Starting phenix.real_space_refine
on Thu Jul 24 11:09:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7m3l_23656/07_2025/7m3l_23656.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7m3l_23656/07_2025/7m3l_23656.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7m3l_23656/07_2025/7m3l_23656.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7m3l_23656/07_2025/7m3l_23656.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7m3l_23656/07_2025/7m3l_23656.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7m3l_23656/07_2025/7m3l_23656.cif"
  }
  resolution = 3.2
  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
-------------------------------------------------------------------------------
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=  -0.000 sd=   0.006
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      23      5.16       5
     C    3875      2.51       5
     N    1044      2.21       5
     O    1171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6113
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A1"
      Number of atoms: 4347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 548, 4347
          Classifications: {'peptide': 548}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 506}
    Chain: "L2"
      Number of atoms: 842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 842
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103}
    Chain: "H2"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 924
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
  Time building chain proxies: 5.01, per 1000 atoms: 0.82
  Number of scatterers: 6113
  At special positions: 0
  Unit cell: (91.528, 104.988, 110.372, 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      23     16.00
     O    1171      8.00
     N    1044      7.00
     C    3875      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYSL2  23 " - pdb=" SG  CYSL2  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYSH2  22 " - pdb=" SG  CYSH2  95 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 871.5 milliseconds
  

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1428

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 15 sheets defined
      6.1% alpha, 30.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A1' and resid 116 through 120
      removed outlier: 3.617A  pdb=" N   VALA1 119 " --> pdb=" O   ALAA1 116 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 122 through 126
      removed outlier: 3.515A  pdb=" N   TRPA1 126 " --> pdb=" O   PROA1 123 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 309 through 313
      removed outlier: 3.846A  pdb=" N   ARGA1 313 " --> pdb=" O   GLNA1 310 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 409 through 413
      removed outlier: 3.581A  pdb=" N   ASPA1 413 " --> pdb=" O   PROA1 410 " (cutoff:3.500A)
    Processing helix  chain 'A1' and resid 425 through 427
      No H-bonds generated for 'chain 'A1' and resid 425 through 427'
    Processing helix  chain 'A1' and resid 443 through 447
    Processing helix  chain 'A1' and resid 554 through 558
      removed outlier: 3.935A  pdb=" N   GLNA1 558 " --> pdb=" O   VALA1 555 " (cutoff:3.500A)
    Processing helix  chain 'L2' and resid 79 through 83
      removed outlier: 3.871A  pdb=" N   LEUL2  83 " --> pdb=" O   ALAL2  80 " (cutoff:3.500A)
    Processing helix  chain 'H2' and resid 28 through 32
      removed outlier: 3.564A  pdb=" N   ASNH2  31 " --> pdb=" O   THRH2  28 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   TYRH2  32 " --> pdb=" O   PHEH2  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H2' and resid 28 through 32'
    Processing helix  chain 'H2' and resid 62 through 65
      removed outlier: 3.960A  pdb=" N   LYSH2  65 " --> pdb=" O   GLUH2  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H2' and resid 62 through 65'
    Processing sheet with id=AA1, first strand: chain 'A1' and resid 49 through 53
      removed outlier: 8.280A  pdb=" N   ASPA1 526 " --> pdb=" O   PHEA1 146 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   PHEA1 146 " --> pdb=" O   ASPA1 526 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   TRPA1 528 " --> pdb=" O   GLUA1 144 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   GLUA1 144 " --> pdb=" O   TRPA1 528 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LYSA1 530 " --> pdb=" O   GLUA1 142 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   GLUA1 142 " --> pdb=" O   LYSA1 530 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LYSA1 532 " --> pdb=" O   SERA1 140 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   SERA1 140 " --> pdb=" O   LYSA1 532 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   VALA1 534 " --> pdb=" O   LEUA1 138 " (cutoff:3.500A)
