Starting phenix.real_space_refine
on Wed Feb 12 02:55:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v4u_21048/02_2025/6v4u_21048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v4u_21048/02_2025/6v4u_21048.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v4u_21048/02_2025/6v4u_21048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v4u_21048/02_2025/6v4u_21048.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v4u_21048/02_2025/6v4u_21048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v4u_21048/02_2025/6v4u_21048.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.039
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    4443      2.51       5
     N    1262      2.21       5
     O    1346      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7074
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 2475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2475
          Classifications: {'peptide': 329}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 4, 'TRANS': 324}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 139
          Unresolved non-hydrogen angles: 171
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 100
    Chain: "A"
      Number of atoms: 2075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 356, 2075
          Classifications: {'peptide': 356}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 221}
          Link IDs: {'PTRANS': 14, 'TRANS': 341}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 785
          Unresolved non-hydrogen angles: 1003
          Unresolved non-hydrogen dihedrals: 630
          Unresolved non-hydrogen chiralities: 93
          Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 20, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 12, 'GLU:plan': 16, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 401
    Chain: "B"
      Number of atoms: 2524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 2524
          Classifications: {'peptide': 421}
          Incomplete info: {'backbone_only': 13, 'truncation_to_alanine': 231}
          Link IDs: {'PTRANS': 12, 'TRANS': 408}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 944
          Unresolved non-hydrogen angles: 1200
          Unresolved non-hydrogen dihedrals: 776
          Unresolved non-hydrogen chiralities: 90
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 19, 'PHE:plan': 14, 'GLU:plan': 24, 'ARG:plan': 21}
          Unresolved non-hydrogen planarities: 541
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ARG C 347 " occ=0.81
      ... (9 atoms not shown)
      pdb=" NH2 ARG C 347 " occ=0.71
  Time building chain proxies: 4.37, per 1000 atoms: 0.62
  Number of scatterers: 7074
  At special positions: 0
  Unit cell: (74.698, 122.964, 155.142, 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    1346      8.00
     N    1262      7.00
     C    4443      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.80
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2070

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      40.5% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'C' and resid 444 through 451
    Processing helix  chain 'A' and resid 55 through 69
      removed outlier: 4.008A  pdb=" N   ILE A  59 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLY A  69 " --> pdb=" O   HIS A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 119
      No H-bonds generated for 'chain 'A' and resid 117 through 119'
    Processing helix  chain 'A' and resid 120 through 125
      removed outlier: 3.511A  pdb=" N   LEU A 125 " --> pdb=" O   LEU A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 141
      removed outlier: 3.631A  pdb=" N   ASP A 133 " --> pdb=" O   ARG A 129 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LYS A 141 " --> pdb=" O   HIS A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 171
      removed outlier: 3.632A  pdb=" N   THR A 162 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLU A 163 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER A 171 " --> pdb=" O   ASP A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 209
      removed outlier: 4.180A  pdb=" N   ILE A 201 " --> pdb=" O   GLU A 197 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASP A 203 " --> pdb=" O   ILE A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 224
    Processing helix  chain 'A' and resid 241 through 249
    Processing helix  chain 'A' and resid 292 through 300
      removed outlier: 3.779A  pdb=" N   TYR A 300 " --> pdb=" O   ARG A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 388
      removed outlier: 3.953A  pdb=" N   LEU A 381 " --> pdb=" O   VAL A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 421
      removed outlier: 3.702A  pdb=" N   LEU A 398 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ASP A 419 " --> pdb=" O   TYR A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 439
