Starting phenix.real_space_refine
on Fri Aug 22 20:22:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sgj_40457/08_2025/8sgj_40457.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sgj_40457/08_2025/8sgj_40457.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sgj_40457/08_2025/8sgj_40457.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sgj_40457/08_2025/8sgj_40457.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sgj_40457/08_2025/8sgj_40457.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sgj_40457/08_2025/8sgj_40457.map"
  }
  resolution = 3.1
  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=   0.002 sd=   0.063
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     S      31      5.16       5
     Na      3      4.78       5
     C    4948      2.51       5
     N    1242      2.21       5
     O    1437      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7667
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 751, 5900
          Classifications: {'peptide': 751}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 724}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 816
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "H"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 941
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Unusual residues: {' CA': 6, ' NA': 3}
          Classifications: {'undetermined': 9, 'water': 1}
          Link IDs: {None: 9}
  Time building chain proxies: 1.51, per 1000 atoms: 0.20
  Number of scatterers: 7667
  At special positions: 0
  Unit cell: (97.11, 100.43, 146.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      6     19.99
     S      31     16.00
     Na      3     11.00
     O    1437      8.00
     N    1242      7.00
     C    4948      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  20 " - pdb=" SG  CYS A 792 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  21 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 419.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1798

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 13 sheets defined
      38.4% alpha, 28.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 72
    Processing helix  chain 'A' and resid 98 through 110
      removed outlier: 3.517A  pdb=" N   LEU A 104 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 124
      removed outlier: 3.511A  pdb=" N   HIS A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 155
      removed outlier: 3.821A  pdb=" N   ILE A 147 " --> pdb=" O   ASN A 143 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ILE A 148 " --> pdb=" O   MET A 144 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   VAL A 155 " --> pdb=" O   CYS A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 189
      removed outlier: 3.784A  pdb=" N   TYR A 180 " --> pdb=" O   SER A 176 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 187 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 220
      removed outlier: 4.507A  pdb=" N   PHE A 207 " --> pdb=" O   THR A 203 " (cutoff:3.500A)
      Proline residue:  A 208  - end of helix
    Processing helix  chain 'A' and resid 223 through 227
      removed outlier: 3.593A  pdb=" N   VAL A 227 " --> pdb=" O   TYR A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 607
    Processing helix  chain 'A' and resid 656 through 666
    Processing helix  chain 'A' and resid 684 through 697
    Processing helix  chain 'A' and resid 708 through 717
      removed outlier: 3.597A  pdb=" N   ILE A 717 " --> pdb=" O   PHE A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 755
      removed outlier: 5.420A  pdb=" N   PHE A 749 " --> pdb=" O   PHE A 745 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   TRP A 750 " --> pdb=" O   LEU A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 764
      removed outlier: 3.725A  pdb=" N   ASN A 764 " --> pdb=" O   GLU A 761 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 761 through 764'
    Processing helix  chain 'A' and resid 765 through 795
      removed outlier: 3.742A  pdb=" N   VAL A 771 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER A 788 " --> pdb=" O   GLY A 784 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE A 794 " --> pdb=" O   PHE A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 805
    Processing helix  chain 'A' and resid 805 through 811
    Processing helix  chain 'A' and resid 811 through 825
      removed outlier: 3.714A  pdb=" N   ASP A 825 " --> pdb=" O   ALA A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 845
      removed outlier: 3.583A  pdb=" N   VAL A 835 " --> pdb=" O   SER A 831 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   VAL A 843 " --> pdb=" O   ASN A 839 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 861