      removed outlier: 5.191A  pdb=" N   LEUA1 138 " --> pdb=" O   VALA1 534 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LYSA1 536 " --> pdb=" O   LEUA1 136 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   LEUA1 136 " --> pdb=" O   LYSA1 536 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   LYSA1 538 " --> pdb=" O   SERA1 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A1' and resid 163 through 167
      removed outlier: 8.280A  pdb=" N   ASPA1 526 " --> pdb=" O   PHEA1 146 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   PHEA1 146 " --> pdb=" O   ASPA1 526 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   TRPA1 528 " --> pdb=" O   GLUA1 144 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   GLUA1 144 " --> pdb=" O   TRPA1 528 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LYSA1 530 " --> pdb=" O   GLUA1 142 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   GLUA1 142 " --> pdb=" O   LYSA1 530 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LYSA1 532 " --> pdb=" O   SERA1 140 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   SERA1 140 " --> pdb=" O   LYSA1 532 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   VALA1 534 " --> pdb=" O   LEUA1 138 " (cutoff:3.500A)
      removed outlier: 5.191A  pdb=" N   LEUA1 138 " --> pdb=" O   VALA1 534 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LYSA1 536 " --> pdb=" O   LEUA1 136 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   LEUA1 136 " --> pdb=" O   LYSA1 536 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   LYSA1 538 " --> pdb=" O   SERA1 134 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A1' and resid 82 through 84
      removed outlier: 6.851A  pdb=" N   ILEA1 105 " --> pdb=" O   PHEA1 212 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   PHEA1 212 " --> pdb=" O   ILEA1 105 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   THRA1 107 " --> pdb=" O   TYRA1 210 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   TYRA1 210 " --> pdb=" O   THRA1 107 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   TRPA1 109 " --> pdb=" O   TRPA1 208 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A1' and resid 82 through 84
      removed outlier: 5.866A  pdb=" N   VALA1 502 " --> pdb=" O   PROA1 108 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A1' and resid 215 through 218
      removed outlier: 3.666A  pdb=" N   GLYA1 235 " --> pdb=" O   ASPA1 215 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   THRA1 217 " --> pdb=" O   TYRA1 233 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   TYRA1 233 " --> pdb=" O   THRA1 217 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A1' and resid 276 through 278
    Processing sheet with id=AA7, first strand: chain 'A1' and resid 335 through 336
      removed outlier: 6.306A  pdb=" N   GLUA1 335 " --> pdb=" O   ALAA1 456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A1' and resid 345 through 346
    Processing sheet with id=AA9, first strand: chain 'A1' and resid 377 through 380
    Processing sheet with id=AB1, first strand: chain 'A1' and resid 415 through 416
    Processing sheet with id=AB2, first strand: chain 'A1' and resid 470 through 472
      removed outlier: 6.811A  pdb=" N   ASPA1 471 " --> pdb=" O   CYSA1 490 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'L2' and resid 4 through 6
      removed outlier: 5.679A  pdb=" N   THRL2  69 " --> pdb=" O   ALAL2  25 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L2' and resid 10 through 13
      removed outlier: 6.333A  pdb=" N   LEUL2  33 " --> pdb=" O   TYRL2  49 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   TYRL2  49 " --> pdb=" O   LEUL2  33 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   TRPL2  35 " --> pdb=" O   LEUL2  47 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H2' and resid 3 through 6
      removed outlier: 3.709A  pdb=" N   THRH2  78 " --> pdb=" O   ASPH2  73 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H2' and resid 57 through 60
      removed outlier: 3.653A  pdb=" N   SERH2  57 " --> pdb=" O   PHEH2  52 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   TRPH2  36 " --> pdb=" O   ILEH2  48 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   TRPH2  50 " --> pdb=" O   METH2  34 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   METH2  34 " --> pdb=" O   TRPH2  50 " (cutoff:3.500A)

