Starting phenix.real_space_refine
on Thu Jun  5 03:48:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vgp_43220/06_2025/8vgp_43220.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vgp_43220/06_2025/8vgp_43220.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vgp_43220/06_2025/8vgp_43220.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vgp_43220/06_2025/8vgp_43220.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vgp_43220/06_2025/8vgp_43220.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vgp_43220/06_2025/8vgp_43220.cif"
  }
  resolution = 2.7
  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=  -0.001 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      34      5.16       5
     C    3157      2.51       5
     N     838      2.21       5
     O    1016      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5046
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1769
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 218, 1758
          Classifications: {'peptide': 218}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 210}
      Conformer: "B"
        Number of residues, atoms: 218, 1758
          Classifications: {'peptide': 218}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 210}
          bond proxies already assigned to first conformer: 1796
    Chain: "H"
      Number of atoms: 1624
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 217, 1613
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 12, 'TRANS': 204}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 217, 1613
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 12, 'TRANS': 204}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1643
    Chain: "L"
      Number of atoms: 1609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1609
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203}
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 25
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1, 'water': 24}
          Link IDs: {None: 24}
    Chain: "H"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "L"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A 400 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 400 " occ=0.50
    residue:
      pdb=" N  AARG H  19 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG H  19 " occ=0.50
  Time building chain proxies: 5.39, per 1000 atoms: 1.07
  Number of scatterers: 5046
  At special positions: 0
  Unit cell: (115.875, 64.1452, 95.1832, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      34     16.00
     O    1016      8.00
     N     838      7.00
     C    3157      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 284 " - pdb=" SG  CYS A 313 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 433 " - pdb=" SG  CYS A 435 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 437 " - pdb=" SG  CYS A 450 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  11 " - pdb=" SG  CYS H 151 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 108 " - pdb=" SG  CYS H 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 126 " - pdb=" SG  CYS L 124 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 141 " - pdb=" SG  CYS L 116 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  40 " - pdb=" SG  CYS L 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  80 " - pdb=" SG  CYS L 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " 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: 1.18
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1178

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 13 sheets defined
      13.6% alpha, 47.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 283 through 290
    Processing helix  chain 'A' and resid 316 through 320
      removed outlier: 4.322A  pdb=" N   GLY A 319 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 345
    Processing helix  chain 'A' and resid 356 through 365
    Processing helix  chain 'A' and resid 394 through 398
    Processing helix  chain 'A' and resid 436 through 441
    Processing helix  chain 'A' and resid 475 through 479
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 73 through 75
      No H-bonds generated for 'chain 'H' and resid 73 through 75'
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'H' and resid 161 through 163
      No H-bonds generated for 'chain 'H' and resid 161 through 163'
    Processing helix  chain 'H' and resid 192 through 194
      No H-bonds generated for 'chain 'H' and resid 192 through 194'
    Processing helix  chain 'H' and resid 207 through 209
      No H-bonds generated for 'chain 'H' and resid 207 through 209'
    Processing helix  chain 'L' and resid 29 through 31
      No H-bonds generated for 'chain 'L' and resid 29 through 31'
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.814A  pdb=" N   PHE L  83 " --> pdb=" O   CYS L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 126