      removed outlier: 3.996A  pdb=" N   ALA A 850 " --> pdb=" O   GLY A 846 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 893
      removed outlier: 4.592A  pdb=" N   LEU A 872 " --> pdb=" O   SER A 868 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   PHE A 874 " --> pdb=" O   GLY A 870 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   SER A 875 " --> pdb=" O   THR A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 905 through 932
      removed outlier: 3.780A  pdb=" N   TYR A 932 " --> pdb=" O   SER A 928 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.816A  pdb=" N   GLU L  84 " --> pdb=" O   THR L  81 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.582A  pdb=" N   SER H  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.614A  pdb=" N   SER H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 79
      removed outlier: 4.365A  pdb=" N   TYR A 228 " --> pdb=" O   GLY A 245 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 161
    Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 195
      removed outlier: 4.262A  pdb=" N   PHE A 865 " --> pdb=" O   VAL A 195 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 443
    Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 384
      removed outlier: 6.894A  pdb=" N   TYR A 381 " --> pdb=" O   THR A 495 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   PHE A 497 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   CYS A 383 " --> pdb=" O   PHE A 497 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   VAL A 458 " --> pdb=" O   GLU A 412 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLU A 412 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
      removed outlier: 5.427A  pdb=" N   LEU A 460 " --> pdb=" O   ARG A 410 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ARG A 410 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
      removed outlier: 5.475A  pdb=" N   ASN A 462 " --> pdb=" O   ASP A 408 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ASP A 408 " --> pdb=" O   ASN A 462 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 574
    Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 515
      removed outlier: 6.842A  pdb=" N   THR A 512 " --> pdb=" O   ILE A 680 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   GLU A 682 " --> pdb=" O   THR A 512 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   VAL A 514 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 511 through 515
      removed outlier: 6.842A  pdb=" N   THR A 512 " --> pdb=" O   ILE A 680 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   GLU A 682 " --> pdb=" O   THR A 512 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   VAL A 514 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ASN A 534 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   VAL A 597 " --> pdb=" O   LYS A 628 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   LYS A 618 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   ARG A 627 " --> pdb=" O   THR A 616 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   THR A 616 " --> pdb=" O   ARG A 627 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 4
    Processing sheet with id=AB1, first strand: chain 'L' and resid 8 through 11
      removed outlier: 6.546A  pdb=" N   LEU L   9 " --> pdb=" O   THR L 106 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 11
      removed outlier: 6.546A  pdb=" N   LEU L   9 " --> pdb=" O   THR L 106 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.466A  pdb=" N   MET H  34 " --> pdb=" O   ALA H  50 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ALA H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.37

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2308
        1.34 -     1.46: 1441
        1.46 -     1.57: 4042
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 7836
  Sorted by residual:
  bond pdb=" CB  TRP A  29 "
       pdb=" CG  TRP A  29 "
    ideal  model  delta    sigma   weight residual
    1.498  1.433  0.065 3.10e-02 1.04e+03 4.33e+00
  bond pdb=" CA  TYR H  60 "
       pdb=" C   TYR H  60 "
    ideal  model  delta    sigma   weight residual
    1.521  1.496  0.025 1.23e-02 6.61e+03 4.16e+00
  bond pdb=" N   TRP A  29 "
       pdb=" CA  TRP A  29 "
    ideal  model  delta    sigma   weight residual
    1.455  1.434  0.021 1.30e-02 5.92e+03 2.69e+00
  bond pdb=" CA  LYS A 697 "
       pdb=" CB  LYS A 697 "
    ideal  model  delta    sigma   weight residual
    1.527  1.567 -0.039 2.48e-02 1.63e+03 2.52e+00
  bond pdb=" C   TYR H  60 "
       pdb=" O   TYR H  60 "
    ideal  model  delta    sigma   weight residual
    1.234  1.218  0.016 1.22e-02 6.72e+03 1.68e+00
