Starting phenix.real_space_refine
on Wed Sep 17 04:16:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7efc_31083/09_2025/7efc_31083.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7efc_31083/09_2025/7efc_31083.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7efc_31083/09_2025/7efc_31083.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7efc_31083/09_2025/7efc_31083.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7efc_31083/09_2025/7efc_31083.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7efc_31083/09_2025/7efc_31083.map"
  }
  resolution = 1.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       4      5.16       5
     C    2392      2.51       5
     N     668      2.21       5
     O     940      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4004
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 946
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 120, 896
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 1, 'TRANS': 118}
      Conformer: "B"
        Number of residues, atoms: 120, 896
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 1, 'TRANS': 118}
          bond proxies already assigned to first conformer: 867
    Chain: "A"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 40, 55
          Unusual residues: {'BTN': 1}
          Classifications: {'undetermined': 1, 'water': 39}
          Link IDs: {None: 39}
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 39, 39
          Classifications: {'water': 39}
          Link IDs: {None: 38}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 39, 39
          Classifications: {'water': 39}
          Link IDs: {None: 38}
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 39, 39
          Classifications: {'water': 39}
          Link IDs: {None: 38}
  Restraints were copied for chains:
    B, C, D
  Residues with excluded nonbonded symmetry interactions: 56
    residue:
      pdb=" N  ASER A  45 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A  45 " occ=0.50
    residue:
      pdb=" N  AALA A  46 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA A  46 " occ=0.50
    residue:
      pdb=" N  AVAL A  47 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL A  47 " occ=0.50
    residue:
      pdb=" N  AGLY A  48 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A  48 " occ=0.50
    residue:
      pdb=" N  AASN A  49 " occ=0.50
      ... (14 atoms not shown)
      pdb=" ND2BASN A  49 " occ=0.50
    residue:
      pdb=" N  AALA A  50 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA A  50 " occ=0.50
    residue:
      pdb=" N  AGLU A  51 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU A  51 " occ=0.50
    residue:
      pdb=" N  ASER A  52 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A  52 " occ=0.50
    residue:
      pdb=" C10ABTN A5100 " occ=0.50
      ... (14 atoms not shown)
      pdb=" S1 ABTN A5100 " occ=0.50
    residue:
      pdb=" O  AHOH A5221 " occ=0.50
    residue:
      pdb=" O   HOH A5223 " occ=0.50
    residue:
      pdb=" O  AHOH A5231 " occ=0.50
    ... (remaining 44 not shown)
  Time building chain proxies: 1.31, per 1000 atoms: 0.33
  Number of scatterers: 4004
  At special positions: 0
  Unit cell: (68.8516, 64.4096, 58.4869, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       4     16.00
     O     940      8.00
     N     668      7.00
     C    2392      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 261.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  888

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 4 sheets defined
      3.3% alpha, 53.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 121
    Processing helix  chain 'B' and resid 118 through 121
    Processing helix  chain 'C' and resid 118 through 121
    Processing helix  chain 'D' and resid 118 through 121
    Processing sheet with id=1, first strand: chain 'A' and resid 19 through 23
      removed outlier: 8.184A  pdb=" N   ARG A  53 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LYS A  80 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL A  55 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ALA A  78 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   THR A  71 " --> pdb=" O   GLY A  94 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   GLY A  94 " --> pdb=" O   THR A  71 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU A  73 " --> pdb=" O   TRP A  92 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   TRP A  92 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   TRP A  75 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   THR A  90 " --> pdb=" O   TRP A  75 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL A  77 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   SER A  88 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TRP A  79 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'B' and resid 19 through 23