    Processing helix  chain 'L' and resid 183 through 187
    Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 301
      removed outlier: 25.594A  pdb=" N   GLU A 308 " --> pdb=" O   ARG A 328 " (cutoff:3.500A)
      removed outlier: 20.837A  pdb=" N   ARG A 328 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
      removed outlier: 14.326A  pdb=" N   LYS A 310 " --> pdb=" O   GLN A 326 " (cutoff:3.500A)
      removed outlier: 9.886A  pdb=" N   GLN A 326 " --> pdb=" O   LYS A 310 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   TYR A 312 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   MET A 489 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   ARG A 327 " --> pdb=" O   THR A 487 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   THR A 487 " --> pdb=" O   ARG A 327 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   TYR A 369 " --> pdb=" O   HIS A 389 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   HIS A 389 " --> pdb=" O   TYR A 369 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 347
      removed outlier: 6.467A  pdb=" N   MET A 489 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   ARG A 327 " --> pdb=" O   THR A 487 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   THR A 487 " --> pdb=" O   ARG A 327 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   TYR A 369 " --> pdb=" O   HIS A 389 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   HIS A 389 " --> pdb=" O   TYR A 369 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 454
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.715A  pdb=" N   ILE H  34 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   GLY H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TYR H  56 " --> pdb=" O   THR H  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.052A  pdb=" N   TYR H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL H  96 " --> pdb=" O   MET H 100C" (cutoff:3.500A)
      removed outlier: 5.906A  pdb=" N   MET H 100C" --> pdb=" O   VAL H  96 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 131
      removed outlier: 6.599A  pdb=" N   CYS H 141 " --> pdb=" O   PRO H 130 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   TYR H 181 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 124 through 131
      removed outlier: 6.599A  pdb=" N   CYS H 141 " --> pdb=" O   PRO H 130 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   TYR H 181 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 159
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6
      removed outlier: 5.525A  pdb=" N   THR L  69 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 9.608A  pdb=" N   GLN L  27 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 9.587A  pdb=" N   SER L  67 " --> pdb=" O   GLN L  27 " (cutoff:3.500A)
      removed outlier: 11.833A  pdb=" N   LEU L  28 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
      removed outlier: 12.058A  pdb=" N   SER L  65 " --> pdb=" O   LEU L  28 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.321A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   LYS L 107 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ALA L  13 " --> pdb=" O   LYS L 107 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   TYR L  49 " --> pdb=" O   VAL L  33 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.761A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 153 through 154

    225 hydrogen bonds defined for protein.
    562 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: 2.18

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1552
        1.34 -     1.46: 1255
        1.46 -     1.58: 2279
        1.58 -     1.71: 0
        1.71 -     1.83: 42
  Bond restraints: 5128
  Sorted by residual:
  bond pdb=" C   THR H 170 "
       pdb=" N   PHE H 171 "
    ideal  model  delta    sigma   weight residual
    1.340  1.228  0.112 5.87e-02 2.90e+02 3.67e+00
  bond pdb=" CG  LEU A 375 "
       pdb=" CD1 LEU A 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.40e+00
  bond pdb=" CD  LYS A 478 "
       pdb=" CE  LYS A 478 "
    ideal  model  delta    sigma   weight residual
    1.520  1.466  0.054 3.00e-02 1.11e+03 3.23e+00
  bond pdb=" CG  LEU L 175 "
       pdb=" CD1 LEU L 175 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.52e+00
  bond pdb=" CB BARG A 400 "
       pdb=" CG BARG A 400 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.47e+00
  ... (remaining 5123 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 6751
        2.60 -     5.20: 182
        5.20 -     7.80: 21
        7.80 -    10.40: 4
       10.40 -    13.00: 1
  Bond angle restraints: 6959
  Sorted by residual:
  angle pdb=" N   PHE A 447 "
        pdb=" CA  PHE A 447 "
        pdb=" C   PHE A 447 "
