Starting phenix.real_space_refine
on Wed Mar  4 02:58:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ny3_8980/03_2026/6ny3_8980.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ny3_8980/03_2026/6ny3_8980.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ny3_8980/03_2026/6ny3_8980.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ny3_8980/03_2026/6ny3_8980.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ny3_8980/03_2026/6ny3_8980.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ny3_8980/03_2026/6ny3_8980.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.110
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     164      5.49       5
     S      21      5.16       5
     C    5880      2.51       5
     N    1863      2.21       5
     O    2286      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s

  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: 10214
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 614
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "D"
      Number of atoms: 485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 485
          Classifications: {'DNA': 24}
          Link IDs: {'rna3p': 23}
    Chain: "Y"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 829
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    Chain: "Y"
      Number of atoms: 5055
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 678, 5055
          Classifications: {'peptide': 678}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 121}
          Link IDs: {'PTRANS': 22, 'TRANS': 655}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 356
          Unresolved non-hydrogen angles: 468
          Unresolved non-hydrogen dihedrals: 249
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'UNK:plan-1': 57, 'ASN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 15, 'GLU:plan': 23, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 237
    Chain: "Y"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 887
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 153
          Unresolved non-hydrogen angles: 223
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'UNK:plan-1': 64, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 79
    Chain: "B"
      Number of atoms: 2344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 2344
          Classifications: {'RNA': 110}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 45}
          Link IDs: {'rna2p': 10, 'rna3p': 99}
          Chain breaks: 2
  Time building chain proxies: 2.55, per 1000 atoms: 0.25
  Number of scatterers: 10214
  At special positions: 0
  Unit cell: (97.2, 139.5, 123.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P     164     15.00
     O    2286      8.00
     N    1863      7.00
     C    5880      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS Y 826 " - pdb=" SG  CYS Y 928 " distance=2.02

  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
  Links applied
    TRANS
      " UNK Y 104 " - " SER Y 103 "
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 408.2 milliseconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1724

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 7 sheets defined
      44.5% alpha, 7.7% beta
      63 base pairs and 99 stacking pairs defined.
    Time for finding SS restraints: 1.51
  Creating SS restraints...
    Processing helix  chain 'Y' and resid 4 through 13
      removed outlier: 3.566A  pdb=" N   ILE Y   8 " --> pdb=" O   ARG Y   4 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG Y   9 " --> pdb=" O   ILE Y   5 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LYS Y  10 " --> pdb=" O   ASN Y   6 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 37 through 42
    Processing helix  chain 'Y' and resid 60 through 88
      removed outlier: 3.641A  pdb=" N   ASN Y  64 " --> pdb=" O   ASN Y  60 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 90 through 98
    Processing helix  chain 'Y' and resid 222 through 260
      removed outlier: 4.440A  pdb=" N   ASP Y 245 " --> pdb=" O   SER Y 241 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 262 through 271
      removed outlier: 4.476A  pdb=" N   ALA Y 268 " --> pdb=" O   LEU Y 264 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 287 through 308
    Processing helix  chain 'Y' and resid 343 through 357
      removed outlier: 3.953A  pdb=" N   LYS Y 357 " --> pdb=" O   LEU Y 353 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 361 through 366
      removed outlier: 3.917A  pdb=" N   TRP Y 365 " --> pdb=" O   GLY Y 361 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 371 through 380
    Processing helix  chain 'Y' and resid 404 through 417
    Processing helix  chain 'Y' and resid 423 through 429
      removed outlier: 4.306A  pdb=" N   ASP Y 427 " --> pdb=" O   GLY Y 423 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 433 through 448
      removed outlier: 3.575A  pdb=" N   LEU Y 440 " --> pdb=" O   LYS Y 436 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   HIS Y 443 " --> pdb=" O   GLY Y 439 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU Y 445 " --> pdb=" O   THR Y 441 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ARG Y 446 " --> pdb=" O   SER Y 442 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 458 through 473
    Processing helix  chain 'Y' and resid 475 through 480