  ... (remaining 7831 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 10356
        1.85 -     3.71: 234
        3.71 -     5.56: 37
        5.56 -     7.42: 7
        7.42 -     9.27: 4
  Bond angle restraints: 10638
  Sorted by residual:
  angle pdb=" N   TRP A  29 "
        pdb=" CA  TRP A  29 "
        pdb=" C   TRP A  29 "
      ideal   model   delta    sigma   weight residual
     110.20  103.08    7.12 1.58e+00 4.01e-01 2.03e+01
  angle pdb=" N   GLN H  82 "
        pdb=" CA  GLN H  82 "
        pdb=" C   GLN H  82 "
      ideal   model   delta    sigma   weight residual
     109.07  115.29   -6.22 1.61e+00 3.86e-01 1.49e+01
  angle pdb=" C   GLY L  51 "
        pdb=" N   THR L  52 "
        pdb=" CA  THR L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  128.36   -6.82 1.91e+00 2.74e-01 1.27e+01
  angle pdb=" C   TYR H  60 "
        pdb=" CA  TYR H  60 "
        pdb=" CB  TYR H  60 "
      ideal   model   delta    sigma   weight residual
     110.45  102.87    7.58 2.15e+00 2.16e-01 1.24e+01
  angle pdb=" C   ILE A 643 "
        pdb=" N   ALA A 644 "
        pdb=" CA  ALA A 644 "
      ideal   model   delta    sigma   weight residual
     121.70  127.93   -6.23 1.80e+00 3.09e-01 1.20e+01
  ... (remaining 10633 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 4166
       17.09 -    34.19: 320
       34.19 -    51.28: 55
       51.28 -    68.37: 5
       68.37 -    85.47: 8
  Dihedral angle restraints: 4554
    sinusoidal: 1746
      harmonic: 2808
  Sorted by residual:
  dihedral pdb=" CA  LEU A 637 "
           pdb=" C   LEU A 637 "
           pdb=" N   SER A 638 "
           pdb=" CA  SER A 638 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.45   17.55     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" C   TYR H  60 "
           pdb=" N   TYR H  60 "
           pdb=" CA  TYR H  60 "
           pdb=" CB  TYR H  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.98   -8.62     0      2.50e+00 1.60e-01 1.19e+01
  dihedral pdb=" CA  GLY A 549 "
           pdb=" C   GLY A 549 "
           pdb=" N   GLY A 550 "
           pdb=" CA  GLY A 550 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.54  -16.46     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 4551 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 860
       0.046 -    0.093: 271
       0.093 -    0.139: 75
       0.139 -    0.186: 6
       0.186 -    0.232: 3
  Chirality restraints: 1215
  Sorted by residual:
  chirality pdb=" CB  THR A 642 "
            pdb=" CA  THR A 642 "
            pdb=" OG1 THR A 642 "
            pdb=" CG2 THR A 642 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  ILE A 717 "
            pdb=" CA  ILE A 717 "
            pdb=" CG1 ILE A 717 "
            pdb=" CG2 ILE A 717 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CB  THR A 877 "
            pdb=" CA  THR A 877 "
            pdb=" OG1 THR A 877 "
            pdb=" CG2 THR A 877 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1212 not shown)

  Planarity restraints: 1332
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  28 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.78e+00
        pdb=" C   ILE A  28 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ILE A  28 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   TRP A  29 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 132 "   -0.042 5.00e-02 4.00e+02   6.34e-02 6.44e+00
        pdb=" N   PRO A 133 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 133 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 133 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 812 "    0.032 5.00e-02 4.00e+02   4.80e-02 3.69e+00
        pdb=" N   PRO A 813 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 813 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 813 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1329 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.58: 84
        2.58 -     3.16: 5975
        3.16 -     3.74: 11638
        3.74 -     4.32: 16557
        4.32 -     4.90: 28278
  Nonbonded interactions: 62532
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 451 "
            pdb="CA    CA A1003 "
     model   vdw
     1.994 2.510
  nonbonded pdb=" OD2 ASP A 421 "
            pdb="CA    CA A1003 "
     model   vdw
     2.115 2.510
  nonbonded pdb=" OD1 ASP A 421 "
            pdb="CA    CA A1003 "
     model   vdw
     2.182 2.510
  nonbonded pdb=" OD1 ASP A 408 "
            pdb=" OG1 THR A 428 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" OG  SER L  64 "
            pdb=" OG1 THR L  75 "
     model   vdw
     2.204 3.040
  ... (remaining 62527 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.310
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.460