      removed outlier: 8.184A  pdb=" N   ARG B  53 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LYS B  80 " --> pdb=" O   ARG B  53 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL B  55 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ALA B  78 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   THR B  71 " --> pdb=" O   GLY B  94 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   GLY B  94 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU B  73 " --> pdb=" O   TRP B  92 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   TRP B  92 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   TRP B  75 " --> pdb=" O   THR B  90 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   THR B  90 " --> pdb=" O   TRP B  75 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL B  77 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   SER B  88 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TRP B  79 " --> pdb=" O   ALA B  86 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'C' and resid 19 through 23
      removed outlier: 8.184A  pdb=" N   ARG C  53 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LYS C  80 " --> pdb=" O   ARG C  53 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL C  55 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ALA C  78 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   THR C  71 " --> pdb=" O   GLY C  94 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   GLY C  94 " --> pdb=" O   THR C  71 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU C  73 " --> pdb=" O   TRP C  92 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   TRP C  92 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   TRP C  75 " --> pdb=" O   THR C  90 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   THR C  90 " --> pdb=" O   TRP C  75 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL C  77 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   SER C  88 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TRP C  79 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing sheet with id=4, first strand: chain 'D' and resid 19 through 23
      removed outlier: 8.184A  pdb=" N   ARG D  53 " --> pdb=" O   LYS D  80 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LYS D  80 " --> pdb=" O   ARG D  53 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL D  55 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ALA D  78 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   THR D  71 " --> pdb=" O   GLY D  94 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   GLY D  94 " --> pdb=" O   THR D  71 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU D  73 " --> pdb=" O   TRP D  92 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   TRP D  92 " --> pdb=" O   LEU D  73 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   TRP D  75 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   THR D  90 " --> pdb=" O   TRP D  75 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL D  77 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   SER D  88 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TRP D  79 " --> pdb=" O   ALA D  86 " (cutoff:3.500A)

    168 hydrogen bonds defined for protein.
    456 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: 0.71

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 548
        1.29 -     1.42: 880
        1.42 -     1.55: 2192
        1.55 -     1.68: 316
        1.68 -     1.81: 8
  Bond restraints: 3944
  Sorted by residual:
  bond pdb=" C   GLY C  94 "
       pdb=" O   GLY C  94 "
    ideal  model  delta    sigma   weight residual
    1.232  1.307 -0.075 1.05e-02 9.07e+03 5.12e+01
  bond pdb=" C   GLY D  94 "
       pdb=" O   GLY D  94 "
    ideal  model  delta    sigma   weight residual
    1.232  1.307 -0.075 1.05e-02 9.07e+03 5.12e+01
  bond pdb=" C   GLY B  94 "
       pdb=" O   GLY B  94 "
    ideal  model  delta    sigma   weight residual
    1.232  1.307 -0.075 1.05e-02 9.07e+03 5.12e+01
  bond pdb=" C   GLY A  94 "
       pdb=" O   GLY A  94 "
    ideal  model  delta    sigma   weight residual
    1.232  1.307 -0.075 1.05e-02 9.07e+03 5.12e+01
  bond pdb=" C   ILE C  17 "
       pdb=" O   ILE C  17 "
    ideal  model  delta    sigma   weight residual
    1.237  1.154  0.083 1.19e-02 7.06e+03 4.86e+01
  ... (remaining 3939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 3396
        2.66 -     5.33: 1508
        5.33 -     7.99: 428
        7.99 -    10.65: 44
       10.65 -    13.32: 24
  Bond angle restraints: 5400
  Sorted by residual:
  angle pdb=" CA  PHE D  29 "
