Starting phenix.real_space_refine
on Sun May 11 06:53:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sgj_40457/05_2025/8sgj_40457.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sgj_40457/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sgj_40457/05_2025/8sgj_40457.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sgj_40457/05_2025/8sgj_40457.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sgj_40457/05_2025/8sgj_40457.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sgj_40457/05_2025/8sgj_40457.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.67, per 1000 atoms: 0.74
  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: 2.21
  Conformation dependent library (CDL) restraints added in 974.3 milliseconds
  

  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: 0.91
  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: 2.61

  Time building geometry restraints manager: 2.55 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:             2.620
  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:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.760
  Find NCS groups from input model:        0.080
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.050
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (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
 TRP   0.020   0.003   TRP A  95 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.028   0.002   PHE A 925 
 TYR   0.029   0.002   TYR A  46 
 ARG   0.009   0.001   ARG L  62 

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

*********************** 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  : 0.866 
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: 0.2214
  time to fit residues: 46.4634
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  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0770
   chunk 41 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 29 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0980
   chunk 57 optimal weight:    0.0030
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.2948

-------------------------------------------------------------------------------
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 834 ASN
** 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 = 0.3766 r_free = 0.3766 target = 0.145559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.108660 restraints weight = 9835.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.93
r_work: 0.3174 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7839  Z= 0.112
  Angle     :  0.524   8.331  10644  Z= 0.285
  Chirality :  0.042   0.144   1215
  Planarity :  0.004   0.047   1332
  Dihedral  :  4.347  18.279   1047
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  7.75 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.27), residues: 966
  helix:  1.32 (0.27), residues: 344
  sheet:  0.48 (0.29), residues: 304
  loop : -0.15 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 165 
 PHE   0.019   0.001   PHE A 925 
 TYR   0.017   0.001   TYR A 184 
 ARG   0.003   0.001   ARG L  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04279 (  408)
  hydrogen bonds       : angle       4.98338 ( 1182)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       0.68772 (    6)
  covalent geometry    : bond        0.00233 ( 7836)
  covalent geometry    : angle       0.52439 (10638)

*********************** 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: 8
    poor density    : 115
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 ASP cc_start: 0.7691 (t70) cc_final: 0.7401 (t0)
REVERT: A  711 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7881 (mm-30)
REVERT: A  897 GLU cc_start: 0.7697 (mp0) cc_final: 0.7474 (pm20)
REVERT: H   13 ARG cc_start: 0.7841 (mmm160) cc_final: 0.7617 (mmm160)
REVERT: H   46 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8098 (mt-10)
  outliers start: 8
  outliers final: 5
  residues processed: 120
  average time/residue: 0.1829
  time to fit residues: 30.3973
Evaluate side-chains
  113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  509 GLU
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 15 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0570
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    1.2702

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

Flipped N/Q/H residues before XYZ refinement:
A 764 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.137367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.100052 restraints weight = 10177.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.93
r_work: 0.3062 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   7839  Z= 0.204
  Angle     :  0.573   9.347  10644  Z= 0.308
  Chirality :  0.044   0.154   1215
  Planarity :  0.004   0.043   1332
  Dihedral  :  4.336  23.930   1047
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  9.81 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.27), residues: 966
  helix:  1.57 (0.27), residues: 344
  sheet:  0.42 (0.29), residues: 309
  loop : -0.24 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 709 
 HIS   0.005   0.001   HIS A 501 
 PHE   0.023   0.002   PHE A 882 
 TYR   0.015   0.002   TYR A 180 
 ARG   0.003   0.001   ARG A 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04482 (  408)
  hydrogen bonds       : angle       4.88317 ( 1182)
  SS BOND              : bond        0.00287 (    3)
  SS BOND              : angle       3.84916 (    6)
  covalent geometry    : bond        0.00491 ( 7836)
  covalent geometry    : angle       0.56540 (10638)