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
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      :  0.004   0.065   7839  Z= 0.184
  Angle     :  0.699   9.269  10644  Z= 0.385
  Chirality :  0.048   0.232   1215
  Planarity :  0.006   0.063   1332
  Dihedral  : 12.734  85.467   2747
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.26), residues: 966
  helix: -0.03 (0.25), residues: 342
  sheet:  0.49 (0.29), residues: 311
  loop : -0.24 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  62 
 TYR   0.029   0.002   TYR A  46 
 PHE   0.028   0.002   PHE A 925 
 TRP   0.020   0.003   TRP A  95 
 HIS   0.003   0.001   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 7836)
  covalent geometry    : angle       0.69925 (10638)
  SS BOND              : bond        0.00255 (    3)
  SS BOND              : angle       0.82376 (    6)
  hydrogen bonds       : bond        0.14458 (  408)
  hydrogen bonds       : angle       6.67707 ( 1182)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8276 (mmm) cc_final: 0.8032 (mmm)
REVERT: A   62 ASP cc_start: 0.7920 (t70) cc_final: 0.7643 (t0)
REVERT: A  162 LYS cc_start: 0.7887 (tttp) cc_final: 0.7024 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0846
  time to fit residues: 17.8325
Evaluate side-chains
  113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 630 HIS
A 764 ASN
A 789 HIS
** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  35 ASN
H   6 GLN
H  82 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.138501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.100912 restraints weight = 10136.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.95
r_work: 0.3049 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7839  Z= 0.211
  Angle     :  0.576   7.435  10644  Z= 0.316
  Chirality :  0.044   0.148   1215
  Planarity :  0.005   0.047   1332
  Dihedral  :  4.440  17.425   1047
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  7.75 %
    Favored  : 90.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.26), residues: 966
  helix:  1.08 (0.27), residues: 344
  sheet:  0.32 (0.29), residues: 311
  loop : -0.22 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 232 
 TYR   0.015   0.002   TYR L  93 
 PHE   0.018   0.002   PHE A 925 
 TRP   0.024   0.002   TRP A 709 
 HIS   0.005   0.001   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 7836)
  covalent geometry    : angle       0.57616 (10638)
  SS BOND              : bond        0.00370 (    3)
  SS BOND              : angle       0.97192 (    6)
  hydrogen bonds       : bond        0.04728 (  408)
  hydrogen bonds       : angle       5.08761 ( 1182)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8374 (mmm) cc_final: 0.7982 (mmm)
REVERT: A   62 ASP cc_start: 0.7806 (t70) cc_final: 0.7521 (t0)
REVERT: A  162 LYS cc_start: 0.7734 (tttp) cc_final: 0.7457 (mtpp)
REVERT: A  181 THR cc_start: 0.8502 (m) cc_final: 0.8197 (p)
REVERT: A  209 ILE cc_start: 0.7547 (mm) cc_final: 0.7292 (mt)
REVERT: A  866 LYS cc_start: 0.8283 (mmmm) cc_final: 0.8067 (mmmm)
REVERT: A  897 GLU cc_start: 0.7710 (mp0) cc_final: 0.7442 (pm20)
REVERT: H   13 ARG cc_start: 0.7856 (mmm160) cc_final: 0.7630 (mmm160)
REVERT: H   46 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8103 (mt-10)
  outliers start: 11
  outliers final: 9
  residues processed: 118
  average time/residue: 0.0647
  time to fit residues: 10.5795
Evaluate side-chains
  112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain H residue   71 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 54 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    1.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.131927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.094837 restraints weight = 10270.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.91
r_work: 0.2962 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   7839  Z= 0.279
  Angle     :  0.608   6.388  10644  Z= 0.331
  Chirality :  0.046   0.173   1215
  Planarity :  0.004   0.047   1332
  Dihedral  :  4.528  15.770   1047
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.38 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.26), residues: 966
  helix:  1.04 (0.26), residues: 348
  sheet:  0.11 (0.29), residues: 293
  loop : -0.44 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 441 
 TYR   0.017   0.002   TYR A 180 
 PHE   0.031   0.002   PHE A 882 
 TRP   0.029   0.002   TRP A 709 
 HIS   0.007   0.002   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00666 ( 7836)
  covalent geometry    : angle       0.60725 (10638)
  SS BOND              : bond        0.00410 (    3)
  SS BOND              : angle       0.96167 (    6)
  hydrogen bonds       : bond        0.04857 (  408)