    126 hydrogen bonds defined for protein.
    288 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: 2.07

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1209
        1.32 -     1.44: 1659
        1.44 -     1.56: 3380
        1.56 -     1.68: 0
        1.68 -     1.81: 38
  Bond restraints: 6286
  Sorted by residual:
  bond pdb=" CA  ASNA1 115 "
       pdb=" CB  ASNA1 115 "
    ideal  model  delta    sigma   weight residual
    1.526  1.479  0.047 1.51e-02 4.39e+03 9.56e+00
  bond pdb=" CB  VALA1 130 "
       pdb=" CG2 VALA1 130 "
    ideal  model  delta    sigma   weight residual
    1.521  1.442  0.079 3.30e-02 9.18e+02 5.77e+00
  bond pdb=" C   LEUA1 422 "
       pdb=" N   PROA1 423 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 4.01e+00
  bond pdb=" CB  CYSH2  95 "
       pdb=" SG  CYSH2  95 "
    ideal  model  delta    sigma   weight residual
    1.808  1.752  0.056 3.30e-02 9.18e+02 2.85e+00
  bond pdb=" N   GLNA1 127 "
       pdb=" CA  GLNA1 127 "
    ideal  model  delta    sigma   weight residual
    1.457  1.479 -0.022 1.29e-02 6.01e+03 2.85e+00
  ... (remaining 6281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.24: 8470
        3.24 -     6.48: 96
        6.48 -     9.72: 11
        9.72 -    12.97: 1
       12.97 -    16.21: 1
  Bond angle restraints: 8579
  Sorted by residual:
  angle pdb=" C   TRPA1 126 "
        pdb=" N   GLNA1 127 "
        pdb=" CA  GLNA1 127 "
      ideal   model   delta    sigma   weight residual
     121.54  130.83   -9.29 1.91e+00 2.74e-01 2.36e+01
  angle pdb=" C   THRL2  31 "
        pdb=" N   ALAL2  32 "
        pdb=" CA  ALAL2  32 "
      ideal   model   delta    sigma   weight residual
     122.46  129.27   -6.81 1.41e+00 5.03e-01 2.33e+01
  angle pdb=" N   GLNA1 127 "
        pdb=" CA  GLNA1 127 "
        pdb=" C   GLNA1 127 "
      ideal   model   delta    sigma   weight residual
     110.80  119.91   -9.11 2.13e+00 2.20e-01 1.83e+01
  angle pdb=" N   ALAL2  32 "
        pdb=" CA  ALAL2  32 "
        pdb=" C   ALAL2  32 "
      ideal   model   delta    sigma   weight residual
     111.30  116.86   -5.56 1.36e+00 5.41e-01 1.67e+01
  angle pdb=" C   ASNA1 421 "
        pdb=" N   LEUA1 422 "
        pdb=" CA  LEUA1 422 "
      ideal   model   delta    sigma   weight residual
     121.03  127.08   -6.05 1.60e+00 3.91e-01 1.43e+01
  ... (remaining 8574 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 3233
       17.26 -    34.53: 361
       34.53 -    51.79: 60
       51.79 -    69.05: 11
       69.05 -    86.31: 9
  Dihedral angle restraints: 3674
    sinusoidal: 1439
      harmonic: 2235
  Sorted by residual:
  dihedral pdb=" CA  LEUA1 422 "
           pdb=" C   LEUA1 422 "
           pdb=" N   PROA1 423 "
           pdb=" CA  PROA1 423 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -126.65  -53.35     0      5.00e+00 4.00e-02 1.14e+02
  dihedral pdb=" CA  TRPA1 126 "
           pdb=" C   TRPA1 126 "
           pdb=" N   GLNA1 127 "
           pdb=" CA  GLNA1 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.14   46.86     0      5.00e+00 4.00e-02 8.78e+01
  dihedral pdb=" CA  GLNA1 159 "
           pdb=" C   GLNA1 159 "
           pdb=" N   PROA1 160 "
           pdb=" CA  PROA1 160 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.03   39.97     0      5.00e+00 4.00e-02 6.39e+01
  ... (remaining 3671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 668
       0.058 -    0.115: 206
       0.115 -    0.173: 40
       0.173 -    0.230: 7
       0.230 -    0.287: 2
  Chirality restraints: 923
  Sorted by residual:
  chirality pdb=" CB  THRA1 265 "
            pdb=" CA  THRA1 265 "
            pdb=" OG1 THRA1 265 "
            pdb=" CG2 THRA1 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.26    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CB  THRA1 158 "
            pdb=" CA  THRA1 158 "
            pdb=" OG1 THRA1 158 "
            pdb=" CG2 THRA1 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CB  ILEA1 330 "
            pdb=" CA  ILEA1 330 "
            pdb=" CG1 ILEA1 330 "
            pdb=" CG2 ILEA1 330 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 920 not shown)

  Planarity restraints: 1122
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRPH2  50 "    0.030 2.00e-02 2.50e+03   2.09e-02 1.09e+01
        pdb=" CG  TRPH2  50 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRPH2  50 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRPH2  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRPH2  50 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRPH2  50 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRPH2  50 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRPH2  50 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ3 TRPH2  50 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRPH2  50 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLNA1 159 "   -0.050 5.00e-02 4.00e+02   7.47e-02 8.94e+00
        pdb=" N   PROA1 160 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PROA1 160 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PROA1 160 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEUA1 422 "   -0.014 2.00e-02 2.50e+03   2.67e-02 7.11e+00
        pdb=" C   LEUA1 422 "    0.046 2.00e-02 2.50e+03
        pdb=" O   LEUA1 422 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PROA1 423 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1119 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 2
        2.22 -     2.89: 2424
        2.89 -     3.56: 7602
        3.56 -     4.23: 14149
        4.23 -     4.90: 24344
  Nonbonded interactions: 48521
  Sorted by model distance:
  nonbonded pdb=" O   GLYA1 227 "
            pdb=" CE1 HISH2 101 "
     model   vdw
     1.551 3.260
  nonbonded pdb=" OD1 ASNA1  93 "
            pdb=" O   GLYH2 102 "
     model   vdw
     1.859 3.040
  nonbonded pdb=" O   GLYA1 227 "
            pdb=" ND1 HISH2 101 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OD2 ASPH2  33 "
            pdb=" OH  TYRH2 104 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OG  SERL2  43 "
            pdb=" O   GLYH2 110 "
     model   vdw
     2.307 3.040
  ... (remaining 48516 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.250
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     18.430
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3856
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.079   6288  Z= 0.385
  Angle     :  0.967  16.208   8583  Z= 0.547
  Chirality :  0.058   0.287    923
  Planarity :  0.008   0.075   1122
  Dihedral  : 15.046  86.313   2240
  Min Nonbonded Distance : 1.551