*********************** 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
  125 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8471 (mmm) cc_final: 0.8057 (mmm)
REVERT: A   62 ASP cc_start: 0.7869 (t70) cc_final: 0.7586 (t0)
REVERT: A  209 ILE cc_start: 0.7554 (mm) cc_final: 0.7323 (mt)
REVERT: A  897 GLU cc_start: 0.7753 (mp0) cc_final: 0.7430 (pm20)
REVERT: L   55 ARG cc_start: 0.8538 (ttp80) cc_final: 0.7949 (ttp80)
REVERT: H   13 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7691 (mmm160)
REVERT: H   46 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8061 (mt-10)
  outliers start: 10
  outliers final: 9
  residues processed: 120
  average time/residue: 0.2027
  time to fit residues: 33.2855
Evaluate side-chains
  111 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   17 VAL
Chi-restraints excluded: chain L residue   31 SER
Chi-restraints excluded: chain H residue   71 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 17 optimal weight:    0.3980
   chunk 19 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 29 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 76 optimal weight:   10.0000
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.137352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.100372 restraints weight = 10044.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.91
r_work: 0.3062 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7839  Z= 0.155
  Angle     :  0.521   8.966  10644  Z= 0.282
  Chirality :  0.042   0.142   1215
  Planarity :  0.004   0.041   1332
  Dihedral  :  4.246  26.614   1047
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.02 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.27), residues: 966
  helix:  1.76 (0.27), residues: 344
  sheet:  0.43 (0.29), residues: 309
  loop : -0.20 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 709 
 HIS   0.004   0.001   HIS A 501 
 PHE   0.016   0.002   PHE A 882 
 TYR   0.012   0.001   TYR A 180 
 ARG   0.002   0.000   ARG A 410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  408)
  hydrogen bonds       : angle       4.70779 ( 1182)
  SS BOND              : bond        0.00286 (    3)
  SS BOND              : angle       3.70672 (    6)
  covalent geometry    : bond        0.00366 ( 7836)
  covalent geometry    : angle       0.51411 (10638)

*********************** 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
  124 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A   53 MET cc_start: 0.8482 (mmm) cc_final: 0.8070 (mmm)
REVERT: A   62 ASP cc_start: 0.7899 (t70) cc_final: 0.7619 (t0)
REVERT: A   94 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8355 (mt)
REVERT: A  658 GLU cc_start: 0.8442 (tt0) cc_final: 0.7905 (mt-10)
REVERT: A  897 GLU cc_start: 0.7776 (mp0) cc_final: 0.7474 (pm20)
REVERT: L   55 ARG cc_start: 0.8559 (ttp80) cc_final: 0.7963 (ttp80)
REVERT: L   95 ASN cc_start: 0.8518 (p0) cc_final: 0.8300 (p0)
REVERT: H   13 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7743 (mmm160)
REVERT: H   46 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8059 (mt-10)
  outliers start: 14
  outliers final: 8
  residues processed: 117
  average time/residue: 0.1827
  time to fit residues: 29.6090
Evaluate side-chains
  110 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 L residue   17 VAL
Chi-restraints excluded: chain L residue   31 SER
Chi-restraints excluded: chain H residue   71 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9980
   chunk 76 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.133201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.096221 restraints weight = 10164.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.90
r_work: 0.2984 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   7839  Z= 0.238
  Angle     :  0.575  10.234  10644  Z= 0.308
  Chirality :  0.044   0.159   1215
  Planarity :  0.004   0.042   1332
  Dihedral  :  4.367  26.819   1047
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.47 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.27), residues: 966
  helix:  1.52 (0.27), residues: 348
  sheet:  0.25 (0.31), residues: 283
  loop : -0.26 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 709 
 HIS   0.005   0.001   HIS A 501 
 PHE   0.016   0.002   PHE A 587 
 TYR   0.015   0.002   TYR A 180 
 ARG   0.003   0.000   ARG A 894 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04488 (  408)
  hydrogen bonds       : angle       4.81055 ( 1182)
  SS BOND              : bond        0.00617 (    3)
  SS BOND              : angle       2.93331 (    6)
  covalent geometry    : bond        0.00578 ( 7836)
  covalent geometry    : angle       0.57062 (10638)