  hydrogen bonds       : angle       5.05425 ( 1182)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8476 (mmm) cc_final: 0.8066 (mmm)
REVERT: A   62 ASP cc_start: 0.7904 (t70) cc_final: 0.7590 (t0)
REVERT: A   94 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8314 (mt)
REVERT: A  658 GLU cc_start: 0.8466 (tt0) cc_final: 0.7889 (mt-10)
REVERT: A  711 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8113 (mm-30)
REVERT: A  764 ASN cc_start: 0.7031 (t0) cc_final: 0.6790 (t0)
REVERT: A  894 ARG cc_start: 0.7075 (mtp85) cc_final: 0.6758 (mtp180)
REVERT: A  897 GLU cc_start: 0.7662 (mp0) cc_final: 0.7322 (pm20)
REVERT: L    6 GLU cc_start: 0.8816 (mp0) cc_final: 0.8591 (mp0)
REVERT: L   55 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8020 (ttp80)
REVERT: L   95 ASN cc_start: 0.8469 (p0) cc_final: 0.8245 (p0)
REVERT: H   46 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8052 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 115
  average time/residue: 0.0689
  time to fit residues: 10.8195
Evaluate side-chains
  112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  118 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.131721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.094777 restraints weight = 10380.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.90
r_work: 0.2957 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   7839  Z= 0.250
  Angle     :  0.564   6.834  10644  Z= 0.306
  Chirality :  0.044   0.151   1215
  Planarity :  0.004   0.045   1332
  Dihedral  :  4.478  15.890   1047
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.35 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.26), residues: 966
  helix:  1.22 (0.27), residues: 344
  sheet:  0.02 (0.30), residues: 293
  loop : -0.44 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  98 
 TYR   0.014   0.002   TYR A 180 
 PHE   0.018   0.002   PHE A 882 
 TRP   0.024   0.002   TRP A 709 
 HIS   0.005   0.001   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 ( 7836)
  covalent geometry    : angle       0.56419 (10638)
  SS BOND              : bond        0.00322 (    3)
  SS BOND              : angle       0.69166 (    6)
  hydrogen bonds       : bond        0.04524 (  408)
  hydrogen bonds       : angle       4.92467 ( 1182)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8572 (mmm) cc_final: 0.8175 (mmm)
REVERT: A   62 ASP cc_start: 0.8010 (t70) cc_final: 0.7687 (t0)
REVERT: A  658 GLU cc_start: 0.8475 (tt0) cc_final: 0.7899 (mt-10)
REVERT: A  764 ASN cc_start: 0.7229 (t0) cc_final: 0.6983 (t0)
REVERT: A  897 GLU cc_start: 0.7656 (mp0) cc_final: 0.7356 (pm20)
REVERT: L   55 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8368 (ttp80)
REVERT: L   95 ASN cc_start: 0.8507 (p0) cc_final: 0.8286 (p0)
  outliers start: 18
  outliers final: 15
  residues processed: 119
  average time/residue: 0.0695
  time to fit residues: 11.4592
Evaluate side-chains
  114 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  614 THR
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  654 THR
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain L residue   11 THR
Chi-restraints excluded: chain L residue   17 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  118 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 26 optimal weight:   20.0000
   chunk 14 optimal weight:    0.0040
   chunk 21 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.8994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.134213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.097282 restraints weight = 10204.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.90
r_work: 0.2995 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7839  Z= 0.145
  Angle     :  0.504   9.413  10644  Z= 0.270
  Chirality :  0.042   0.145   1215
  Planarity :  0.003   0.039   1332
  Dihedral  :  4.283  16.397   1047
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.16 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.27), residues: 966
  helix:  1.67 (0.27), residues: 341
  sheet:  0.01 (0.29), residues: 304
  loop : -0.37 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 894 
 TYR   0.012   0.001   TYR A 892 
 PHE   0.014   0.001   PHE A 587 
 TRP   0.015   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7836)
  covalent geometry    : angle       0.50355 (10638)
  SS BOND              : bond        0.00195 (    3)
  SS BOND              : angle       0.51546 (    6)
  hydrogen bonds       : bond        0.03952 (  408)
  hydrogen bonds       : angle       4.67206 ( 1182)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8479 (mmm) cc_final: 0.8096 (mmm)
REVERT: A   62 ASP cc_start: 0.7872 (t70) cc_final: 0.7579 (t0)