    Processing helix  chain 'Y' and resid 481 through 501
      removed outlier: 4.371A  pdb=" N   TYR Y 485 " --> pdb=" O   GLU Y 481 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ALA Y 486 " --> pdb=" O   LYS Y 482 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 502 through 504
      No H-bonds generated for 'chain 'Y' and resid 502 through 504'
    Processing helix  chain 'Y' and resid 602 through 610
    Processing helix  chain 'Y' and resid 711 through 728
      removed outlier: 3.884A  pdb=" N   ARG Y 728 " --> pdb=" O   VAL Y 724 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 738 through 762
      removed outlier: 3.904A  pdb=" N   ASN Y 742 " --> pdb=" O   SER Y 738 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   HIS Y 762 " --> pdb=" O   HIS Y 758 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 783 through 787
    Processing helix  chain 'Y' and resid 790 through 802
      removed outlier: 4.049A  pdb=" N   TYR Y 802 " --> pdb=" O   ALA Y 798 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 886 through 892
    Processing helix  chain 'Y' and resid 897 through 904
    Processing helix  chain 'Y' and resid 906 through 914
      removed outlier: 3.747A  pdb=" N   UNK Y 910 " --> pdb=" O   UNK Y 906 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 945 through 950
    Processing helix  chain 'Y' and resid 965 through 978
      removed outlier: 3.534A  pdb=" N   ARG Y 976 " --> pdb=" O   ALA Y 972 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'Y' and resid 18 through 19
    Processing sheet with id=AA2, first strand: chain 'Y' and resid 27 through 29
      removed outlier: 3.605A  pdb=" N   ASN Y 626 " --> pdb=" O   THR Y 651 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   GLU Y 653 " --> pdb=" O   LEU Y 624 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   LEU Y 624 " --> pdb=" O   GLU Y 653 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG Y 510 " --> pdb=" O   GLU Y 631 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'Y' and resid 27 through 29
      removed outlier: 3.605A  pdb=" N   ASN Y 626 " --> pdb=" O   THR Y 651 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   GLU Y 653 " --> pdb=" O   LEU Y 624 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   LEU Y 624 " --> pdb=" O   GLU Y 653 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Y' and resid 33 through 34
      removed outlier: 3.695A  pdb=" N   ARG Y  33 " --> pdb=" O   ALA Y 600 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Y' and resid 518 through 519
      removed outlier: 4.031A  pdb=" N   SER Y 518 " --> pdb=" O   GLN Y 527 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'Y' and resid 557 through 558
      removed outlier: 4.036A  pdb=" N   ARG Y 557 " --> pdb=" O   THR Y 586 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'Y' and resid 669 through 670
      removed outlier: 6.363A  pdb=" N   ILE Y 669 " --> pdb=" O   VAL Y 767 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   ALA Y 769 " --> pdb=" O   ILE Y 669 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   LEU Y 766 " --> pdb=" O   SER Y 812 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   THR Y 814 " --> pdb=" O   LEU Y 766 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   PHE Y 768 " --> pdb=" O   THR Y 814 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    250 hydrogen bonds defined for protein.
    732 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      153 hydrogen bonds
      288 hydrogen bond angles
      0 basepair planarities
      63 basepair parallelities
      99 stacking parallelities
  Total time for adding SS restraints: 2.46

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1454
        1.32 -     1.44: 3695
        1.44 -     1.57: 5236
        1.57 -     1.69: 323
        1.69 -     1.81: 34
  Bond restraints: 10742
  Sorted by residual:
  bond pdb=" CA  HIS Y 199 "
       pdb=" CB  HIS Y 199 "
    ideal  model  delta    sigma   weight residual
    1.530  1.488  0.042 1.69e-02 3.50e+03 6.27e+00
  bond pdb=" CA  LEU Y 615 "
       pdb=" CB  LEU Y 615 "
    ideal  model  delta    sigma   weight residual
    1.531  1.449  0.082 3.28e-02 9.30e+02 6.18e+00
  bond pdb=" CG  LEU Y 585 "
       pdb=" CD1 LEU Y 585 "
    ideal  model  delta    sigma   weight residual
    1.521  1.441  0.080 3.30e-02 9.18e+02 5.95e+00
  bond pdb=" C   SER Y 197 "
       pdb=" N   ILE Y 198 "
    ideal  model  delta    sigma   weight residual
    1.332  1.300  0.032 1.36e-02 5.41e+03 5.40e+00
  bond pdb=" C   ASN Y 501 "
       pdb=" N   PRO Y 502 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.020 8.40e-03 1.42e+04 5.39e+00
  ... (remaining 10737 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.27: 14984
        3.27 -     6.55: 273
        6.55 -     9.82: 30
        9.82 -    13.09: 4
       13.09 -    16.37: 1
  Bond angle restraints: 15292
  Sorted by residual:
  angle pdb=" N   GLY Y 572 "
        pdb=" CA  GLY Y 572 "
        pdb=" C   GLY Y 572 "
      ideal   model   delta    sigma   weight residual
     113.18  129.55  -16.37 2.37e+00 1.78e-01 4.77e+01
  angle pdb=" CA  TRP Y 534 "
        pdb=" CB  TRP Y 534 "
        pdb=" CG  TRP Y 534 "
      ideal   model   delta    sigma   weight residual
     113.60  125.99  -12.39 1.90e+00 2.77e-01 4.25e+01
  angle pdb=" N   SER Y 197 "