        pdb=" CB  PHE D  29 "
        pdb=" CG  PHE D  29 "
      ideal   model   delta    sigma   weight residual
     113.80  124.22  -10.42 1.00e+00 1.00e+00 1.08e+02
  angle pdb=" CA  PHE B  29 "
        pdb=" CB  PHE B  29 "
        pdb=" CG  PHE B  29 "
      ideal   model   delta    sigma   weight residual
     113.80  124.22  -10.42 1.00e+00 1.00e+00 1.08e+02
  angle pdb=" CA  PHE A  29 "
        pdb=" CB  PHE A  29 "
        pdb=" CG  PHE A  29 "
      ideal   model   delta    sigma   weight residual
     113.80  124.22  -10.42 1.00e+00 1.00e+00 1.08e+02
  angle pdb=" CA  PHE C  29 "
        pdb=" CB  PHE C  29 "
        pdb=" CG  PHE C  29 "
      ideal   model   delta    sigma   weight residual
     113.80  124.22  -10.42 1.00e+00 1.00e+00 1.08e+02
  angle pdb=" CA  ILE A  17 "
        pdb=" C   ILE A  17 "
        pdb=" O   ILE A  17 "
      ideal   model   delta    sigma   weight residual
     120.85  110.38   10.47 1.06e+00 8.90e-01 9.75e+01
  ... (remaining 5395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.54: 2008
       16.54 -    33.08: 160
       33.08 -    49.62: 20
       49.62 -    66.16: 12
       66.16 -    82.70: 12
  Dihedral angle restraints: 2212
    sinusoidal: 788
      harmonic: 1424
  Sorted by residual:
  dihedral pdb=" CA ASER B  52 "
           pdb=" C  ASER B  52 "
           pdb=" N   ARG B  53 "
           pdb=" CA  ARG B  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.36  -28.64     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA ASER D  52 "
           pdb=" C  ASER D  52 "
           pdb=" N   ARG D  53 "
           pdb=" CA  ARG D  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.36  -28.64     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA ASER A  52 "
           pdb=" C  ASER A  52 "
           pdb=" N   ARG A  53 "
           pdb=" CA  ARG A  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.36  -28.64     0      5.00e+00 4.00e-02 3.28e+01
  ... (remaining 2209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 412
       0.080 -    0.160: 164
       0.160 -    0.241: 20
       0.241 -    0.321: 0
       0.321 -    0.401: 8
  Chirality restraints: 604
  Sorted by residual:
  chirality pdb=" CB  VAL A  31 "
            pdb=" CA  VAL A  31 "
            pdb=" CG1 VAL A  31 "
            pdb=" CG2 VAL A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.23   -0.40 2.00e-01 2.50e+01 4.02e+00
  chirality pdb=" CB  VAL C  31 "
            pdb=" CA  VAL C  31 "
            pdb=" CG1 VAL C  31 "
            pdb=" CG2 VAL C  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.23   -0.40 2.00e-01 2.50e+01 4.02e+00
  chirality pdb=" CB  VAL B  31 "
            pdb=" CA  VAL B  31 "
            pdb=" CG1 VAL B  31 "
            pdb=" CG2 VAL B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.23   -0.40 2.00e-01 2.50e+01 4.02e+00
  ... (remaining 601 not shown)

  Planarity restraints: 684
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3 ABTN C5100 "   -0.063 2.00e-02 2.50e+03   2.15e-01 6.96e+02
        pdb=" C4 ABTN C5100 "    0.172 2.00e-02 2.50e+03
        pdb=" C5 ABTN C5100 "    0.172 2.00e-02 2.50e+03
        pdb=" N1 ABTN C5100 "   -0.270 2.00e-02 2.50e+03
        pdb=" N2 ABTN C5100 "   -0.272 2.00e-02 2.50e+03
        pdb=" O3 ABTN C5100 "    0.262 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3 ABTN A5100 "   -0.063 2.00e-02 2.50e+03   2.15e-01 6.96e+02
        pdb=" C4 ABTN A5100 "    0.172 2.00e-02 2.50e+03
        pdb=" C5 ABTN A5100 "    0.172 2.00e-02 2.50e+03
        pdb=" N1 ABTN A5100 "   -0.270 2.00e-02 2.50e+03
        pdb=" N2 ABTN A5100 "   -0.272 2.00e-02 2.50e+03
        pdb=" O3 ABTN A5100 "    0.262 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3 ABTN B5100 "    0.063 2.00e-02 2.50e+03   2.15e-01 6.96e+02
        pdb=" C4 ABTN B5100 "   -0.172 2.00e-02 2.50e+03
        pdb=" C5 ABTN B5100 "   -0.172 2.00e-02 2.50e+03
        pdb=" N1 ABTN B5100 "    0.270 2.00e-02 2.50e+03
        pdb=" N2 ABTN B5100 "    0.272 2.00e-02 2.50e+03
        pdb=" O3 ABTN B5100 "   -0.262 2.00e-02 2.50e+03
  ... (remaining 681 not shown)

  Histogram of nonbonded interaction distances:
        0.00 -     0.98: 2
        0.98 -     1.96: 0
        1.96 -     2.94: 1438
        2.94 -     3.92: 11594
        3.92 -     4.90: 22880
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 35914
  Sorted by model distance:
  nonbonded pdb=" O   HOH A5223 "
            pdb=" O   HOH C5223 "
     model   vdw
     0.001 3.040
  nonbonded pdb=" O   HOH B5223 "
            pdb=" O   HOH D5223 "
     model   vdw
     0.001 3.040
  nonbonded pdb=" O  AASN C  49 "
            pdb=" OD1AASN C  49 "
     model   vdw
     2.057 3.040
  nonbonded pdb=" O  AASN D  49 "
            pdb=" OD1AASN D  49 "