      ideal   model   delta    sigma   weight residual
     112.89  118.86   -5.97 1.24e+00 6.50e-01 2.32e+01
  angle pdb=" CA  LEU L  73 "
        pdb=" CB  LEU L  73 "
        pdb=" CG  LEU L  73 "
      ideal   model   delta    sigma   weight residual
     116.30  129.30  -13.00 3.50e+00 8.16e-02 1.38e+01
  angle pdb=" N   GLN A 462 "
        pdb=" CA  GLN A 462 "
        pdb=" C   GLN A 462 "
      ideal   model   delta    sigma   weight residual
     112.34  116.82   -4.48 1.30e+00 5.92e-01 1.19e+01
  angle pdb=" C   GLU H 152 "
        pdb=" N   CYS H 153 "
        pdb=" CA  CYS H 153 "
      ideal   model   delta    sigma   weight residual
     121.80  129.92   -8.12 2.44e+00 1.68e-01 1.11e+01
  angle pdb=" CA  CYS L 124 "
        pdb=" CB  CYS L 124 "
        pdb=" SG  CYS L 124 "
      ideal   model   delta    sigma   weight residual
     114.40  107.12    7.28 2.30e+00 1.89e-01 1.00e+01
  ... (remaining 6954 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 2790
       17.67 -    35.35: 183
       35.35 -    53.02: 37
       53.02 -    70.69: 10
       70.69 -    88.37: 15
  Dihedral angle restraints: 3035
    sinusoidal: 1174
      harmonic: 1861
  Sorted by residual:
  dihedral pdb=" CD BARG H  19 "
           pdb=" NE BARG H  19 "
           pdb=" CZ BARG H  19 "
           pdb=" NH1BARG H  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -74.63   74.63     1      1.00e+01 1.00e-02 7.06e+01
  dihedral pdb=" CD BARG A 400 "
           pdb=" NE BARG A 400 "
           pdb=" CZ BARG A 400 "
           pdb=" NH1BARG A 400 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   71.95  -71.95     1      1.00e+01 1.00e-02 6.62e+01
  dihedral pdb=" CA  PHE H  98 "
           pdb=" C   PHE H  98 "
           pdb=" N   LEU H  99 "
           pdb=" CA  LEU H  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.97  -29.03     0      5.00e+00 4.00e-02 3.37e+01
  ... (remaining 3032 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 433
       0.050 -    0.099: 226
       0.099 -    0.149: 78
       0.149 -    0.199: 11
       0.199 -    0.248: 2
  Chirality restraints: 750
  Sorted by residual:
  chirality pdb=" CA  TYR A 476 "
            pdb=" N   TYR A 476 "
            pdb=" C   TYR A 476 "
            pdb=" CB  TYR A 476 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  TYR H 100A"
            pdb=" N   TYR H 100A"
            pdb=" C   TYR H 100A"
            pdb=" CB  TYR H 100A"
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CB  ILE A 324 "
            pdb=" CA  ILE A 324 "
            pdb=" CG1 ILE A 324 "
            pdb=" CG2 ILE A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.91e-01
  ... (remaining 747 not shown)

  Planarity restraints: 890
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD BARG H  19 "    0.904 9.50e-02 1.11e+02   4.06e-01 1.11e+02
        pdb=" NE BARG H  19 "   -0.075 2.00e-02 2.50e+03
        pdb=" CZ BARG H  19 "    0.046 2.00e-02 2.50e+03
        pdb=" NH1BARG H  19 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH2BARG H  19 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD BARG A 400 "    0.874 9.50e-02 1.11e+02   3.93e-01 1.05e+02
        pdb=" NE BARG A 400 "   -0.074 2.00e-02 2.50e+03
        pdb=" CZ BARG A 400 "    0.048 2.00e-02 2.50e+03
        pdb=" NH1BARG A 400 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH2BARG A 400 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD AARG A 400 "    0.243 9.50e-02 1.11e+02   1.10e-01 9.11e+00
        pdb=" NE AARG A 400 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ AARG A 400 "    0.020 2.00e-02 2.50e+03
        pdb=" NH1AARG A 400 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH2AARG A 400 "    0.001 2.00e-02 2.50e+03
  ... (remaining 887 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 183
        2.70 -     3.25: 4731
        3.25 -     3.80: 7880
        3.80 -     4.35: 11345
        4.35 -     4.90: 18704
  Nonbonded interactions: 42843
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 451 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" O   HOH A 714 "
            pdb=" O   HOH A 722 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OG  SER L   7 "
            pdb=" O   HOH L 301 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" NZ  LYS L 190 "
            pdb=" OD1 ASN L 210 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   HOH A 709 "
            pdb=" O   HOH A 716 "
     model   vdw
     2.250 3.040
  ... (remaining 42838 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=0.50 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:             56.580
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     20.300
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:22.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   99.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