        pdb=" CA  SER Y 197 "
        pdb=" C   SER Y 197 "
      ideal   model   delta    sigma   weight residual
     114.64  104.98    9.66 1.52e+00 4.33e-01 4.04e+01
  angle pdb=" C   ILE Y 198 "
        pdb=" N   HIS Y 199 "
        pdb=" CA  HIS Y 199 "
      ideal   model   delta    sigma   weight residual
     121.54  131.42   -9.88 1.91e+00 2.74e-01 2.68e+01
  angle pdb=" N   THR Y 954 "
        pdb=" CA  THR Y 954 "
        pdb=" C   THR Y 954 "
      ideal   model   delta    sigma   weight residual
     114.62  109.13    5.49 1.14e+00 7.69e-01 2.32e+01
  ... (remaining 15287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.22: 5796
       34.22 -    68.44: 555
       68.44 -   102.65: 46
      102.65 -   136.87: 1
      136.87 -   171.09: 4
  Dihedral angle restraints: 6402
    sinusoidal: 3745
      harmonic: 2657
  Sorted by residual:
  dihedral pdb=" CA  ILE Y 198 "
           pdb=" C   ILE Y 198 "
           pdb=" N   HIS Y 199 "
           pdb=" CA  HIS Y 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.16  -41.84     0      5.00e+00 4.00e-02 7.00e+01
  dihedral pdb=" O4'   U B  17 "
           pdb=" C1'   U B  17 "
           pdb=" N1    U B  17 "
           pdb=" C2    U B  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   64.29  167.71     1      1.70e+01 3.46e-03 6.57e+01
  dihedral pdb=" CA  GLY Y 367 "
           pdb=" C   GLY Y 367 "
           pdb=" N   VAL Y 368 "
           pdb=" CA  VAL Y 368 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.98  -34.02     0      5.00e+00 4.00e-02 4.63e+01
  ... (remaining 6399 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1507
       0.068 -    0.137: 250
       0.137 -    0.205: 48
       0.205 -    0.273: 6
       0.273 -    0.341: 5
  Chirality restraints: 1816
  Sorted by residual:
  chirality pdb=" CB  ILE Y 677 "
            pdb=" CA  ILE Y 677 "
            pdb=" CG1 ILE Y 677 "
            pdb=" CG2 ILE Y 677 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" C3'   G B  44 "
            pdb=" C4'   G B  44 "
            pdb=" O3'   G B  44 "
            pdb=" C2'   G B  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.17   -0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" C3'   G B  30 "
            pdb=" C4'   G B  30 "
            pdb=" O3'   G B  30 "
            pdb=" C2'   G B  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.17   -0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 1813 not shown)

  Planarity restraints: 1364
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP Y 534 "   -0.025 2.00e-02 2.50e+03   1.97e-02 9.70e+00
        pdb=" CG  TRP Y 534 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP Y 534 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP Y 534 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP Y 534 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP Y 534 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP Y 534 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP Y 534 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP Y 534 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP Y 534 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  56 "   -0.039 2.00e-02 2.50e+03   1.85e-02 9.41e+00
        pdb=" N9    A B  56 "    0.045 2.00e-02 2.50e+03
        pdb=" C8    A B  56 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A B  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A B  56 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A B  56 "    0.000 2.00e-02 2.50e+03
        pdb=" N6    A B  56 "   -0.011 2.00e-02 2.50e+03
        pdb=" N1    A B  56 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    A B  56 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A B  56 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    A B  56 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN Y 501 "    0.047 5.00e-02 4.00e+02   7.08e-02 8.02e+00
        pdb=" N   PRO Y 502 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 502 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 502 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1361 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2340
        2.78 -     3.31: 8487
        3.31 -     3.84: 18053
        3.84 -     4.37: 19591
        4.37 -     4.90: 30769
  Nonbonded interactions: 79240
  Sorted by model distance:
  nonbonded pdb=" OH  TYR Y 196 "
            pdb=" O   SER Y 221 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O4    U B  65 "
            pdb=" O6    G B  87 "
     model   vdw
     2.295 2.432
  nonbonded pdb=" OG1 THR Y 603 "
            pdb=" OP2   A B  18 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   SER Y 204 "
            pdb=" OG  SER Y 204 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   SER Y 661 "
            pdb=" OG  SER Y 661 "
     model   vdw
     2.334 3.040
  ... (remaining 79235 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.530
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.560
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.082  10744  Z= 0.410
  Angle     :  1.131  16.367  15297  Z= 0.624
  Chirality :  0.056   0.341   1816
  Planarity :  0.007   0.071   1363
  Dihedral  : 22.552 171.087   4672
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 16.88 %
    Favored  : 82.48 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 11.51 %
