.0619
  time to fit residues: 5.7733
Evaluate side-chains
  53 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 2 optimal weight:    0.4980
   chunk 84 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 106 optimal weight:    8.9990
   chunk 68 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.071512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.059671 restraints weight = 31274.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.061608 restraints weight = 16458.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.062905 restraints weight = 10878.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.063737 restraints weight = 8210.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.064345 restraints weight = 6793.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8543  Z= 0.097
  Angle     :  0.480   7.953  11610  Z= 0.246
  Chirality :  0.038   0.140   1362
  Planarity :  0.003   0.034   1460
  Dihedral  :  5.937  69.609   1178
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 20.02 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.26), residues: 1077
  helix:  2.48 (0.24), residues: 479
  sheet: -0.97 (0.43), residues: 144
  loop : -0.85 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 175 
 TYR   0.011   0.001   TYR A1004 
 PHE   0.011   0.001   PHE A 405 
 TRP   0.006   0.001   TRP A 787 
 HIS   0.002   0.000   HIS A 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 8543)
  covalent geometry    : angle       0.47984 (11610)
  hydrogen bonds       : bond        0.04090 (  403)
  hydrogen bonds       : angle       3.60905 ( 1182)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A  246 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.8221 (t80)
REVERT: A 1136 MET cc_start: 0.7663 (mmm) cc_final: 0.7378 (mmm)
  outliers start: 11
  outliers final: 7
  residues processed: 52
  average time/residue: 0.0523
  time to fit residues: 4.5889
Evaluate side-chains
  47 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 89 optimal weight:    0.4980
   chunk 71 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 104 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 106 optimal weight:    0.7980
   overall best weight:    1.0184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.071179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.059379 restraints weight = 31285.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.061313 restraints weight = 16447.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.062613 restraints weight = 10838.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.063423 restraints weight = 8153.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.064056 restraints weight = 6734.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8543  Z= 0.105
  Angle     :  0.497  10.435  11610  Z= 0.249
  Chirality :  0.038   0.141   1362
  Planarity :  0.003   0.031   1460
  Dihedral  :  5.844  71.674   1178
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 20.13 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.26), residues: 1077
  helix:  2.55 (0.24), residues: 479
  sheet: -0.86 (0.42), residues: 144
  loop : -0.82 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 175 
 TYR   0.008   0.001   TYR A1004 
 PHE   0.010   0.001   PHE A 405 
 TRP   0.007   0.001   TRP A 787 
 HIS   0.002   0.000   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8543)
  covalent geometry    : angle       0.49703 (11610)
  hydrogen bonds       : bond        0.04118 (  403)
  hydrogen bonds       : angle       3.58516 ( 1182)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  246 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8212 (t80)
REVERT: A 1136 MET cc_start: 0.7824 (mmm) cc_final: 0.7496 (mmm)
  outliers start: 18
  outliers final: 12
  residues processed: 54
  average time/residue: 0.0641
  time to fit residues: 5.6616
Evaluate side-chains
  52 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:    8.9990
   chunk 96 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0570
   chunk 65 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    2.0106

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.070527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.059044 restraints weight = 31273.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.060893 restraints weight = 16688.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.062130 restraints weight = 11106.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.062991 restraints weight = 8428.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.063522 restraints weight = 6926.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8543  Z= 0.160
  Angle     :  0.540  11.628  11610  Z= 0.271
  Chirality :  0.039   0.143   1362
  Planarity :  0.003   0.030   1460
  Dihedral  :  5.951  75.439   1178
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 20.58 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.26), residues: 1077
  helix:  2.49 (0.24), residues: 479
  sheet: -0.63 (0.45), residues: 134
  loop : -0.85 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 260 
 TYR   0.012   0.001   TYR A 625 
 PHE   0.013   0.001   PHE A 499 
 TRP   0.007   0.001   TRP A 787 
 HIS   0.003   0.001   HIS A 691 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8543)
  covalent geometry    : angle       0.54015 (11610)
  hydrogen bonds       : bond        0.04798 (  403)
  hydrogen bonds       : angle       3.78185 ( 1182)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  246 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8237 (t80)
REVERT: A 1136 MET cc_start: 0.7954 (mmm) cc_final: 0.7677 (mmm)
  outliers start: 16
  outliers final: 15
  residues processed: 51
  average time/residue: 0.0627
  time to fit residues: 5.3163
Evaluate side-chains
  54 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0060
   chunk 70 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 106 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.5800

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.069272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.057607 restraints weight = 31445.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.059522 restraints weight = 16206.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.060796 restraints weight = 10571.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.061677 restraints weight = 7926.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.062173 restraints weight = 6471.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8543  Z= 0.132
  Angle     :  0.522  12.337  11610  Z= 0.261
  Chirality :  0.038   0.141   1362
  Planarity :  0.003   0.031   1460
  Dihedral  :  5.875  71.683   1178
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.70 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.27), residues: 1077
  helix:  2.50 (0.24), residues: 479
  sheet: -0.78 (0.43), residues: 144
  loop : -0.84 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 634 
 TYR   0.010   0.001   TYR A 625 
 PHE   0.011   0.001   PHE A 499 
 TRP   0.006   0.001   TRP A 137 
 HIS   0.002   0.001   HIS A 691 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8543)
  covalent geometry    : angle       0.52173 (11610)
  hydrogen bonds       : bond        0.04549 (  403)
  hydrogen bonds       : angle       3.70346 ( 1182)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  246 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8247 (t80)
REVERT: A 1136 MET cc_start: 0.7931 (mmm) cc_final: 0.7655 (mmm)
  outliers start: 15
  outliers final: 13
  residues processed: 49
  average time/residue: 0.0627
  time to fit residues: 5.1009
Evaluate side-chains
  51 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 83 optimal weight:    0.0170
   chunk 31 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.0622

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.071023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.059252 restraints weight = 31281.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.061162 restraints weight = 16355.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.062465 restraints weight = 10823.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.063368 restraints weight = 8151.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.063985 restraints weight = 6658.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8543  Z= 0.105
  Angle     :  0.500  12.320  11610  Z= 0.250
  Chirality :  0.038   0.141   1362
  Planarity :  0.003   0.031   1460
  Dihedral  :  5.757  69.005   1178
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.70 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.27), residues: 1077
  helix:  2.56 (0.24), residues: 479
  sheet: -0.71 (0.43), residues: 144
  loop : -0.80 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 175 
 TYR   0.008   0.001   TYR A1004 
 PHE   0.010   0.001   PHE A1164 
 TRP   0.006   0.001   TRP A 137 
 HIS   0.002   0.000   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8543)
  covalent geometry    : angle       0.50020 (11610)
  hydrogen bonds       : bond        0.04145 (  403)
  hydrogen bonds       : angle       3.57145 ( 1182)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1192.69 seconds
wall clock time: 21 minutes 17.12 seconds (1277.12 seconds total)