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.10 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 10.98 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.28 %

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: -3.19 (0.25), residues: 769
  helix: -4.56 (0.44), residues: 18
  sheet: -1.97 (0.30), residues: 234
  loop : -2.20 (0.22), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.003   TRPH2  50 
 HIS   0.009   0.002   HISA1 403 
 PHE   0.020   0.003   PHEA1  45 
 TYR   0.030   0.003   TYRA1 342 
 ARG   0.006   0.001   ARGH2  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25357 (  121)
  hydrogen bonds       : angle      11.13522 (  288)
  SS BOND              : bond        0.00779 (    2)
  SS BOND              : angle       1.50850 (    4)
  covalent geometry    : bond        0.00903 ( 6286)
  covalent geometry    : angle       0.96622 ( 8579)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 78
  average time/residue: 0.2723
  time to fit residues: 26.4485
Evaluate side-chains
  39 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 56 optimal weight:    9.9990
   chunk 31 optimal weight:   30.0000
   chunk 19 optimal weight:   30.0000
   chunk 38 optimal weight:    0.0170
   chunk 30 optimal weight:    9.9990
   chunk 58 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    5.6026

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

Flipped N/Q/H residues before XYZ refinement:
A1  47 ASN
A1  70 HIS
A1 167 ASN
A1 181 ASN
** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1 231 ASN
A1 234 HIS
** A1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1 384 HIS
A1 403 HIS
A1 416 GLN
A1 419 ASN
A1 466 ASN
A1 468 GLN
A1 483 HIS
A1 550 GLN
L2  37 GLN
L2  53 ASN
** H2  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H2 101 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.055867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.048667 restraints weight = 59847.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 7.38
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6701
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   6288  Z= 0.190
  Angle     :  0.701  10.244   8583  Z= 0.365
  Chirality :  0.046   0.157    923
  Planarity :  0.006   0.063   1122
  Dihedral  :  6.434  65.089    839
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.11 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 15.04 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