    Favored  : 88.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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: -5.86 (0.20), residues: 782
  helix: -3.34 (0.18), residues: 349
  sheet: -4.27 (0.40), residues: 92
  loop : -4.33 (0.24), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Y 787 
 TYR   0.022   0.003   TYR Y 732 
 PHE   0.039   0.004   PHE Y 609 
 TRP   0.053   0.003   TRP Y 534 
 HIS   0.019   0.004   HIS Y 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00909 (10742)
  covalent geometry    : angle       1.13080 (15292)
  SS BOND              : bond        0.00789 (    1)
  SS BOND              : angle       2.50922 (    2)
  hydrogen bonds       : bond        0.15717 (  400)
  hydrogen bonds       : angle       6.77320 ( 1020)
  link_TRANS           : bond        0.00138 (    1)
  link_TRANS           : angle       0.78483 (    3)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.238 
Fit side-chains
REVERT: Y  498 LEU cc_start: 0.8628 (mt) cc_final: 0.8302 (mt)
REVERT: Y  950 ASN cc_start: 0.8438 (p0) cc_final: 0.8233 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1304
  time to fit residues: 14.9848
Evaluate side-chains
  64 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
Y  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.152242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.114717 restraints weight = 13855.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.117704 restraints weight = 8016.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.119625 restraints weight = 5720.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.120894 restraints weight = 4667.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.121485 restraints weight = 4118.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10744  Z= 0.139
  Angle     :  0.686   9.151  15297  Z= 0.361
  Chirality :  0.038   0.215   1816
  Planarity :  0.005   0.047   1363
  Dihedral  : 23.301 179.454   3232
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 14.83 %
    Favored  : 84.91 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.79 %
    Favored  : 81.41 %
  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: -4.01 (0.26), residues: 782
  helix: -1.24 (0.26), residues: 337
  sheet: -3.84 (0.45), residues: 92
  loop : -3.81 (0.26), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG Y 475 
 TYR   0.011   0.001   TYR Y 528 
 PHE   0.024   0.002   PHE Y 503 
 TRP   0.027   0.002   TRP Y 534 
 HIS   0.005   0.001   HIS Y 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (10742)
  covalent geometry    : angle       0.68583 (15292)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       1.12620 (    2)
  hydrogen bonds       : bond        0.05329 (  400)
  hydrogen bonds       : angle       4.33183 ( 1020)
  link_TRANS           : bond        0.00057 (    1)
  link_TRANS           : angle       0.76550 (    3)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.284 
Fit side-chains
REVERT: Y  219 TYR cc_start: 0.8522 (m-10) cc_final: 0.8282 (m-10)
REVERT: Y  316 ARG cc_start: 0.8490 (tpp80) cc_final: 0.8093 (mmt90)
REVERT: Y  585 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8046 (pp)
REVERT: Y  639 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5703 (pt)
  outliers start: 17
  outliers final: 5
  residues processed: 90
  average time/residue: 0.1079
  time to fit residues: 13.4873
Evaluate side-chains
  73 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   21 VAL
Chi-restraints excluded: chain Y residue  585 LEU
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0870
   chunk 39 optimal weight:    0.0060
   chunk 49 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0980
   overall best weight:    0.3774

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.159115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.121997 restraints weight = 13974.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.125092 restraints weight = 7926.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.127116 restraints weight = 5611.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.128232 restraints weight = 4558.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.128969 restraints weight = 4038.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10744  Z= 0.118
  Angle     :  0.615   7.874  15297  Z= 0.324
  Chirality :  0.035   0.208   1816
  Planarity :  0.004   0.045   1363
  Dihedral  : 23.115 179.671   3232
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.45 %
    Favored  : 85.55 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 19.08 %
    Favored  : 77.63 %
  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: -3.06 (0.29), residues: 782
  helix: -0.29 (0.28), residues: 346
  sheet: -3.37 (0.50), residues: 91
  loop : -3.57 (0.28), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Y 299 
 TYR   0.012   0.001   TYR Y 196 
 PHE   0.019   0.001   PHE Y 775 
 TRP   0.020   0.001   TRP Y 534 
 HIS   0.004   0.001   HIS Y 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (10742)
  covalent geometry    : angle       0.61486 (15292)
  SS BOND              : bond        0.00005 (    1)
  SS BOND              : angle       0.79766 (    2)
  hydrogen bonds       : bond        0.04328 (  400)
  hydrogen bonds       : angle       3.82056 ( 1020)
  link_TRANS           : bond        0.00005 (    1)