     model   vdw
     2.057 3.040
  nonbonded pdb=" O  AASN A  49 "
            pdb=" OD1AASN A  49 "
     model   vdw
     2.057 3.040
  ... (remaining 35909 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.94
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:             0.340
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.840
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  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:8.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
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      :  0.032   0.090   3944  Z= 2.144
  Angle     :  3.162  13.316   5400  Z= 2.201
  Chirality :  0.090   0.401    604
  Planarity :  0.016   0.215    684
  Dihedral  : 14.879  82.705   1324
  Min Nonbonded Distance : 0.001

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  2.54 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  4.30 %
    Favored  : 93.55 %
  Cbeta Deviations :  3.60 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.33), residues: 512
  helix:  None (None), residues: 0
  sheet:  0.30 (0.29), residues: 244
  loop : -1.41 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG D  53 
 TYR   0.002   0.001   TYR B  60 
 PHE   0.002   0.001   PHE D 130 
 TRP   0.004   0.001   TRP C  92 
 HIS   0.001   0.000   HIS C 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.03226 ( 3944)
  covalent geometry    : angle       3.16201 ( 5400)
  hydrogen bonds       : bond        0.13857 (  168)
  hydrogen bonds       : angle       9.73459 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 SER cc_start: 0.8217 (m) cc_final: 0.7789 (p)
REVERT: A   53 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7498 (ttp80)
REVERT: A   69 SER cc_start: 0.7845 (m) cc_final: 0.7634 (t)
REVERT: A  103 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7435 (mtm-85)
REVERT: B   27 SER cc_start: 0.8218 (m) cc_final: 0.7790 (p)
REVERT: B   53 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7499 (ttp80)
REVERT: B   69 SER cc_start: 0.7845 (m) cc_final: 0.7635 (t)
REVERT: B  103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7434 (mtm-85)
REVERT: C   27 SER cc_start: 0.8215 (m) cc_final: 0.7788 (p)
REVERT: C   53 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7498 (ttp80)
REVERT: C   69 SER cc_start: 0.7844 (m) cc_final: 0.7634 (t)
REVERT: C  103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7433 (mtm-85)
REVERT: D   27 SER cc_start: 0.8217 (m) cc_final: 0.7788 (p)
REVERT: D   53 ARG cc_start: 0.7715 (ttp-110) cc_final: 0.7500 (ttp80)
REVERT: D   69 SER cc_start: 0.7844 (m) cc_final: 0.7634 (t)
REVERT: D  103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7435 (mtm-85)
  outliers start: 4
  outliers final: 4
  residues processed: 64
  average time/residue: 0.6083
  time to fit residues: 40.1896
Evaluate side-chains
  52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain D residue   28 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0970
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:   30.0000
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.4151 r_free = 0.4151 target = 0.169510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.141194 restraints weight = 8168.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 1.82
r_work: 0.3703 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3595 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3594
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3590 r_free = 0.3590    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3590
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.114   3944  Z= 0.332
  Angle     :  1.284  17.671   5400  Z= 0.716
  Chirality :  0.068   0.438    604
  Planarity :  0.012   0.094    684
  Dihedral  :  9.685  59.086    636
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  9.68 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.05 (0.33), residues: 512
  helix: -4.83 (0.28), residues: 24
  sheet: -0.61 (0.26), residues: 280
  loop : -1.88 (0.40), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.003   ARG B  53 
 TYR   0.143   0.009   TYR B  43 
 PHE   0.118   0.017   PHE B  29 
 TRP   0.070   0.007   TRP B 108 
 HIS   0.010   0.002   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00695 ( 3944)
  covalent geometry    : angle       1.28449 ( 5400)
  hydrogen bonds       : bond        0.06664 (  168)
  hydrogen bonds       : angle       9.08511 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 0
  residues processed: 61
  average time/residue: 0.6203
  time to fit residues: 38.9867
Evaluate side-chains
  48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 29 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 107 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.160979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.138025 restraints weight = 3616.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 1.16