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: -2.35 (0.27), residues: 769
  helix: -4.48 (0.74), residues: 12
  sheet: -1.43 (0.31), residues: 244
  loop : -1.60 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRPH2  50 
 HIS   0.006   0.002   HISH2 101 
 PHE   0.015   0.002   PHEA1 266 
 TYR   0.013   0.001   TYRL2  92 
 ARG   0.004   0.001   ARGA1  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04111 (  121)
  hydrogen bonds       : angle       7.20587 (  288)
  SS BOND              : bond        0.00991 (    2)
  SS BOND              : angle       1.22963 (    4)
  covalent geometry    : bond        0.00417 ( 6286)
  covalent geometry    : angle       0.70109 ( 8579)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1   47 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7219 (m-40)
REVERT: L2    4 MET cc_start: 0.6673 (mmm) cc_final: 0.4619 (tpp)
REVERT: L2   17 ASP cc_start: 0.9288 (t0) cc_final: 0.9053 (t0)
REVERT: L2   24 LYS cc_start: 0.9262 (mmtm) cc_final: 0.9057 (mmmt)
REVERT: H2   65 LYS cc_start: 0.9603 (mmmt) cc_final: 0.9356 (mmmt)
  outliers start: 15
  outliers final: 7
  residues processed: 60
  average time/residue: 0.2749
  time to fit residues: 21.1112
Evaluate side-chains
  43 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   47 ASN
Chi-restraints excluded: chain A1 residue  106 VAL
Chi-restraints excluded: chain A1 residue  132 THR
Chi-restraints excluded: chain A1 residue  324 TYR
Chi-restraints excluded: chain A1 residue  482 LEU
Chi-restraints excluded: chain L2 residue    5 THR
Chi-restraints excluded: chain H2 residue   18 VAL
Chi-restraints excluded: chain H2 residue   51 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 14 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 51 optimal weight:    0.9990
   chunk 66 optimal weight:   50.0000
   chunk 37 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 11 optimal weight:   30.0000
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A1  47 ASN
** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1 242 GLN
** A1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H2  43 GLN
H2  81 GLN
H2  83 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.057035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.049906 restraints weight = 61378.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 7.24
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6595
moved from start:          0.4866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6288  Z= 0.102
  Angle     :  0.586   8.172   8583  Z= 0.294
  Chirality :  0.043   0.140    923
  Planarity :  0.005   0.067   1122
  Dihedral  :  5.628  58.880    839
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.63 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.49 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.28), residues: 769
  helix: -4.54 (0.69), residues: 12
  sheet: -1.22 (0.32), residues: 229
  loop : -1.24 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRPH2  50 
 HIS   0.003   0.001   HISA1 222 
 PHE   0.012   0.001   PHEA1 527 
 TYR   0.007   0.001   TYRH2 104 
 ARG   0.002   0.000   ARGA1 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03046 (  121)
  hydrogen bonds       : angle       6.16880 (  288)
  SS BOND              : bond        0.00229 (    2)
  SS BOND              : angle       0.46528 (    4)
  covalent geometry    : bond        0.00235 ( 6286)
  covalent geometry    : angle       0.58580 ( 8579)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L2    4 MET cc_start: 0.6699 (mmm) cc_final: 0.4595 (tpp)
  outliers start: 16
  outliers final: 6
  residues processed: 54
  average time/residue: 0.3064
  time to fit residues: 21.6034
Evaluate side-chains
  41 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue  106 VAL
Chi-restraints excluded: chain A1 residue  132 THR
Chi-restraints excluded: chain A1 residue  324 TYR
Chi-restraints excluded: chain A1 residue  482 LEU
Chi-restraints excluded: chain A1 residue  494 CYS
Chi-restraints excluded: chain H2 residue   51 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 50 optimal weight:   20.0000
   chunk 30 optimal weight:   20.0000
   chunk 61 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 32 optimal weight:   50.0000
   chunk 38 optimal weight:    7.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1 365 GLN ** 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 = 0.3827 r_free = 0.3827 target = 0.051886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.045699 restraints weight = 71484.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 6.55
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.7718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6288  Z= 0.221
  Angle     :  0.723  13.884   8583  Z= 0.362
  Chirality :  0.045   0.193    923
  Planarity :  0.005   0.054   1122
  Dihedral  :  5.846  57.783    839
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.24 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 14.59 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.29), residues: 769
  helix: -4.15 (1.05), residues: 12
  sheet: -0.87 (0.33), residues: 224
  loop : -1.11 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRPH2  50 
 HIS   0.007   0.002   HISL2   8 
 PHE   0.024   0.002   PHEA1  53 
 TYR   0.012   0.001   TYRA1 510 
 ARG   0.011   0.001   ARGL2  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03470 (  121)
  hydrogen bonds       : angle       6.10354 (  288)
  SS BOND              : bond        0.00560 (    2)
  SS BOND              : angle       1.34477 (    4)
  covalent geometry    : bond        0.00446 ( 6286)
  covalent geometry    : angle       0.72276 ( 8579)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 33
  time to evaluate  : 1.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L2    4 MET cc_start: 0.8005 (mmm) cc_final: 0.7506 (tpp)
REVERT: L2   24 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8982 (mmmt)
REVERT: L2   47 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8766 (mp)
  outliers start: 25
  outliers final: 13
  residues processed: 56
  average time/residue: 0.2487
  time to fit residues: 18.0386
Evaluate side-chains