      removed outlier: 3.862A  pdb=" N   LYS A 428 " --> pdb=" O   LYS A 424 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   SER A 429 " --> pdb=" O   LYS A 425 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ASP A 436 " --> pdb=" O   ASN A 432 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   LEU A 437 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ASP A 438 " --> pdb=" O   LYS A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 459
      removed outlier: 4.472A  pdb=" N   MET A 449 " --> pdb=" O   LEU A 445 " (cutoff:3.500A)
      Proline residue:  A 457  - end of helix
    Processing helix  chain 'A' and resid 465 through 474
    Processing helix  chain 'B' and resid 83 through 98
      removed outlier: 5.647A  pdb=" N   TYR B  89 " --> pdb=" O   PHE B  85 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   PHE B  90 " --> pdb=" O   ASP B  86 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ASP B  98 " --> pdb=" O   ILE B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 217
      removed outlier: 3.738A  pdb=" N   ALA B 174 " --> pdb=" O   GLN B 170 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   GLU B 175 " --> pdb=" O   GLU B 171 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ARG B 178 " --> pdb=" O   ALA B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 253
    Processing helix  chain 'B' and resid 321 through 340
      removed outlier: 3.543A  pdb=" N   THR B 334 " --> pdb=" O   TYR B 330 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU B 335 " --> pdb=" O   PHE B 331 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ALA B 336 " --> pdb=" O   THR B 332 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN B 337 " --> pdb=" O   GLN B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 359
    Processing helix  chain 'B' and resid 366 through 382
    Processing helix  chain 'B' and resid 707 through 716
    Processing helix  chain 'B' and resid 719 through 730
      removed outlier: 3.955A  pdb=" N   ALA B 723 " --> pdb=" O   PHE B 719 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLY B 730 " --> pdb=" O   SER B 726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 740 through 746
      removed outlier: 3.592A  pdb=" N   LEU B 746 " --> pdb=" O   ILE B 742 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 747 through 752
      removed outlier: 3.507A  pdb=" N   LEU B 750 " --> pdb=" O   VAL B 747 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ALA B 751 " --> pdb=" O   THR B 748 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ILE B 752 " --> pdb=" O   ALA B 749 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 747 through 752'
    Processing helix  chain 'B' and resid 771 through 779
      removed outlier: 3.936A  pdb=" N   MET B 775 " --> pdb=" O   PRO B 771 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   PHE B 777 " --> pdb=" O   HIS B 773 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 825 through 832
    Processing helix  chain 'B' and resid 842 through 868
    Processing helix  chain 'B' and resid 880 through 892
    Processing helix  chain 'B' and resid 900 through 914
    Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 39
      removed outlier: 3.638A  pdb=" N   LEU C  37 " --> pdb=" O   LEU C 430 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU C  39 " --> pdb=" O   ILE C 428 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE C 428 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ILE C 429 " --> pdb=" O   THR C 421 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 50
      removed outlier: 6.835A  pdb=" N   ALA C  60 " --> pdb=" O   ARG C  47 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LEU C  49 " --> pdb=" O   ALA C  58 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   ALA C  58 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67
    Processing sheet with id=AA4, first strand: chain 'C' and resid 105 through 109
      removed outlier: 4.084A  pdb=" N   VAL C 117 " --> pdb=" O   GLN C 127 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   GLN C 127 " --> pdb=" O   VAL C 117 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 140 through 141
    Processing sheet with id=AA6, first strand: chain 'C' and resid 180 through 181
    Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 332
    Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 43
      removed outlier: 3.631A  pdb=" N   ARG A  40 " --> pdb=" O   PHE A  30 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA A  27 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   THR A 109 " --> pdb=" O   TRP A  33 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 85 through 87
    Processing sheet with id=AB1, first strand: chain 'B' and resid 784 through 786
      removed outlier: 8.209A  pdb=" N   LEU B 785 " --> pdb=" O   LEU B 733 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   VAL B 735 " --> pdb=" O   LEU B 785 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   THR B 732 " --> pdb=" O   SER B 808 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LEU B 810 " --> pdb=" O   THR B 732 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   VAL B 734 " --> pdb=" O   LEU B 810 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    322 hydrogen bonds defined for protein.