r_work: 0.3669 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3566 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   3944  Z= 0.297
  Angle     :  0.860   8.272   5400  Z= 0.472
  Chirality :  0.049   0.177    604
  Planarity :  0.005   0.029    684
  Dihedral  :  8.527  46.828    632
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.03 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  9.41 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.35), residues: 512
  helix:  None (None), residues: 0
  sheet:  0.26 (0.24), residues: 292
  loop : -0.06 (0.47), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG A  84 
 TYR   0.017   0.003   TYR B  22 
 PHE   0.026   0.005   PHE A  29 
 TRP   0.021   0.004   TRP D  75 
 HIS   0.008   0.003   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 ( 3944)
  covalent geometry    : angle       0.86037 ( 5400)
  hydrogen bonds       : bond        0.05530 (  168)
  hydrogen bonds       : angle       8.36748 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 54
  average time/residue: 0.7063
  time to fit residues: 39.2090
Evaluate side-chains
  51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 19 optimal weight:   20.0000
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.164870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.140805 restraints weight = 4611.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 1.33
r_work: 0.3706 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3606 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3603
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3603 r_free = 0.3603    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3603 r_free = 0.3603    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3603
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3944  Z= 0.119
  Angle     :  0.637   7.726   5400  Z= 0.332
  Chirality :  0.042   0.145    604
  Planarity :  0.003   0.019    684
  Dihedral  :  6.780  47.673    632
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 10.22 %
    Favored  : 89.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.34), residues: 512
  helix: -5.08 (0.18), residues: 24
  sheet:  0.48 (0.25), residues: 296
  loop : -0.19 (0.46), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  53 
 TYR   0.012   0.001   TYR C  22 
 PHE   0.018   0.003   PHE C  29 
 TRP   0.014   0.002   TRP D  75 
 HIS   0.002   0.001   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 3944)
  covalent geometry    : angle       0.63678 ( 5400)
  hydrogen bonds       : bond        0.04347 (  168)
  hydrogen bonds       : angle       7.35852 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 49
  average time/residue: 0.7473
  time to fit residues: 37.6472
Evaluate side-chains
  48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   28 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 41 optimal weight:    0.5980
   chunk 31 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.164787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.140967 restraints weight = 4365.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 1.30
r_work: 0.3709 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3608 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3603
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3603 r_free = 0.3603    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3944  Z= 0.117
  Angle     :  0.624   7.866   5400  Z= 0.325
  Chirality :  0.042   0.148    604
  Planarity :  0.003   0.021    684
  Dihedral  :  6.666  46.228    632
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  9.68 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.34), residues: 512
  helix: -5.19 (0.15), residues: 24
  sheet:  0.66 (0.26), residues: 296
  loop :  0.04 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  53 
 TYR   0.011   0.001   TYR C  22 
 PHE   0.013   0.002   PHE C  29 
 TRP   0.012   0.002   TRP B 108 
 HIS   0.002   0.001   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 3944)
  covalent geometry    : angle       0.62370 ( 5400)
  hydrogen bonds       : bond        0.04338 (  168)
  hydrogen bonds       : angle       7.16136 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 50
  average time/residue: 0.7345
  time to fit residues: 37.6868
Evaluate side-chains
  45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain B residue   28 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    4.5588

-------------------------------------------------------------------------------