  link_TRANS           : angle       1.00728 (    3)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.283 
Fit side-chains
REVERT: Y   35 MET cc_start: 0.8161 (mtp) cc_final: 0.7895 (mtm)
REVERT: Y  219 TYR cc_start: 0.8275 (m-10) cc_final: 0.8009 (m-10)
REVERT: Y  316 ARG cc_start: 0.8630 (tpp80) cc_final: 0.8348 (tpt-90)
REVERT: Y  528 TYR cc_start: 0.8408 (m-80) cc_final: 0.8023 (m-80)
REVERT: Y  639 ILE cc_start: 0.6023 (OUTLIER) cc_final: 0.5708 (pt)
REVERT: Y  765 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7152 (p)
REVERT: Y  960 LYS cc_start: 0.8602 (tppt) cc_final: 0.8232 (tptt)
  outliers start: 20
  outliers final: 11
  residues processed: 98
  average time/residue: 0.0921
  time to fit residues: 13.0031
Evaluate side-chains
  83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  280 LEU
Chi-restraints excluded: chain Y residue  341 VAL
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  503 PHE
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  594 LEU
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  765 VAL
Chi-restraints excluded: chain Y residue  782 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0070
   chunk 14 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 81 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    0.8600

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.155873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.118045 restraints weight = 13955.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.121157 restraints weight = 7930.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.123125 restraints weight = 5607.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.124441 restraints weight = 4540.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.125179 restraints weight = 4007.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10744  Z= 0.132
  Angle     :  0.624  10.095  15297  Z= 0.324
  Chirality :  0.036   0.209   1816
  Planarity :  0.004   0.044   1363
  Dihedral  : 23.049 179.867   3232
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 13.81 %
    Favored  : 86.06 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.38 %
    Favored  : 75.82 %
  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: -2.50 (0.30), residues: 782
  helix:  0.26 (0.29), residues: 338
  sheet: -3.01 (0.59), residues: 74
  loop : -3.36 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Y 475 
 TYR   0.011   0.001   TYR Y 528 
 PHE   0.028   0.001   PHE Y 775 
 TRP   0.025   0.001   TRP Y 534 
 HIS   0.015   0.002   HIS Y 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10742)
  covalent geometry    : angle       0.62361 (15292)
  SS BOND              : bond        0.00134 (    1)
  SS BOND              : angle       0.67023 (    2)
  hydrogen bonds       : bond        0.04599 (  400)
  hydrogen bonds       : angle       3.64494 ( 1020)
  link_TRANS           : bond        0.00046 (    1)
  link_TRANS           : angle       1.11799 (    3)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.288 
Fit side-chains
REVERT: Y   35 MET cc_start: 0.8228 (mtp) cc_final: 0.7897 (mtm)
REVERT: Y  219 TYR cc_start: 0.8413 (m-10) cc_final: 0.8073 (m-10)
REVERT: Y  233 MET cc_start: 0.8311 (mmp) cc_final: 0.7977 (mmp)
REVERT: Y  530 ASN cc_start: 0.8987 (m-40) cc_final: 0.8646 (m-40)
REVERT: Y  639 ILE cc_start: 0.6002 (OUTLIER) cc_final: 0.5668 (pt)
  outliers start: 17
  outliers final: 11
  residues processed: 85
  average time/residue: 0.0932
  time to fit residues: 11.6870
Evaluate side-chains
  75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  341 VAL
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  932 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 4 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 40 optimal weight:    0.0970
   chunk 64 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.158286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.120888 restraints weight = 14016.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.123803 restraints weight = 8332.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.125659 restraints weight = 6046.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.126861 restraints weight = 4966.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.127453 restraints weight = 4426.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10744  Z= 0.118
  Angle     :  0.604  11.176  15297  Z= 0.313
  Chirality :  0.035   0.209   1816
  Planarity :  0.004   0.044   1363
  Dihedral  : 22.995 179.499   3232
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.32 %
    Favored  : 85.55 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.89 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.30), residues: 782
  helix:  0.52 (0.29), residues: 344
  sheet: -3.09 (0.54), residues: 91
  loop : -3.20 (0.30), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y 706 
 TYR   0.010   0.001   TYR Y 196 
 PHE   0.031   0.001   PHE Y 775 
 TRP   0.018   0.001   TRP Y 534 
 HIS   0.008   0.001   HIS Y 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (10742)
  covalent geometry    : angle       0.60438 (15292)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       0.45707 (    2)
  hydrogen bonds       : bond        0.04299 (  400)
  hydrogen bonds       : angle       3.52965 ( 1020)