REVERT: A   94 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8310 (mt)
REVERT: A  658 GLU cc_start: 0.8409 (tt0) cc_final: 0.7878 (mt-10)
REVERT: A  764 ASN cc_start: 0.7255 (t0) cc_final: 0.6948 (t0)
REVERT: A  897 GLU cc_start: 0.7678 (mp0) cc_final: 0.7369 (pm20)
REVERT: L   55 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8021 (ttp80)
REVERT: L   95 ASN cc_start: 0.8445 (p0) cc_final: 0.8232 (p0)
REVERT: H   10 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7475 (mt-10)
  outliers start: 17
  outliers final: 13
  residues processed: 119
  average time/residue: 0.0629
  time to fit residues: 10.5354
Evaluate side-chains
  113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  698 THR
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain L residue   11 THR
Chi-restraints excluded: chain L residue   17 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  118 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 789 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.134472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.097372 restraints weight = 10155.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.91
r_work: 0.2998 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   7839  Z= 0.145
  Angle     :  0.527   9.749  10644  Z= 0.280
  Chirality :  0.042   0.171   1215
  Planarity :  0.003   0.039   1332
  Dihedral  :  4.310  25.639   1047
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.65 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.27), residues: 966
  helix:  1.87 (0.27), residues: 340
  sheet:  0.04 (0.30), residues: 304
  loop : -0.30 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  62 
 TYR   0.011   0.001   TYR A 180 
 PHE   0.018   0.001   PHE A 925 
 TRP   0.015   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7836)
  covalent geometry    : angle       0.51816 (10638)
  SS BOND              : bond        0.00451 (    3)
  SS BOND              : angle       4.07943 (    6)
  hydrogen bonds       : bond        0.03923 (  408)
  hydrogen bonds       : angle       4.63565 ( 1182)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8452 (mmm) cc_final: 0.8058 (mmm)
REVERT: A   62 ASP cc_start: 0.7824 (t70) cc_final: 0.7551 (t0)
REVERT: A   94 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8301 (mt)
REVERT: A  658 GLU cc_start: 0.8403 (tt0) cc_final: 0.7872 (mt-10)
REVERT: A  711 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8133 (mm-30)
REVERT: A  764 ASN cc_start: 0.7283 (t0) cc_final: 0.6913 (t0)
REVERT: A  897 GLU cc_start: 0.7641 (mp0) cc_final: 0.7318 (pm20)
REVERT: L   55 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8002 (ttp80)
REVERT: H   10 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7452 (mt-10)
REVERT: H   43 GLN cc_start: 0.8478 (mp10) cc_final: 0.8187 (mp10)
REVERT: H   81 MET cc_start: 0.8961 (ttp) cc_final: 0.8660 (tmm)
  outliers start: 18
  outliers final: 16
  residues processed: 119
  average time/residue: 0.0777
  time to fit residues: 12.6658
Evaluate side-chains
  117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain A residue  698 THR
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain L residue   11 THR
Chi-restraints excluded: chain L residue   17 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  118 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0270
   chunk 55 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   chunk 89 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
L   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.099307 restraints weight = 10130.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.93
r_work: 0.3052 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059   7839  Z= 0.109
  Angle     :  0.502   9.347  10644  Z= 0.264
  Chirality :  0.041   0.149   1215
  Planarity :  0.004   0.050   1332
  Dihedral  :  4.185  27.644   1047
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.50 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.28), residues: 966
  helix:  2.05 (0.27), residues: 344
  sheet:  0.20 (0.30), residues: 313
  loop : -0.16 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 894 
 TYR   0.009   0.001   TYR A 180 
 PHE   0.013   0.001   PHE A 587 
 TRP   0.012   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7836)
  covalent geometry    : angle       0.49582 (10638)
  SS BOND              : bond        0.00582 (    3)
  SS BOND              : angle       3.26617 (    6)
  hydrogen bonds       : bond        0.03644 (  408)
  hydrogen bonds       : angle       4.46928 ( 1182)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8488 (mmm) cc_final: 0.8087 (mmm)
REVERT: A   62 ASP cc_start: 0.7955 (t70) cc_final: 0.7675 (t0)