  43 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 29
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue   54 LEU
Chi-restraints excluded: chain A1 residue  132 THR
Chi-restraints excluded: chain A1 residue  322 THR
Chi-restraints excluded: chain A1 residue  324 TYR
Chi-restraints excluded: chain A1 residue  336 VAL
Chi-restraints excluded: chain A1 residue  539 LEU
Chi-restraints excluded: chain L2 residue    5 THR
Chi-restraints excluded: chain L2 residue   47 LEU
Chi-restraints excluded: chain H2 residue    2 VAL
Chi-restraints excluded: chain H2 residue    9 LEU
Chi-restraints excluded: chain H2 residue   15 SER
Chi-restraints excluded: chain H2 residue   18 VAL
Chi-restraints excluded: chain H2 residue   51 ILE
Chi-restraints excluded: chain H2 residue   63 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 74 optimal weight:   20.0000
   chunk 29 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A1 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1 143 GLN
** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1 446 ASN
A1 468 GLN
A1 560 ASN
H2  39 GLN
H2  81 GLN
H2  83 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.051617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.045054 restraints weight = 66575.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 6.74
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.8585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6288  Z= 0.124
  Angle     :  0.563   7.858   8583  Z= 0.285
  Chirality :  0.042   0.148    923
  Planarity :  0.004   0.058   1122
  Dihedral  :  5.291  55.921    839
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.11 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.69 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.29), residues: 769
  helix: -5.46 (0.44), residues: 6
  sheet: -0.60 (0.32), residues: 230
  loop : -0.91 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRPH2  50 
 HIS   0.004   0.001   HISL2   8 
 PHE   0.007   0.001   PHEA1 527 
 TYR   0.007   0.001   TYRA1 510 
 ARG   0.003   0.000   ARGA1 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02770 (  121)
  hydrogen bonds       : angle       5.58308 (  288)
  SS BOND              : bond        0.00327 (    2)
  SS BOND              : angle       1.06480 (    4)
  covalent geometry    : bond        0.00274 ( 6286)
  covalent geometry    : angle       0.56290 ( 8579)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: A1  143 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8588 (mm110)
REVERT: L2    4 MET cc_start: 0.8586 (mmm) cc_final: 0.7481 (tpp)
REVERT: L2   27 GLN cc_start: 0.9002 (pp30) cc_final: 0.8698 (pp30)
  outliers start: 11
  outliers final: 4
  residues processed: 43
  average time/residue: 0.2623
  time to fit residues: 14.6529
Evaluate side-chains
  31 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue  143 GLN
Chi-restraints excluded: chain A1 residue  324 TYR
Chi-restraints excluded: chain A1 residue  433 THR
Chi-restraints excluded: chain L2 residue  107 LYS
Chi-restraints excluded: chain H2 residue   51 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 29 optimal weight:    0.6980
   chunk 6 optimal weight:   30.0000
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:   20.0000
   chunk 38 optimal weight:    0.0980
   chunk 73 optimal weight:    9.9990
   chunk 71 optimal weight:    7.9990
   chunk 14 optimal weight:   30.0000
   chunk 49 optimal weight:    7.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    4.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A1 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1 222 HIS ** 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 = 0.3805 r_free = 0.3805 target = 0.050465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.044146 restraints weight = 67457.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 6.56
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.9440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6288  Z= 0.136
  Angle     :  0.591   9.171   8583  Z= 0.297
  Chirality :  0.042   0.128    923
  Planarity :  0.004   0.049   1122
  Dihedral  :  5.207  54.622    839
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.50 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.59 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.30), residues: 769
  helix: -5.46 (0.44), residues: 6
  sheet: -0.44 (0.33), residues: 226
  loop : -0.84 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRPH2  50 
 HIS   0.004   0.001   HISA1 222 
 PHE   0.010   0.001   PHEA1 261 
 TYR   0.009   0.001   TYRA1 510 
 ARG   0.007   0.000   ARGL2  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02732 (  121)
  hydrogen bonds       : angle       5.33048 (  288)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.64674 (    4)
  covalent geometry    : bond        0.00307 ( 6286)
  covalent geometry    : angle       0.59133 ( 8579)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L2    4 MET cc_start: 0.8856 (mmm) cc_final: 0.8185 (tpp)
REVERT: L2   24 LYS cc_start: 0.9602 (mmmt) cc_final: 0.9395 (mmmt)
  outliers start: 12
  outliers final: 11
  residues processed: 43
  average time/residue: 0.2463
  time to fit residues: 13.7724
Evaluate side-chains
  38 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 27
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue  132 THR
Chi-restraints excluded: chain A1 residue  322 THR
Chi-restraints excluded: chain A1 residue  324 TYR
Chi-restraints excluded: chain A1 residue  336 VAL
Chi-restraints excluded: chain A1 residue  494 CYS
Chi-restraints excluded: chain L2 residue    5 THR
Chi-restraints excluded: chain L2 residue    8 HIS
Chi-restraints excluded: chain L2 residue  107 LYS
Chi-restraints excluded: chain H2 residue    9 LEU
Chi-restraints excluded: chain H2 residue   15 SER
Chi-restraints excluded: chain H2 residue   51 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 4 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 61 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 70 optimal weight:   20.0000
   chunk 18 optimal weight:   30.0000
   chunk 52 optimal weight:    6.9990
   overall best weight:    8.5990