  link_TRANS           : bond        0.00040 (    1)
  link_TRANS           : angle       1.05675 (    3)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.287 
Fit side-chains
REVERT: Y   35 MET cc_start: 0.8187 (mtp) cc_final: 0.7829 (mtm)
REVERT: Y  219 TYR cc_start: 0.8271 (m-10) cc_final: 0.7992 (m-10)
REVERT: Y  639 ILE cc_start: 0.6084 (OUTLIER) cc_final: 0.5769 (pt)
REVERT: Y  765 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7313 (p)
  outliers start: 23
  outliers final: 14
  residues processed: 88
  average time/residue: 0.0898
  time to fit residues: 11.7003
Evaluate side-chains
  79 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  341 VAL
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  594 LEU
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  765 VAL
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  932 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 17 optimal weight:   20.0000
   chunk 64 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 59 optimal weight:    0.4980
   chunk 61 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.155814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.117673 restraints weight = 14095.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.120707 restraints weight = 8156.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.122714 restraints weight = 5834.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.123872 restraints weight = 4755.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.124741 restraints weight = 4206.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10744  Z= 0.139
  Angle     :  0.622  11.905  15297  Z= 0.321
  Chirality :  0.035   0.211   1816
  Planarity :  0.004   0.045   1363
  Dihedral  : 22.971 178.822   3232
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.83 %
    Favored  : 85.04 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 21.38 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.30), residues: 782
  helix:  0.62 (0.30), residues: 344
  sheet: -3.12 (0.55), residues: 82
  loop : -3.13 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Y 706 
 TYR   0.014   0.001   TYR Y 528 
 PHE   0.019   0.001   PHE Y 775 
 TRP   0.023   0.001   TRP Y 534 
 HIS   0.005   0.001   HIS Y 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10742)
  covalent geometry    : angle       0.62191 (15292)
  SS BOND              : bond        0.00320 (    1)
  SS BOND              : angle       0.39446 (    2)
  hydrogen bonds       : bond        0.04606 (  400)
  hydrogen bonds       : angle       3.52006 ( 1020)
  link_TRANS           : bond        0.00026 (    1)
  link_TRANS           : angle       1.06244 (    3)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.281 
Fit side-chains
REVERT: Y   35 MET cc_start: 0.8248 (mtp) cc_final: 0.7918 (mtm)
REVERT: Y  219 TYR cc_start: 0.8373 (m-10) cc_final: 0.8084 (m-10)
REVERT: Y  381 ASN cc_start: 0.8778 (t0) cc_final: 0.8305 (t0)
REVERT: Y  639 ILE cc_start: 0.6137 (OUTLIER) cc_final: 0.5801 (pt)
  outliers start: 20
  outliers final: 15
  residues processed: 77
  average time/residue: 0.0886
  time to fit residues: 10.0212
Evaluate side-chains
  77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   21 VAL
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue   56 VAL
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  311 LYS
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  949 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.151580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.112858 restraints weight = 14046.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.115755 restraints weight = 8290.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.117667 restraints weight = 6014.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.118735 restraints weight = 4957.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.119512 restraints weight = 4428.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10744  Z= 0.177
  Angle     :  0.663  11.934  15297  Z= 0.342
  Chirality :  0.037   0.216   1816
  Planarity :  0.004   0.045   1363
  Dihedral  : 22.975 177.049   3232
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.96 %
    Favored  : 84.91 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 21.05 %
    Favored  : 75.00 %
  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: -2.14 (0.30), residues: 782
  helix:  0.58 (0.29), residues: 344
  sheet: -2.82 (0.61), residues: 74
  loop : -3.25 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Y 706 
 TYR   0.016   0.002   TYR Y 528 
 PHE   0.018   0.002   PHE Y 775 
 TRP   0.025   0.001   TRP Y 534 
 HIS   0.005   0.002   HIS Y  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (10742)
  covalent geometry    : angle       0.66289 (15292)
  SS BOND              : bond        0.00300 (    1)
  SS BOND              : angle       0.46206 (    2)
  hydrogen bonds       : bond        0.05313 (  400)
  hydrogen bonds       : angle       3.62933 ( 1020)
  link_TRANS           : bond        0.00098 (    1)
  link_TRANS           : angle       0.97119 (    3)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.193 
Fit side-chains
REVERT: Y   35 MET cc_start: 0.8325 (mtp) cc_final: 0.8038 (mtm)
REVERT: Y  219 TYR cc_start: 0.8546 (m-10) cc_final: 0.8184 (m-10)
REVERT: Y  639 ILE cc_start: 0.6060 (OUTLIER) cc_final: 0.5695 (pt)