*********************** 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
  126 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8539 (mmm) cc_final: 0.8107 (mmm)
REVERT: A   62 ASP cc_start: 0.7937 (t70) cc_final: 0.7623 (t0)
REVERT: A   94 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8398 (mt)
REVERT: A  658 GLU cc_start: 0.8475 (tt0) cc_final: 0.7904 (mt-10)
REVERT: A  764 ASN cc_start: 0.7170 (t0) cc_final: 0.6623 (t0)
REVERT: A  894 ARG cc_start: 0.7629 (mtt-85) cc_final: 0.7173 (mtt-85)
REVERT: A  897 GLU cc_start: 0.7794 (mp0) cc_final: 0.7457 (pm20)
REVERT: L   55 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8050 (ttp80)
REVERT: L   95 ASN cc_start: 0.8498 (p0) cc_final: 0.8293 (p0)
  outliers start: 14
  outliers final: 11
  residues processed: 120
  average time/residue: 0.1957
  time to fit residues: 32.4055
Evaluate side-chains
  116 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
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  577 ASP
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  641 ILE
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   17 VAL
Chi-restraints excluded: chain L residue   31 SER
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 48 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.136087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.099165 restraints weight = 9986.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.89
r_work: 0.3041 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7839  Z= 0.127
  Angle     :  0.503   9.397  10644  Z= 0.269
  Chirality :  0.041   0.143   1215
  Planarity :  0.003   0.039   1332
  Dihedral  :  4.216  25.569   1047
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.04 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.27), residues: 966
  helix:  1.91 (0.27), residues: 343
  sheet:  0.26 (0.31), residues: 289
  loop : -0.21 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.016   0.001   PHE A 925 
 TYR   0.010   0.001   TYR L  93 
 ARG   0.002   0.000   ARG A 894 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03860 (  408)
  hydrogen bonds       : angle       4.57915 ( 1182)
  SS BOND              : bond        0.00228 (    3)
  SS BOND              : angle       2.43383 (    6)
  covalent geometry    : bond        0.00292 ( 7836)
  covalent geometry    : angle       0.50027 (10638)

*********************** 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
  122 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A   53 MET cc_start: 0.8492 (mmm) cc_final: 0.8085 (mmm)
REVERT: A   62 ASP cc_start: 0.7925 (t70) cc_final: 0.7624 (t0)
REVERT: A  658 GLU cc_start: 0.8404 (tt0) cc_final: 0.7890 (mt-10)
REVERT: A  711 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8101 (mm-30)
REVERT: A  764 ASN cc_start: 0.7235 (t0) cc_final: 0.6986 (t0)
REVERT: L   55 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8014 (ttp80)
REVERT: H   10 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7134 (mt-10)
  outliers start: 14
  outliers final: 12
  residues processed: 115
  average time/residue: 0.2066
  time to fit residues: 32.3834
Evaluate side-chains
  112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
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  620 LEU
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  641 ILE
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  863 GLU
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 97 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9980
   chunk 26 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.132564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.097355 restraints weight = 10163.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.80
r_work: 0.3011 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7839  Z= 0.168
  Angle     :  0.523  10.293  10644  Z= 0.279
  Chirality :  0.042   0.157   1215
  Planarity :  0.004   0.041   1332
  Dihedral  :  4.195  23.851   1047
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.27), residues: 966
  helix:  1.89 (0.27), residues: 345
  sheet:  0.22 (0.30), residues: 304
  loop : -0.16 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 501 
 PHE   0.015   0.001   PHE A 587 
 TYR   0.013   0.001   TYR A 180 
 ARG   0.004   0.000   ARG H  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  408)
  hydrogen bonds       : angle       4.61813 ( 1182)
  SS BOND              : bond        0.00298 (    3)
  SS BOND              : angle       2.51118 (    6)
  covalent geometry    : bond        0.00400 ( 7836)
  covalent geometry    : angle       0.51973 (10638)