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      :  0.010   0.112   5141  Z= 0.394
  Angle     :  1.022  12.996   6985  Z= 0.549
  Chirality :  0.063   0.248    750
  Planarity :  0.021   0.406    890
  Dihedral  : 14.339  88.368   1818
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.00 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  5.99 %
    Favored  : 93.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    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: -0.76 (0.32), residues: 646
  helix: -2.77 (0.56), residues: 42
  sheet:  0.45 (0.31), residues: 266
  loop : -0.98 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP H  33 
 HIS   0.013   0.003   HIS H  35 
 PHE   0.024   0.004   PHE H  98 
 TYR   0.022   0.005   TYR A 353 
 ARG   0.019   0.004   ARG A 327 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17839 (  188)
  hydrogen bonds       : angle       8.68279 (  562)
  SS BOND              : bond        0.00749 (   13)
  SS BOND              : angle       1.62910 (   26)
  covalent geometry    : bond        0.00980 ( 5128)
  covalent geometry    : angle       1.01941 ( 6959)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
REVERT: H  141 CYS cc_start: 0.7481 (m) cc_final: 0.6963 (m)
  outliers start: 4
  outliers final: 0
  residues processed: 92
  average time/residue: 1.5596
  time to fit residues: 148.5404
Evaluate side-chains
  65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    0.1980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 362 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.073803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.055178 restraints weight = 40368.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 5.26
r_work: 0.2537 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2546
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2546
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5141  Z= 0.162
  Angle     :  0.690   9.496   6985  Z= 0.365
  Chirality :  0.046   0.137    750
  Planarity :  0.004   0.048    890
  Dihedral  :  5.476  26.440    704
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.12 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 10.53 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    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:  0.01 (0.34), residues: 646
  helix: -1.90 (0.64), residues: 45
  sheet:  0.71 (0.31), residues: 276
  loop : -0.25 (0.37), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  33 
 HIS   0.006   0.001   HIS A 402 
 PHE   0.021   0.002   PHE H  98 
 TYR   0.011   0.001   TYR A 391 
 ARG   0.008   0.001   ARG L 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04073 (  188)
  hydrogen bonds       : angle       6.05896 (  562)
  SS BOND              : bond        0.00484 (   13)
  SS BOND              : angle       1.63849 (   26)
  covalent geometry    : bond        0.00376 ( 5128)
  covalent geometry    : angle       0.68410 ( 6959)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
REVERT: A  464 GLN cc_start: 0.8729 (mp10) cc_final: 0.8436 (mp10)
REVERT: H   31 ASP cc_start: 0.9221 (m-30) cc_final: 0.8978 (m-30)
REVERT: H   82 MET cc_start: 0.9188 (mtp) cc_final: 0.8970 (mtm)
REVERT: L  123 GLU cc_start: 0.9225 (mp0) cc_final: 0.8782 (mp0)
REVERT: L  125 LEU cc_start: 0.8543 (mm) cc_final: 0.8068 (mt)
REVERT: L  167 ASP cc_start: 0.8673 (t0) cc_final: 0.8191 (t0)
  outliers start: 5
  outliers final: 1
  residues processed: 71
  average time/residue: 1.7699
  time to fit residues: 129.8531
Evaluate side-chains
  64 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0870
   overall best weight:    0.6562

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

Flipped N/Q/H residues before XYZ refinement:
A 465 ASN
H 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.073155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.054820 restraints weight = 34825.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 4.97
r_work: 0.2526 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2535 r_free = 0.2535    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2535 r_free = 0.2535    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5141  Z= 0.161
  Angle     :  0.645   9.488   6985  Z= 0.340
  Chirality :  0.045   0.165    750
  Planarity :  0.004   0.046    890
  Dihedral  :  5.162  25.305    704
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.12 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 12.16 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    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:  0.17 (0.34), residues: 646
  helix: -1.43 (0.69), residues: 46
  sheet:  0.76 (0.31), residues: 276
  loop : -0.13 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.004   0.001   HIS A 402 