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

Flipped N/Q/H residues before XYZ refinement:
A1  85 ASN
A1 147 ASN
** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.047260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.040785 restraints weight = 71485.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 7.29
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          1.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082   6288  Z= 0.246
  Angle     :  0.753  13.349   8583  Z= 0.378
  Chirality :  0.044   0.173    923
  Planarity :  0.005   0.053   1122
  Dihedral  :  6.166  54.729    839
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.15 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.05 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.30), residues: 769
  helix: -5.49 (0.41), residues: 6
  sheet: -0.40 (0.36), residues: 215
  loop : -0.94 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRPH2  50 
 HIS   0.009   0.002   HISL2   8 
 PHE   0.020   0.002   PHEL2  71 
 TYR   0.023   0.002   TYRA1 510 
 ARG   0.006   0.001   ARGA1 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03442 (  121)
  hydrogen bonds       : angle       6.21066 (  288)
  SS BOND              : bond        0.00615 (    2)
  SS BOND              : angle       1.14948 (    4)
  covalent geometry    : bond        0.00526 ( 6286)
  covalent geometry    : angle       0.75259 ( 8579)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 30
  time to evaluate  : 1.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A1  319 MET cc_start: 0.6755 (mmm) cc_final: 0.6319 (mmt)
REVERT: A1  331 MET cc_start: 0.7512 (mmm) cc_final: 0.7052 (tmm)
REVERT: A1  569 MET cc_start: 0.8879 (mmm) cc_final: 0.8414 (mmm)
REVERT: L2    6 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8127 (mm-40)
REVERT: L2   42 GLN cc_start: 0.9441 (mm110) cc_final: 0.9023 (mp10)
REVERT: H2   34 MET cc_start: 0.8671 (tpp) cc_final: 0.8335 (tpp)
  outliers start: 20
  outliers final: 9
  residues processed: 48
  average time/residue: 0.4172
  time to fit residues: 28.3065
Evaluate side-chains
  39 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 29
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue  322 THR
Chi-restraints excluded: chain A1 residue  324 TYR
Chi-restraints excluded: chain A1 residue  336 VAL
Chi-restraints excluded: chain A1 residue  433 THR
Chi-restraints excluded: chain A1 residue  494 CYS
Chi-restraints excluded: chain L2 residue    6 GLN
Chi-restraints excluded: chain L2 residue    8 HIS
Chi-restraints excluded: chain H2 residue    9 LEU
Chi-restraints excluded: chain H2 residue   15 SER
Chi-restraints excluded: chain H2 residue   63 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   chunk 3 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 56 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A1 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H2   5 GLN
** H2  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H2  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.047400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.041050 restraints weight = 71050.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 6.99
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          1.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6288  Z= 0.143
  Angle     :  0.653  11.142   8583  Z= 0.324
  Chirality :  0.043   0.150    923
  Planarity :  0.004   0.050   1122
  Dihedral  :  5.516  56.698    839
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.63 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 19.10 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.30), residues: 769
  helix: -5.47 (0.43), residues: 6
  sheet: -0.35 (0.35), residues: 222
  loop : -0.83 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRPH2  50 
 HIS   0.003   0.001   HISA1 222 
 PHE   0.008   0.001   PHEA1 535 
 TYR   0.010   0.001   TYRA1 510 
 ARG   0.005   0.000   ARGH2  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02817 (  121)
  hydrogen bonds       : angle       5.51112 (  288)
  SS BOND              : bond        0.00807 (    2)
  SS BOND              : angle       1.19544 (    4)
  covalent geometry    : bond        0.00324 ( 6286)
  covalent geometry    : angle       0.65243 ( 8579)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 31
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: A1  319 MET cc_start: 0.6571 (mmm) cc_final: 0.6136 (mmt)
REVERT: A1  330 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8348 (tt)
REVERT: L2    4 MET cc_start: 0.9118 (tpt) cc_final: 0.8843 (tpp)
REVERT: L2    6 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8276 (mm-40)
REVERT: H2   34 MET cc_start: 0.8800 (tpp) cc_final: 0.8508 (tpp)
  outliers start: 12
  outliers final: 7
  residues processed: 42
  average time/residue: 0.2374
  time to fit residues: 13.8080
Evaluate side-chains
  38 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue  322 THR
Chi-restraints excluded: chain A1 residue  324 TYR
Chi-restraints excluded: chain A1 residue  330 ILE
Chi-restraints excluded: chain A1 residue  336 VAL
Chi-restraints excluded: chain A1 residue  433 THR
Chi-restraints excluded: chain A1 residue  494 CYS
Chi-restraints excluded: chain L2 residue    6 GLN
Chi-restraints excluded: chain H2 residue    9 LEU
Chi-restraints excluded: chain H2 residue   15 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 43 optimal weight:    9.9990
   chunk 69 optimal weight:   20.0000
   chunk 61 optimal weight:   50.0000
   chunk 72 optimal weight:   50.0000
   chunk 25 optimal weight:    7.9990
   chunk 41 optimal weight:   30.0000
   chunk 49 optimal weight:    7.9990
   chunk 4 optimal weight:   20.0000
   chunk 59 optimal weight:   50.0000
   chunk 37 optimal weight:   10.0000
   overall best weight:    7.3390