REVERT: Y  794 ASP cc_start: 0.8752 (t0) cc_final: 0.8398 (t0)
  outliers start: 24
  outliers final: 20
  residues processed: 80
  average time/residue: 0.0849
  time to fit residues: 10.1811
Evaluate side-chains
  83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   21 VAL
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  247 ILE
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  418 TYR
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  517 PHE
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  785 THR
Chi-restraints excluded: chain Y residue  823 CYS
Chi-restraints excluded: chain Y residue  949 LEU
Chi-restraints excluded: chain Y residue  952 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.153868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.115291 restraints weight = 14043.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.118293 restraints weight = 8260.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.120263 restraints weight = 5942.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.121402 restraints weight = 4871.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.122222 restraints weight = 4327.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10744  Z= 0.147
  Angle     :  0.632  12.805  15297  Z= 0.327
  Chirality :  0.036   0.215   1816
  Planarity :  0.004   0.045   1363
  Dihedral  : 22.947 176.614   3232
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.71 %
    Favored  : 85.17 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.04 %
    Favored  : 74.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.30), residues: 782
  helix:  0.57 (0.29), residues: 351
  sheet: -3.05 (0.58), residues: 81
  loop : -3.24 (0.29), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Y 706 
 TYR   0.015   0.001   TYR Y 528 
 PHE   0.038   0.002   PHE Y 775 
 TRP   0.023   0.001   TRP Y 534 
 HIS   0.004   0.001   HIS Y 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10742)
  covalent geometry    : angle       0.63165 (15292)
  SS BOND              : bond        0.00212 (    1)
  SS BOND              : angle       0.36825 (    2)
  hydrogen bonds       : bond        0.04875 (  400)
  hydrogen bonds       : angle       3.59379 ( 1020)
  link_TRANS           : bond        0.00037 (    1)
  link_TRANS           : angle       0.98521 (    3)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.304 
Fit side-chains
REVERT: Y   35 MET cc_start: 0.8336 (mtp) cc_final: 0.8024 (mtm)
REVERT: Y  219 TYR cc_start: 0.8456 (m-10) cc_final: 0.8081 (m-10)
REVERT: Y  381 ASN cc_start: 0.8845 (t0) cc_final: 0.8398 (t0)
REVERT: Y  639 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5719 (pt)
  outliers start: 20
  outliers final: 18
  residues processed: 84
  average time/residue: 0.0859
  time to fit residues: 10.8910
Evaluate side-chains
  81 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  311 LYS
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  418 TYR
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  517 PHE
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  785 THR
Chi-restraints excluded: chain Y residue  949 LEU
Chi-restraints excluded: chain Y residue  952 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 85 optimal weight:    6.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.155592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.117058 restraints weight = 14008.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.120075 restraints weight = 8212.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.122068 restraints weight = 5911.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.123111 restraints weight = 4838.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.124018 restraints weight = 4323.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10744  Z= 0.132
  Angle     :  0.624  13.598  15297  Z= 0.322
  Chirality :  0.036   0.212   1816
  Planarity :  0.004   0.044   1363
  Dihedral  : 22.906 176.642   3232
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.96 %
    Favored  : 85.04 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.53 %
    Favored  : 74.34 %
  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: -1.86 (0.31), residues: 782
  helix:  0.85 (0.30), residues: 344
  sheet: -2.94 (0.59), residues: 81
  loop : -3.06 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Y 706 
 TYR   0.015   0.001   TYR Y 575 
 PHE   0.034   0.002   PHE Y 775 
 TRP   0.018   0.001   TRP Y 534 
 HIS   0.004   0.001   HIS Y 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10742)
  covalent geometry    : angle       0.62291 (15292)
  SS BOND              : bond        0.00220 (    1)
  SS BOND              : angle       2.68574 (    2)
  hydrogen bonds       : bond        0.04604 (  400)
  hydrogen bonds       : angle       3.54999 ( 1020)
  link_TRANS           : bond        0.00022 (    1)
  link_TRANS           : angle       1.03681 (    3)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.281 
Fit side-chains
REVERT: Y   35 MET cc_start: 0.8264 (mtp) cc_final: 0.7943 (mtm)
REVERT: Y  381 ASN cc_start: 0.8819 (t0) cc_final: 0.8373 (t0)
REVERT: Y  409 ASP cc_start: 0.8634 (m-30) cc_final: 0.8217 (m-30)
REVERT: Y  639 ILE cc_start: 0.6095 (OUTLIER) cc_final: 0.5775 (pt)
REVERT: Y  794 ASP cc_start: 0.8731 (t0) cc_final: 0.8379 (t0)