 PHE   0.022   0.002   PHE H  98 
 TYR   0.010   0.001   TYR A 353 
 ARG   0.007   0.001   ARG A 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03693 (  188)
  hydrogen bonds       : angle       5.67653 (  562)
  SS BOND              : bond        0.00377 (   13)
  SS BOND              : angle       1.58922 (   26)
  covalent geometry    : bond        0.00390 ( 5128)
  covalent geometry    : angle       0.63876 ( 6959)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 GLN cc_start: 0.8797 (mm110) cc_final: 0.8552 (mm-40)
REVERT: A  458 MET cc_start: 0.8977 (mmm) cc_final: 0.8547 (mmp)
REVERT: A  464 GLN cc_start: 0.8707 (mp10) cc_final: 0.8447 (mp10)
REVERT: H   31 ASP cc_start: 0.9227 (m-30) cc_final: 0.8949 (m-30)
REVERT: H   82 MET cc_start: 0.9226 (mtp) cc_final: 0.8848 (mtm)
REVERT: L  123 GLU cc_start: 0.9221 (mp0) cc_final: 0.8790 (mp0)
REVERT: L  142 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8574 (ttt-90)
REVERT: L  167 ASP cc_start: 0.8686 (t0) cc_final: 0.8190 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 70
  average time/residue: 2.0608
  time to fit residues: 149.5979
Evaluate side-chains
  64 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
H 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.072198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.053264 restraints weight = 45943.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.2702 rms_B_bonded: 5.51
r_work: 0.2491 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2491
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2496 r_free = 0.2496    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2496 r_free = 0.2496    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   5141  Z= 0.197
  Angle     :  0.650   9.426   6985  Z= 0.341
  Chirality :  0.046   0.146    750
  Planarity :  0.004   0.043    890
  Dihedral  :  5.146  26.938    704
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.97 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.79 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    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:  0.22 (0.35), residues: 646
  helix: -1.40 (0.71), residues: 46
  sheet:  0.82 (0.32), residues: 282
  loop : -0.16 (0.38), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.018   0.002   PHE H  98 
 TYR   0.012   0.001   TYR H  91 
 ARG   0.007   0.001   ARG A 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03775 (  188)
  hydrogen bonds       : angle       5.64072 (  562)
  SS BOND              : bond        0.00398 (   13)
  SS BOND              : angle       1.55624 (   26)
  covalent geometry    : bond        0.00479 ( 5128)
  covalent geometry    : angle       0.64375 ( 6959)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 GLN cc_start: 0.8824 (mm110) cc_final: 0.8570 (mm-40)
REVERT: A  458 MET cc_start: 0.9045 (mmm) cc_final: 0.8743 (mmp)
REVERT: H   31 ASP cc_start: 0.9258 (m-30) cc_final: 0.8980 (m-30)
REVERT: H  211 LYS cc_start: 0.9480 (ttmm) cc_final: 0.9246 (ttmm)
REVERT: L  142 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8661 (ttt-90)
REVERT: L  167 ASP cc_start: 0.8644 (t0) cc_final: 0.8276 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 71
  average time/residue: 1.5910
  time to fit residues: 117.1276
Evaluate side-chains
  67 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain L residue  122 ASP
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
H 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.072744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.054250 restraints weight = 30047.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.2729 rms_B_bonded: 4.75
r_work: 0.2537 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2544
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2544 r_free = 0.2544    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2544 r_free = 0.2544    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2544
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5141  Z= 0.159
  Angle     :  0.637   9.383   6985  Z= 0.335
  Chirality :  0.045   0.149    750
  Planarity :  0.004   0.040    890
  Dihedral  :  5.021  29.055    704
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.12 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.43 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    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:  0.25 (0.35), residues: 646
  helix: -1.49 (0.68), residues: 47
  sheet:  0.85 (0.32), residues: 282
  loop : -0.12 (0.38), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A 402 
 PHE   0.020   0.001   PHE H  98 
 TYR   0.011   0.001   TYR H  91 
 ARG   0.008   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03418 (  188)
  hydrogen bonds       : angle       5.42647 (  562)
  SS BOND              : bond        0.00342 (   13)