REVERT: A   94 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8420 (mt)
REVERT: A  658 GLU cc_start: 0.8403 (tt0) cc_final: 0.7892 (mt-10)
REVERT: A  764 ASN cc_start: 0.7247 (t0) cc_final: 0.6885 (t0)
REVERT: A  897 GLU cc_start: 0.7613 (mp0) cc_final: 0.7269 (pm20)
REVERT: L   55 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8064 (ttp80)
REVERT: H   10 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7431 (mt-10)
REVERT: H   43 GLN cc_start: 0.8458 (mp10) cc_final: 0.8151 (mp10)
REVERT: H   81 MET cc_start: 0.8984 (ttp) cc_final: 0.8686 (tmm)
  outliers start: 18
  outliers final: 14
  residues processed: 123
  average time/residue: 0.0642
  time to fit residues: 11.0080
Evaluate side-chains
  117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  698 THR
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain L residue   11 THR
Chi-restraints excluded: chain L residue   17 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  118 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.134811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.097691 restraints weight = 10211.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.92
r_work: 0.3008 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7839  Z= 0.149
  Angle     :  0.515  11.851  10644  Z= 0.271
  Chirality :  0.042   0.156   1215
  Planarity :  0.003   0.038   1332
  Dihedral  :  4.190  26.321   1047
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.38 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.28), residues: 966
  helix:  2.01 (0.27), residues: 344
  sheet:  0.14 (0.30), residues: 313
  loop : -0.11 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 894 
 TYR   0.012   0.001   TYR A 180 
 PHE   0.026   0.001   PHE A 925 
 TRP   0.016   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7836)
  covalent geometry    : angle       0.50965 (10638)
  SS BOND              : bond        0.00289 (    3)
  SS BOND              : angle       3.04331 (    6)
  hydrogen bonds       : bond        0.03830 (  408)
  hydrogen bonds       : angle       4.49972 ( 1182)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8490 (mmm) cc_final: 0.8081 (mmm)
REVERT: A   62 ASP cc_start: 0.7858 (t70) cc_final: 0.7583 (t0)
REVERT: A   94 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8390 (mt)
REVERT: A  658 GLU cc_start: 0.8379 (tt0) cc_final: 0.7852 (mt-10)
REVERT: A  711 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8155 (mm-30)
REVERT: A  764 ASN cc_start: 0.7284 (t0) cc_final: 0.6914 (t0)
REVERT: L   55 ARG cc_start: 0.8567 (ttp80) cc_final: 0.8039 (ttp80)
REVERT: H   10 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7450 (mt-10)
REVERT: H   43 GLN cc_start: 0.8397 (mp10) cc_final: 0.8100 (mp10)
  outliers start: 17
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0670
  time to fit residues: 10.6936
Evaluate side-chains
  111 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain A residue  698 THR
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain L residue   11 THR
Chi-restraints excluded: chain L residue   17 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  118 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 71 optimal weight:    0.0970
   chunk 3 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 4 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 89 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.5178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.134414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.099074 restraints weight = 10107.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.83
r_work: 0.3057 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7839  Z= 0.110
  Angle     :  0.502  11.527  10644  Z= 0.264
  Chirality :  0.041   0.160   1215
  Planarity :  0.003   0.036   1332
  Dihedral  :  4.121  25.467   1047
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.38 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.28), residues: 966
  helix:  2.16 (0.28), residues: 344
  sheet:  0.16 (0.30), residues: 313
  loop : -0.03 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 547 
 TYR   0.009   0.001   TYR A 180 
 PHE   0.012   0.001   PHE A 587 
 TRP   0.011   0.001   TRP A  29 
 HIS   0.003   0.001   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7836)
  covalent geometry    : angle       0.49741 (10638)
  SS BOND              : bond        0.00267 (    3)
  SS BOND              : angle       2.75912 (    6)
  hydrogen bonds       : bond        0.03595 (  408)
  hydrogen bonds       : angle       4.40085 ( 1182)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8490 (mmm) cc_final: 0.8079 (mmm)
REVERT: A   94 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8401 (mt)