*********************** 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
  122 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8503 (mmm) cc_final: 0.8080 (mmm)
REVERT: A   62 ASP cc_start: 0.7936 (t70) cc_final: 0.7625 (t0)
REVERT: A   94 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8372 (mt)
REVERT: A  658 GLU cc_start: 0.8436 (tt0) cc_final: 0.7904 (mt-10)
REVERT: A  764 ASN cc_start: 0.7259 (t0) cc_final: 0.6703 (t0)
REVERT: L   55 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8042 (ttp80)
REVERT: H   10 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7259 (mt-10)
REVERT: H   13 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7234 (mmp-170)
REVERT: H   43 GLN cc_start: 0.8490 (mp10) cc_final: 0.8230 (mp10)
REVERT: H   81 MET cc_start: 0.8886 (ttp) cc_final: 0.8590 (tmm)
  outliers start: 17
  outliers final: 14
  residues processed: 115
  average time/residue: 0.2061
  time to fit residues: 32.5825
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  : 0.841 
-------------------------------------------------------------------------------
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  577 ASP
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  641 ILE
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   17 VAL
Chi-restraints excluded: chain L residue   31 SER
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.135513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.098383 restraints weight = 10159.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.93
r_work: 0.3037 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7839  Z= 0.136
  Angle     :  0.505  11.341  10644  Z= 0.266
  Chirality :  0.041   0.144   1215
  Planarity :  0.003   0.038   1332
  Dihedral  :  4.131  23.086   1047
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.53 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.27), residues: 966
  helix:  1.99 (0.27), residues: 344
  sheet:  0.21 (0.30), residues: 304
  loop : -0.10 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.019   0.001   PHE A 925 
 TYR   0.011   0.001   TYR A 180 
 ARG   0.002   0.000   ARG H  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03777 (  408)
  hydrogen bonds       : angle       4.52572 ( 1182)
  SS BOND              : bond        0.00261 (    3)
  SS BOND              : angle       2.32803 (    6)
  covalent geometry    : bond        0.00320 ( 7836)
  covalent geometry    : angle       0.50231 (10638)

*********************** 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
  121 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8473 (mmm) cc_final: 0.8048 (mmm)
REVERT: A   62 ASP cc_start: 0.7935 (t70) cc_final: 0.7628 (t0)
REVERT: A   94 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8365 (mt)
REVERT: A  160 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8419 (m)
REVERT: A  166 LEU cc_start: 0.7150 (mt) cc_final: 0.6785 (mt)
REVERT: A  658 GLU cc_start: 0.8386 (tt0) cc_final: 0.7863 (mt-10)
REVERT: A  764 ASN cc_start: 0.7231 (t0) cc_final: 0.6713 (t0)
REVERT: L   55 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8040 (ttp80)
REVERT: H   10 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7234 (mt-10)
REVERT: H   13 ARG cc_start: 0.7798 (mmm160) cc_final: 0.6950 (mmm160)
REVERT: H   43 GLN cc_start: 0.8418 (mp10) cc_final: 0.8101 (mp10)
  outliers start: 18
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1921
  time to fit residues: 30.0100
Evaluate side-chains
  115 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
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  160 THR
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  641 ILE
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.136182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.098978 restraints weight = 10175.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.94
r_work: 0.3043 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7839  Z= 0.127
  Angle     :  0.498  10.440  10644  Z= 0.263
  Chirality :  0.041   0.144   1215
  Planarity :  0.003   0.037   1332
  Dihedral  :  4.066  22.263   1047
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.77 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.28), residues: 966
  helix:  2.07 (0.27), residues: 344
  sheet:  0.24 (0.30), residues: 303
  loop : -0.08 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.013   0.001   PHE A 587 
 TYR   0.010   0.001   TYR A 180 
 ARG   0.003   0.000   ARG H  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03738 (  408)
  hydrogen bonds       : angle       4.46391 ( 1182)
  SS BOND              : bond        0.00270 (    3)
  SS BOND              : angle       2.23943 (    6)
  covalent geometry    : bond        0.00296 ( 7836)
  covalent geometry    : angle       0.49491 (10638)