REVERT: Y  920 GLN cc_start: 0.6709 (tp-100) cc_final: 0.6268 (tp-100)
  outliers start: 19
  outliers final: 17
  residues processed: 83
  average time/residue: 0.0829
  time to fit residues: 10.2778
Evaluate side-chains
  81 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  311 LYS
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  418 TYR
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  517 PHE
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  949 LEU
Chi-restraints excluded: chain Y residue  952 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 90 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 76 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.155372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.116941 restraints weight = 13964.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.119929 restraints weight = 8219.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.121801 restraints weight = 5930.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.123150 restraints weight = 4865.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.123575 restraints weight = 4310.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10744  Z= 0.135
  Angle     :  0.622  13.118  15297  Z= 0.321
  Chirality :  0.036   0.212   1816
  Planarity :  0.004   0.044   1363
  Dihedral  : 22.895 176.674   3232
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.45 %
    Favored  : 85.42 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.70 %
    Favored  : 74.18 %
  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: -1.87 (0.31), residues: 782
  helix:  0.84 (0.30), residues: 345
  sheet: -2.87 (0.59), residues: 81
  loop : -3.09 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Y 706 
 TYR   0.016   0.001   TYR Y 575 
 PHE   0.037   0.002   PHE Y 775 
 TRP   0.024   0.001   TRP Y 534 
 HIS   0.004   0.001   HIS Y 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10742)
  covalent geometry    : angle       0.62117 (15292)
  SS BOND              : bond        0.00096 (    1)
  SS BOND              : angle       2.41897 (    2)
  hydrogen bonds       : bond        0.04655 (  400)
  hydrogen bonds       : angle       3.55443 ( 1020)
  link_TRANS           : bond        0.00013 (    1)
  link_TRANS           : angle       1.03391 (    3)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.277 
Fit side-chains
REVERT: Y   35 MET cc_start: 0.8266 (mtp) cc_final: 0.7956 (mtm)
REVERT: Y  381 ASN cc_start: 0.8842 (t0) cc_final: 0.8403 (t0)
REVERT: Y  409 ASP cc_start: 0.8641 (m-30) cc_final: 0.8217 (m-30)
REVERT: Y  639 ILE cc_start: 0.6117 (OUTLIER) cc_final: 0.5794 (pt)
REVERT: Y  794 ASP cc_start: 0.8768 (t0) cc_final: 0.8400 (t0)
REVERT: Y  920 GLN cc_start: 0.6702 (tp-100) cc_final: 0.6254 (tp-100)
  outliers start: 19
  outliers final: 18
  residues processed: 79
  average time/residue: 0.0856
  time to fit residues: 10.1289
Evaluate side-chains
  83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   21 VAL
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  311 LYS
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  418 TYR
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  517 PHE
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  949 LEU
Chi-restraints excluded: chain Y residue  952 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 51 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0970
   chunk 83 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0670
   chunk 81 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 85 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.4916

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.159536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.121387 restraints weight = 13962.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.124501 restraints weight = 8152.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.126556 restraints weight = 5830.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.127640 restraints weight = 4746.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.128605 restraints weight = 4226.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10744  Z= 0.113
  Angle     :  0.596  13.945  15297  Z= 0.308
  Chirality :  0.035   0.208   1816
  Planarity :  0.003   0.044   1363
  Dihedral  : 22.861 178.693   3232
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.71 %
    Favored  : 85.29 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 23.19 %
    Favored  : 73.52 %
  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: -1.68 (0.31), residues: 782
  helix:  1.03 (0.30), residues: 346
  sheet: -2.87 (0.59), residues: 81
  loop : -3.01 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Y 706 
 TYR   0.013   0.001   TYR Y 528 
 PHE   0.036   0.001   PHE Y 775 
 TRP   0.014   0.001   TRP Y 534 
 HIS   0.004   0.001   HIS Y 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10742)
  covalent geometry    : angle       0.59507 (15292)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       2.36207 (    2)
  hydrogen bonds       : bond        0.04246 (  400)
  hydrogen bonds       : angle       3.48704 ( 1020)
  link_TRANS           : bond        0.00068 (    1)
  link_TRANS           : angle       1.08526 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1579.70 seconds
wall clock time: 27 minutes 57.66 seconds (1677.66 seconds total)