  SS BOND              : angle       1.45630 (   26)
  covalent geometry    : bond        0.00387 ( 5128)
  covalent geometry    : angle       0.63213 ( 6959)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 GLN cc_start: 0.8808 (mm110) cc_final: 0.8563 (mm-40)
REVERT: A  458 MET cc_start: 0.9038 (mmm) cc_final: 0.8729 (mmp)
REVERT: H   31 ASP cc_start: 0.9270 (m-30) cc_final: 0.8971 (m-30)
REVERT: H  211 LYS cc_start: 0.9476 (ttmm) cc_final: 0.9235 (ttmm)
REVERT: L  142 ARG cc_start: 0.8827 (tpp80) cc_final: 0.8623 (ttt-90)
REVERT: L  167 ASP cc_start: 0.8619 (t0) cc_final: 0.8229 (t0)
  outliers start: 10
  outliers final: 4
  residues processed: 70
  average time/residue: 1.5106
  time to fit residues: 109.6210
Evaluate side-chains
  66 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 62 optimal weight:    0.1980
   chunk 35 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.1980
   chunk 44 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
H 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.073466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.055218 restraints weight = 33186.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.2744 rms_B_bonded: 4.89
r_work: 0.2545 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5141  Z= 0.134
  Angle     :  0.635   9.328   6985  Z= 0.330
  Chirality :  0.044   0.141    750
  Planarity :  0.004   0.041    890
  Dihedral  :  4.881  30.296    704
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.28 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.61 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  0.34 (0.35), residues: 646
  helix: -1.50 (0.68), residues: 47
  sheet:  0.92 (0.32), residues: 282
  loop : -0.05 (0.39), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 402 
 PHE   0.020   0.001   PHE H  98 
 TYR   0.011   0.001   TYR A 391 
 ARG   0.008   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03164 (  188)
  hydrogen bonds       : angle       5.23038 (  562)
  SS BOND              : bond        0.00336 (   13)
  SS BOND              : angle       1.45804 (   26)
  covalent geometry    : bond        0.00328 ( 5128)
  covalent geometry    : angle       0.62990 ( 6959)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 GLN cc_start: 0.8826 (mm110) cc_final: 0.8579 (mm-40)
REVERT: A  458 MET cc_start: 0.8925 (mmm) cc_final: 0.8515 (mmp)
REVERT: H   31 ASP cc_start: 0.9226 (m-30) cc_final: 0.8928 (m-30)
REVERT: H  197 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8517 (tp-100)
REVERT: H  211 LYS cc_start: 0.9479 (ttmm) cc_final: 0.9235 (ttmm)
REVERT: L    3 GLN cc_start: 0.8593 (mp10) cc_final: 0.8137 (mp10)
REVERT: L  142 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8049 (ttp80)
  outliers start: 11
  outliers final: 5
  residues processed: 70
  average time/residue: 1.7136
  time to fit residues: 124.1731
Evaluate side-chains
  66 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain L residue  122 ASP
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
H 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.072926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.054588 restraints weight = 33763.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.2726 rms_B_bonded: 4.94
r_work: 0.2527 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2527
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5141  Z= 0.157
  Angle     :  0.642   9.187   6985  Z= 0.336
  Chirality :  0.045   0.144    750
  Planarity :  0.004   0.044    890
  Dihedral  :  4.863  27.403    704
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.59 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.97 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    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:  0.38 (0.35), residues: 646
  helix: -1.48 (0.67), residues: 47
  sheet:  0.98 (0.32), residues: 282
  loop : -0.06 (0.38), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.020   0.001   PHE H  98 
 TYR   0.011   0.001   TYR H  91 
 ARG   0.010   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (  188)
  hydrogen bonds       : angle       5.24430 (  562)
  SS BOND              : bond        0.00336 (   13)
  SS BOND              : angle       1.53503 (   26)
  covalent geometry    : bond        0.00384 ( 5128)
  covalent geometry    : angle       0.63678 ( 6959)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 GLN cc_start: 0.8841 (mm110) cc_final: 0.8589 (mm-40)
REVERT: A  458 MET cc_start: 0.8948 (mmm) cc_final: 0.8634 (mmp)
REVERT: H   31 ASP cc_start: 0.9232 (m-30) cc_final: 0.8944 (m-30)
REVERT: H  197 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8432 (tp-100)
REVERT: H  211 LYS cc_start: 0.9464 (ttmm) cc_final: 0.9261 (ttmm)
REVERT: L    3 GLN cc_start: 0.8647 (mp10) cc_final: 0.8158 (mp10)