*********************** 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
  123 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A   53 MET cc_start: 0.8496 (mmm) cc_final: 0.8073 (mmm)
REVERT: A   62 ASP cc_start: 0.7978 (t70) cc_final: 0.7667 (t0)
REVERT: A   94 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8423 (mt)
REVERT: A  166 LEU cc_start: 0.7211 (mt) cc_final: 0.6848 (mt)
REVERT: A  658 GLU cc_start: 0.8384 (tt0) cc_final: 0.7866 (mt-10)
REVERT: A  711 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8123 (mm-30)
REVERT: A  764 ASN cc_start: 0.7199 (t0) cc_final: 0.6696 (t0)
REVERT: L   55 ARG cc_start: 0.8614 (ttp80) cc_final: 0.8086 (ttp80)
REVERT: H   10 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7251 (mt-10)
REVERT: H   13 ARG cc_start: 0.7808 (mmm160) cc_final: 0.7029 (mmm160)
  outliers start: 18
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1956
  time to fit residues: 30.9926
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  : 0.801 
-------------------------------------------------------------------------------
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  577 ASP
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  641 ILE
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   17 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   74 LYS
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 66 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0270
   chunk 22 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.136697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.099609 restraints weight = 10106.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.93
r_work: 0.3055 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7839  Z= 0.118
  Angle     :  0.498  12.051  10644  Z= 0.262
  Chirality :  0.041   0.144   1215
  Planarity :  0.003   0.037   1332
  Dihedral  :  4.030  21.045   1047
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.89 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.28), residues: 966
  helix:  2.14 (0.27), residues: 344
  sheet:  0.25 (0.30), residues: 303
  loop : -0.05 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.029   0.001   PHE A 925 
 TYR   0.010   0.001   TYR A 180 
 ARG   0.004   0.000   ARG H  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03643 (  408)
  hydrogen bonds       : angle       4.41567 ( 1182)
  SS BOND              : bond        0.00244 (    3)
  SS BOND              : angle       1.94285 (    6)
  covalent geometry    : bond        0.00272 ( 7836)
  covalent geometry    : angle       0.49583 (10638)

********************** 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
  123 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A   53 MET cc_start: 0.8502 (mmm) cc_final: 0.8082 (mmm)
REVERT: A   62 ASP cc_start: 0.7939 (t70) cc_final: 0.7651 (t0)
REVERT: A   94 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8410 (mt)
REVERT: A  160 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8456 (m)
REVERT: A  166 LEU cc_start: 0.7174 (mt) cc_final: 0.6810 (mt)
REVERT: A  658 GLU cc_start: 0.8381 (tt0) cc_final: 0.7940 (mt-10)
REVERT: A  711 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8125 (mm-30)
REVERT: A  764 ASN cc_start: 0.7163 (t0) cc_final: 0.6694 (t0)
REVERT: L   55 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8061 (ttp80)
REVERT: H   10 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7282 (mt-10)
REVERT: H   13 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7014 (mmm160)
REVERT: H   81 MET cc_start: 0.8789 (ttp) cc_final: 0.8583 (tmm)
REVERT: H   84 ARG cc_start: 0.8222 (ptp-110) cc_final: 0.7918 (ptp-170)
  outliers start: 18
  outliers final: 15
  residues processed: 115
  average time/residue: 0.1980
  time to fit residues: 31.2990
Evaluate side-chains
  119 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
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  160 THR
Chi-restraints excluded: chain A residue  372 SER
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  641 ILE
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   17 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   74 LYS
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 95 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 26 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    0.3980
   chunk 44 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3665 r_free = 0.3665 target = 0.136383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.099255 restraints weight = 10095.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.92
r_work: 0.3048 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7839  Z= 0.128
  Angle     :  0.505  11.647  10644  Z= 0.265
  Chirality :  0.041   0.144   1215
  Planarity :  0.003   0.038   1332
  Dihedral  :  4.018  20.395   1047
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.28 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.89 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.28), residues: 966
  helix:  2.14 (0.27), residues: 344
  sheet:  0.26 (0.30), residues: 303
  loop : -0.03 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  29 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.017   0.001   PHE A 882 
 TYR   0.010   0.001   TYR A 180 
 ARG   0.002   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03680 (  408)
  hydrogen bonds       : angle       4.40502 ( 1182)
  SS BOND              : bond        0.00280 (    3)
  SS BOND              : angle       1.97999 (    6)
  covalent geometry    : bond        0.00300 ( 7836)
  covalent geometry    : angle       0.50327 (10638)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3981.14 seconds
wall clock time: 69 minutes 48.53 seconds (4188.53 seconds total)