REVERT: A  160 THR cc_start: 0.8674 (m) cc_final: 0.8437 (m)
REVERT: A  658 GLU cc_start: 0.8375 (tt0) cc_final: 0.7863 (mt-10)
REVERT: A  711 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8150 (mm-30)
REVERT: A  764 ASN cc_start: 0.7248 (t0) cc_final: 0.6905 (t0)
REVERT: L   55 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8030 (ttp80)
REVERT: H   10 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7451 (mt-10)
REVERT: H   43 GLN cc_start: 0.8342 (mp10) cc_final: 0.8082 (mp10)
REVERT: H   84 ARG cc_start: 0.8313 (ptp-110) cc_final: 0.7847 (ptp-170)
  outliers start: 18
  outliers final: 17
  residues processed: 116
  average time/residue: 0.0630
  time to fit residues: 10.2629
Evaluate side-chains
  119 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain A residue  698 THR
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain L residue   11 THR
Chi-restraints excluded: chain L residue   17 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  118 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 66 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.135694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.098502 restraints weight = 10116.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.92
r_work: 0.3040 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7839  Z= 0.132
  Angle     :  0.507  12.757  10644  Z= 0.266
  Chirality :  0.041   0.162   1215
  Planarity :  0.003   0.037   1332
  Dihedral  :  4.104  24.821   1047
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.50 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.28), residues: 966
  helix:  2.14 (0.28), residues: 344
  sheet:  0.17 (0.30), residues: 313
  loop :  0.00 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 547 
 TYR   0.010   0.001   TYR A 180 
 PHE   0.019   0.001   PHE A 882 
 TRP   0.019   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7836)
  covalent geometry    : angle       0.50310 (10638)
  SS BOND              : bond        0.00305 (    3)
  SS BOND              : angle       2.72435 (    6)
  hydrogen bonds       : bond        0.03690 (  408)
  hydrogen bonds       : angle       4.40760 ( 1182)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8479 (mmm) cc_final: 0.8059 (mmm)
REVERT: A   94 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8381 (mt)
REVERT: A  160 THR cc_start: 0.8663 (m) cc_final: 0.8425 (m)
REVERT: A  658 GLU cc_start: 0.8373 (tt0) cc_final: 0.7929 (mt-10)
REVERT: A  711 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8139 (mm-30)
REVERT: A  764 ASN cc_start: 0.7278 (t0) cc_final: 0.6931 (t0)
REVERT: L   55 ARG cc_start: 0.8556 (ttp80) cc_final: 0.8026 (ttp80)
REVERT: H   10 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7473 (mt-10)
REVERT: H   84 ARG cc_start: 0.8298 (ptp-110) cc_final: 0.7857 (ptp-170)
  outliers start: 19
  outliers final: 18
  residues processed: 113
  average time/residue: 0.0717
  time to fit residues: 11.4888
Evaluate side-chains
  115 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain A residue  698 THR
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain L residue   11 THR
Chi-restraints excluded: chain L residue   17 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  118 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0070
   chunk 79 optimal weight:    0.0570
   chunk 18 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.4516

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.137190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.100314 restraints weight = 10068.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.91
r_work: 0.3057 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7839  Z= 0.105
  Angle     :  0.497  11.319  10644  Z= 0.262
  Chirality :  0.041   0.153   1215
  Planarity :  0.003   0.036   1332
  Dihedral  :  4.045  23.666   1047
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.97 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.62 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.28), residues: 966
  helix:  2.24 (0.28), residues: 344
  sheet:  0.24 (0.30), residues: 303
  loop :  0.06 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 547 
 TYR   0.009   0.001   TYR A 180 
 PHE   0.016   0.001   PHE A 882 
 TRP   0.016   0.001   TRP A  29 
 HIS   0.003   0.000   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7836)
  covalent geometry    : angle       0.49489 (10638)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       2.06669 (    6)
  hydrogen bonds       : bond        0.03491 (  408)
  hydrogen bonds       : angle       4.32561 ( 1182)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1586.66 seconds
wall clock time: 27 minutes 53.36 seconds (1673.36 seconds total)