REVERT: L  142 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8665 (ttt-90)
  outliers start: 10
  outliers final: 5
  residues processed: 68
  average time/residue: 1.6277
  time to fit residues: 114.7192
Evaluate side-chains
  65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain L residue  122 ASP
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0970
   chunk 13 optimal weight:    0.1980
   chunk 35 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
H 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.073132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.054729 restraints weight = 37522.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 5.15
r_work: 0.2542 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2549 r_free = 0.2549    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2549 r_free = 0.2549    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5141  Z= 0.140
  Angle     :  0.656  10.184   6985  Z= 0.342
  Chirality :  0.044   0.151    750
  Planarity :  0.004   0.048    890
  Dihedral  :  4.845  30.660    704
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.28 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 14.88 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  0.43 (0.35), residues: 646
  helix: -1.39 (0.68), residues: 47
  sheet:  1.03 (0.32), residues: 273
  loop : -0.03 (0.37), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 402 
 PHE   0.020   0.001   PHE H  98 
 TYR   0.011   0.001   TYR A 391 
 ARG   0.011   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03126 (  188)
  hydrogen bonds       : angle       5.16242 (  562)
  SS BOND              : bond        0.00322 (   13)
  SS BOND              : angle       2.17476 (   26)
  covalent geometry    : bond        0.00340 ( 5128)
  covalent geometry    : angle       0.64390 ( 6959)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 GLN cc_start: 0.8847 (mm110) cc_final: 0.8601 (mm-40)
REVERT: A  458 MET cc_start: 0.8912 (mmm) cc_final: 0.8508 (mmp)
REVERT: H   31 ASP cc_start: 0.9221 (m-30) cc_final: 0.8929 (m-30)
REVERT: H   43 LYS cc_start: 0.8993 (mmtm) cc_final: 0.8732 (mmtm)
REVERT: H  117 LYS cc_start: 0.8781 (tptp) cc_final: 0.8565 (tmtt)
REVERT: H  197 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8405 (tp-100)
REVERT: H  211 LYS cc_start: 0.9473 (ttmm) cc_final: 0.9254 (ttmm)
REVERT: L    3 GLN cc_start: 0.8628 (mp10) cc_final: 0.8108 (mp10)
REVERT: L  142 ARG cc_start: 0.8923 (tpp80) cc_final: 0.8689 (ttt-90)
  outliers start: 7
  outliers final: 5
  residues processed: 67
  average time/residue: 1.6473
  time to fit residues: 114.2597
Evaluate side-chains
  67 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain L residue  122 ASP
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 15 optimal weight:    0.2980
   chunk 51 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
H 176 GLN
L  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.073227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.054875 restraints weight = 34620.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 4.99
r_work: 0.2544 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2544
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2550
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2550 r_free = 0.2550    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2550 r_free = 0.2550    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2550
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5141  Z= 0.152
  Angle     :  0.676  10.199   6985  Z= 0.352
  Chirality :  0.044   0.150    750
  Planarity :  0.004   0.052    890
  Dihedral  :  4.850  29.058    704
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.44 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 15.06 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    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:  0.48 (0.35), residues: 646
  helix: -1.30 (0.68), residues: 47
  sheet:  1.07 (0.32), residues: 273
  loop : -0.01 (0.37), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.021   0.001   PHE H  98 
 TYR   0.011   0.001   TYR A 391 
 ARG   0.013   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03157 (  188)
  hydrogen bonds       : angle       5.16739 (  562)
  SS BOND              : bond        0.00325 (   13)
  SS BOND              : angle       2.07370 (   26)
  covalent geometry    : bond        0.00374 ( 5128)
  covalent geometry    : angle       0.66565 ( 6959)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 GLN cc_start: 0.8846 (mm110) cc_final: 0.8600 (mm-40)
REVERT: A  458 MET cc_start: 0.8929 (mmm) cc_final: 0.8515 (mmp)
REVERT: H   31 ASP cc_start: 0.9218 (m-30) cc_final: 0.8919 (m-30)
REVERT: H   43 LYS cc_start: 0.9023 (mmtm) cc_final: 0.8754 (mmtm)
REVERT: H  117 LYS cc_start: 0.8794 (tptp) cc_final: 0.8587 (tmtt)