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 = 0.4054 r_free = 0.4054 target = 0.161864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.137795 restraints weight = 4271.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.28
r_work: 0.3661 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3558 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3944  Z= 0.238
  Angle     :  0.777   9.015   5400  Z= 0.408
  Chirality :  0.046   0.149    604
  Planarity :  0.004   0.023    684
  Dihedral  :  7.776  46.540    632
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  9.41 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.36), residues: 512
  helix:  None (None), residues: 0
  sheet:  0.49 (0.25), residues: 296
  loop :  0.88 (0.48), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.002   ARG B  84 
 TYR   0.016   0.002   TYR C  22 
 PHE   0.017   0.003   PHE C  29 
 TRP   0.016   0.003   TRP C  92 
 HIS   0.006   0.003   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 3944)
  covalent geometry    : angle       0.77691 ( 5400)
  hydrogen bonds       : bond        0.05398 (  168)
  hydrogen bonds       : angle       7.75149 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 47
  average time/residue: 0.8220
  time to fit residues: 39.5863
Evaluate side-chains
  46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   69 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 36 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
C  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.162517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.138396 restraints weight = 4432.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 1.31
r_work: 0.3670 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3567 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3944  Z= 0.156
  Angle     :  0.668   8.499   5400  Z= 0.351
  Chirality :  0.044   0.164    604
  Planarity :  0.003   0.023    684
  Dihedral  :  7.037  46.043    632
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  9.14 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.33), residues: 512
  helix: -5.22 (0.15), residues: 24
  sheet:  0.48 (0.25), residues: 304
  loop : -0.21 (0.42), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 103 
 TYR   0.012   0.002   TYR C  22 
 PHE   0.009   0.002   PHE C  29 
 TRP   0.012   0.002   TRP B 108 
 HIS   0.003   0.002   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3944)
  covalent geometry    : angle       0.66786 ( 5400)
  hydrogen bonds       : bond        0.04970 (  168)
  hydrogen bonds       : angle       7.40670 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 4
  residues processed: 51
  average time/residue: 0.7353
  time to fit residues: 38.5606
Evaluate side-chains
  48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   69 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 12 optimal weight:   20.0000
   chunk 1 optimal weight:    5.9990
   chunk 5 optimal weight:    0.4980
   chunk 25 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    4.6988

-------------------------------------------------------------------------------
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 = 0.4041 r_free = 0.4041 target = 0.161063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.137477 restraints weight = 4016.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 1.24
r_work: 0.3656 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3551
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3551 r_free = 0.3551    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3551 r_free = 0.3551    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3551
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3944  Z= 0.243
  Angle     :  0.758   9.010   5400  Z= 0.406
  Chirality :  0.048   0.164    604
  Planarity :  0.004   0.033    684
  Dihedral  :  7.859  45.540    632
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 10.22 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.33), residues: 512
  helix: -5.21 (0.15), residues: 24
  sheet:  0.35 (0.25), residues: 304
  loop : -0.24 (0.43), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG A 103 
 TYR   0.019   0.002   TYR C  22 
 PHE   0.007   0.002   PHE D  29 
 TRP   0.014   0.003   TRP C  92 
 HIS   0.006   0.003   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 3944)
  covalent geometry    : angle       0.75768 ( 5400)
  hydrogen bonds       : bond        0.05602 (  168)
  hydrogen bonds       : angle       7.76235 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 46
  average time/residue: 0.7201
  time to fit residues: 34.1204
Evaluate side-chains
  47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   69 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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 = 0.4070 r_free = 0.4070 target = 0.163334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.139885 restraints weight = 4082.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 1.26