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

Flipped N/Q/H residues before XYZ refinement:
** A1 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2  43 GLN ** 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 = 0.3637 r_free = 0.3637 target = 0.046646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.040107 restraints weight = 69935.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 6.83
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          1.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6288  Z= 0.199
  Angle     :  0.708  13.498   8583  Z= 0.346
  Chirality :  0.044   0.161    923
  Planarity :  0.004   0.050   1122
  Dihedral  :  5.561  54.493    839
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.76 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 20.15 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.30), residues: 769
  helix: -5.47 (0.43), residues: 6
  sheet: -0.41 (0.35), residues: 222
  loop : -0.83 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRPH2  50 
 HIS   0.005   0.001   HISA1 222 
 PHE   0.008   0.001   PHEA1 535 
 TYR   0.018   0.001   TYRA1 510 
 ARG   0.018   0.001   ARGH2  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03051 (  121)
  hydrogen bonds       : angle       5.53336 (  288)
  SS BOND              : bond        0.00444 (    2)
  SS BOND              : angle       0.56176 (    4)
  covalent geometry    : bond        0.00440 ( 6286)
  covalent geometry    : angle       0.70758 ( 8579)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.656 
Fit side-chains
REVERT: A1  518 MET cc_start: 0.7737 (tpp) cc_final: 0.7350 (tpp)
REVERT: L2    4 MET cc_start: 0.8870 (tpt) cc_final: 0.8621 (tpp)
REVERT: L2   42 GLN cc_start: 0.9568 (mm110) cc_final: 0.9095 (mp10)
REVERT: H2   34 MET cc_start: 0.8807 (tpp) cc_final: 0.8498 (tpp)
  outliers start: 7
  outliers final: 7
  residues processed: 36
  average time/residue: 0.2023
  time to fit residues: 10.2357
Evaluate side-chains
  35 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue  322 THR
Chi-restraints excluded: chain A1 residue  324 TYR
Chi-restraints excluded: chain A1 residue  336 VAL
Chi-restraints excluded: chain A1 residue  494 CYS
Chi-restraints excluded: chain L2 residue    8 HIS
Chi-restraints excluded: chain H2 residue    9 LEU
Chi-restraints excluded: chain H2 residue   15 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 70 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   chunk 32 optimal weight:   30.0000
   chunk 47 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 26 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A1 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2  43 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.047115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.040703 restraints weight = 73428.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 7.12
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          1.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6288  Z= 0.143
  Angle     :  0.679  16.801   8583  Z= 0.334
  Chirality :  0.043   0.153    923
  Planarity :  0.004   0.052   1122
  Dihedral  :  5.404  54.296    839
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.76 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 20.15 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

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: -0.93 (0.30), residues: 769
  helix: -5.45 (0.45), residues: 6
  sheet: -0.25 (0.34), residues: 223
  loop : -0.73 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRPH2  50 
 HIS   0.004   0.001   HISA1 222 
 PHE   0.007   0.001   PHEL2  71 
 TYR   0.010   0.001   TYRA1 510 
 ARG   0.005   0.000   ARGH2  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02743 (  121)
  hydrogen bonds       : angle       5.37843 (  288)
  SS BOND              : bond        0.00241 (    2)
  SS BOND              : angle       0.95869 (    4)
  covalent geometry    : bond        0.00328 ( 6286)
  covalent geometry    : angle       0.67883 ( 8579)

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

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

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1538 Ramachandran restraints generated.
    769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.694 
Fit side-chains
REVERT: L2    4 MET cc_start: 0.8790 (tpt) cc_final: 0.8558 (tpp)
REVERT: L2    6 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8373 (mm110)
REVERT: L2   42 GLN cc_start: 0.9610 (mm110) cc_final: 0.9202 (mp10)
REVERT: H2   34 MET cc_start: 0.8796 (tpp) cc_final: 0.8442 (tpp)
  outliers start: 7
  outliers final: 5
  residues processed: 36
  average time/residue: 0.1969
  time to fit residues: 9.8803
Evaluate side-chains
  36 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A1 residue  322 THR
Chi-restraints excluded: chain A1 residue  336 VAL
Chi-restraints excluded: chain A1 residue  494 CYS
Chi-restraints excluded: chain L2 residue    6 GLN
Chi-restraints excluded: chain L2 residue    8 HIS
Chi-restraints excluded: chain H2 residue    9 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 1 optimal weight:   20.0000
   chunk 50 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 27 optimal weight:   20.0000
   chunk 4 optimal weight:    5.9990
   chunk 65 optimal weight:   50.0000
   chunk 30 optimal weight:    9.9990
   chunk 19 optimal weight:   30.0000
   chunk 44 optimal weight:   20.0000
   overall best weight:    8.5990

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

Flipped N/Q/H residues before XYZ refinement:
A1 181 ASN
** A1 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.046317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.039839 restraints weight = 73953.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 7.52
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          1.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6288  Z= 0.227
  Angle     :  0.768  16.320   8583  Z= 0.374
  Chirality :  0.044   0.159    923
  Planarity :  0.004   0.048   1122
  Dihedral  :  5.749  53.142    839
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.19 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 20.00 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.30), residues: 769
  helix: -5.46 (0.43), residues: 6
  sheet: -0.36 (0.35), residues: 218
  loop : -0.83 (0.27), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRPH2  50 
 HIS   0.006   0.001   HISA1 222 
 PHE   0.015   0.001   PHEA1 535 
 TYR   0.025   0.001   TYRA1 510 
 ARG   0.010   0.001   ARGA1 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03179 (  121)
  hydrogen bonds       : angle       5.78923 (  288)
  SS BOND              : bond        0.00502 (    2)
  SS BOND              : angle       0.47371 (    4)
  covalent geometry    : bond        0.00489 ( 6286)
  covalent geometry    : angle       0.76798 ( 8579)

===============================================================================
Job complete
usr+sys time: 3562.88 seconds
wall clock time: 64 minutes 18.37 seconds (3858.37 seconds total)