REVERT: H  211 LYS cc_start: 0.9454 (ttmm) cc_final: 0.9179 (ttmm)
REVERT: L  142 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8698 (ttt-90)
  outliers start: 7
  outliers final: 5
  residues processed: 67
  average time/residue: 1.7195
  time to fit residues: 119.2759
Evaluate side-chains
  68 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain L residue  122 ASP
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 33 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H 176 GLN
L 210 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.072722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.054150 restraints weight = 40450.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.2721 rms_B_bonded: 5.26
r_work: 0.2516 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2521
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2521 r_free = 0.2521    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2521 r_free = 0.2521    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2521
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   5141  Z= 0.183
  Angle     :  0.683  10.556   6985  Z= 0.355
  Chirality :  0.045   0.150    750
  Planarity :  0.004   0.055    890
  Dihedral  :  4.906  28.288    704
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.44 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.52 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    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:  0.48 (0.35), residues: 646
  helix: -1.25 (0.69), residues: 47
  sheet:  0.99 (0.31), residues: 289
  loop :  0.01 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.020   0.002   PHE H  98 
 TYR   0.012   0.001   TYR H  91 
 ARG   0.013   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03338 (  188)
  hydrogen bonds       : angle       5.25185 (  562)
  SS BOND              : bond        0.00343 (   13)
  SS BOND              : angle       2.08826 (   26)
  covalent geometry    : bond        0.00447 ( 5128)
  covalent geometry    : angle       0.67267 ( 6959)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 GLN cc_start: 0.8860 (mm110) cc_final: 0.8607 (mm-40)
REVERT: A  458 MET cc_start: 0.8954 (mmm) cc_final: 0.8637 (mmp)
REVERT: H   31 ASP cc_start: 0.9243 (m-30) cc_final: 0.8968 (m-30)
REVERT: H  197 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8540 (tp-100)
REVERT: H  211 LYS cc_start: 0.9449 (ttmm) cc_final: 0.9219 (ttmm)
REVERT: L  142 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8702 (ttt-90)
  outliers start: 11
  outliers final: 6
  residues processed: 68
  average time/residue: 1.5168
  time to fit residues: 106.9298
Evaluate side-chains
  70 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain H residue   11 CYS
Chi-restraints excluded: chain L residue   40 CYS
Chi-restraints excluded: chain L residue  122 ASP
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0870
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.4960

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

Flipped N/Q/H residues before XYZ refinement:
H 176 GLN
L 210 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.072948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.054234 restraints weight = 47243.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.2729 rms_B_bonded: 5.58
r_work: 0.2518 rms_B_bonded: 5.05 restraints_weight: 2.0000
r_work (final): 0.2518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2525
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2525 r_free = 0.2525    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2525 r_free = 0.2525    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2525
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5141  Z= 0.148
  Angle     :  0.683  10.134   6985  Z= 0.356
  Chirality :  0.044   0.143    750
  Planarity :  0.004   0.055    890
  Dihedral  :  4.845  27.997    704
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.44 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.52 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.16 %
    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:  0.50 (0.35), residues: 646
  helix: -1.30 (0.68), residues: 47
  sheet:  0.99 (0.31), residues: 289
  loop :  0.05 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 402 
 PHE   0.021   0.001   PHE H  98 
 TYR   0.011   0.001   TYR A 391 
 ARG   0.013   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03164 (  188)
  hydrogen bonds       : angle       5.16536 (  562)
  SS BOND              : bond        0.00320 (   13)
  SS BOND              : angle       1.97469 (   26)
  covalent geometry    : bond        0.00366 ( 5128)
  covalent geometry    : angle       0.67400 ( 6959)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5456.31 seconds
wall clock time: 97 minutes 10.44 seconds (5830.44 seconds total)