r_work: 0.3694 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3591 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3583
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3944  Z= 0.130
  Angle     :  0.655   8.595   5400  Z= 0.337
  Chirality :  0.043   0.161    604
  Planarity :  0.003   0.024    684
  Dihedral  :  6.941  47.134    632
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  9.68 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.33), residues: 512
  helix: -5.24 (0.15), residues: 24
  sheet:  0.51 (0.25), residues: 304
  loop : -0.24 (0.42), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 103 
 TYR   0.014   0.001   TYR C  22 
 PHE   0.005   0.001   PHE B  29 
 TRP   0.012   0.002   TRP B 108 
 HIS   0.002   0.001   HIS D  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3944)
  covalent geometry    : angle       0.65487 ( 5400)
  hydrogen bonds       : bond        0.04709 (  168)
  hydrogen bonds       : angle       7.31747 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 5
  residues processed: 50
  average time/residue: 0.6885
  time to fit residues: 35.4141
Evaluate side-chains
  46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   69 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0470
   chunk 42 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.8084

-------------------------------------------------------------------------------
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 = 0.4067 r_free = 0.4067 target = 0.163253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.138802 restraints weight = 4621.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 1.35
r_work: 0.3679 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3577 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3944  Z= 0.134
  Angle     :  0.645   8.747   5400  Z= 0.337
  Chirality :  0.044   0.158    604
  Planarity :  0.003   0.023    684
  Dihedral  :  7.000  47.669    632
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  9.41 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.33), residues: 512
  helix: -5.27 (0.15), residues: 24
  sheet:  0.53 (0.25), residues: 304
  loop : -0.17 (0.42), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 103 
 TYR   0.016   0.001   TYR C  22 
 PHE   0.006   0.002   PHE A  29 
 TRP   0.012   0.002   TRP B 108 
 HIS   0.002   0.001   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3944)
  covalent geometry    : angle       0.64452 ( 5400)
  hydrogen bonds       : bond        0.04739 (  168)
  hydrogen bonds       : angle       7.30513 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 5
  residues processed: 50
  average time/residue: 0.7535
  time to fit residues: 38.7453
Evaluate side-chains
  48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   69 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:   20.0000
   chunk 11 optimal weight:    9.9990
   chunk 37 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0170
   chunk 19 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 39 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    1.5222

-------------------------------------------------------------------------------
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 = 0.4077 r_free = 0.4077 target = 0.164058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.138169 restraints weight = 5869.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 1.53
r_work: 0.3673 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3567 r_free = 0.3567    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3566 r_free = 0.3566    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3944  Z= 0.126
  Angle     :  0.648   8.184   5400  Z= 0.333
  Chirality :  0.044   0.160    604
  Planarity :  0.003   0.022    684
  Dihedral  :  6.903  48.293    632
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  9.68 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.33), residues: 512
  helix: -5.28 (0.15), residues: 24
  sheet:  0.61 (0.25), residues: 304
  loop : -0.15 (0.42), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 103 
 TYR   0.015   0.001   TYR C  22 
 PHE   0.007   0.002   PHE D  29 
 TRP   0.012   0.002   TRP B 108 
 HIS   0.002   0.001   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 3944)
  covalent geometry    : angle       0.64837 ( 5400)
  hydrogen bonds       : bond        0.04588 (  168)
  hydrogen bonds       : angle       7.17855 (  456)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2580.06 seconds
wall clock time: 44 minutes 45.01 seconds (2685.01 seconds total)