    945 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.78

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2456
        1.34 -     1.46: 1512
        1.46 -     1.58: 3169
        1.58 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 7167
  Sorted by residual:
  bond pdb=" N   GLU A 442 "
       pdb=" CA  GLU A 442 "
    ideal  model  delta    sigma   weight residual
    1.456  1.469 -0.013 1.25e-02 6.40e+03 1.12e+00
  bond pdb=" CA  ASP C 163 "
       pdb=" CB  ASP C 163 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 7.14e-01
  bond pdb=" C   LYS B 762 "
       pdb=" N   PRO B 763 "
    ideal  model  delta    sigma   weight residual
    1.334  1.351 -0.017 2.34e-02 1.83e+03 5.56e-01
  bond pdb=" CA  THR C 123 "
       pdb=" CB  THR C 123 "
    ideal  model  delta    sigma   weight residual
    1.530  1.543 -0.013 1.69e-02 3.50e+03 5.55e-01
  bond pdb=" CA  SER A  23 "
       pdb=" C   SER A  23 "
    ideal  model  delta    sigma   weight residual
    1.525  1.540 -0.015 2.10e-02 2.27e+03 5.11e-01
  ... (remaining 7162 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 9696
        1.64 -     3.28: 89
        3.28 -     4.93: 23
        4.93 -     6.57: 7
        6.57 -     8.21: 2
  Bond angle restraints: 9817
  Sorted by residual:
  angle pdb=" N   ILE A 224 "
        pdb=" CA  ILE A 224 "
        pdb=" C   ILE A 224 "
      ideal   model   delta    sigma   weight residual
     111.91  109.33    2.58 8.90e-01 1.26e+00 8.43e+00
  angle pdb=" C   GLU A 442 "
        pdb=" CA  GLU A 442 "
        pdb=" CB  GLU A 442 "
      ideal   model   delta    sigma   weight residual
     109.62  114.66   -5.04 1.79e+00 3.12e-01 7.92e+00
  angle pdb=" C   LEU C 162 "
        pdb=" N   ASP C 163 "
        pdb=" CA  ASP C 163 "
      ideal   model   delta    sigma   weight residual
     121.54  126.91   -5.37 1.91e+00 2.74e-01 7.90e+00
  angle pdb=" C   THR C 122 "
        pdb=" N   THR C 123 "
        pdb=" CA  THR C 123 "
      ideal   model   delta    sigma   weight residual
     121.54  126.21   -4.67 1.91e+00 2.74e-01 5.97e+00
  angle pdb=" C   MET C 255 "
        pdb=" N   GLN C 256 "
        pdb=" CA  GLN C 256 "
      ideal   model   delta    sigma   weight residual
     121.54  125.61   -4.07 1.91e+00 2.74e-01 4.54e+00
  ... (remaining 9812 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.74: 3825
       11.74 -    23.48: 238
       23.48 -    35.22: 79
       35.22 -    46.96: 22
       46.96 -    58.70: 2
  Dihedral angle restraints: 4166
    sinusoidal: 999
      harmonic: 3167
  Sorted by residual:
  dihedral pdb=" CA  GLN B 365 "
           pdb=" C   GLN B 365 "
           pdb=" N   HIS B 366 "
           pdb=" CA  HIS B 366 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.33  -18.67     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  PHE B  85 "
           pdb=" C   PHE B  85 "
           pdb=" N   ASP B  86 "
           pdb=" CA  ASP B  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.38   17.62     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  LEU B 711 "
           pdb=" CB  LEU B 711 "
           pdb=" CG  LEU B 711 "
           pdb=" CD1 LEU B 711 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.03   44.97     3      1.50e+01 4.44e-03 8.09e+00
  ... (remaining 4163 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 712
       0.028 -    0.056: 330
       0.056 -    0.084: 95
       0.084 -    0.112: 79
       0.112 -    0.140: 10
  Chirality restraints: 1226
  Sorted by residual:
  chirality pdb=" CA  ASP C 163 "
            pdb=" N   ASP C 163 "
            pdb=" C   ASP C 163 "
            pdb=" CB  ASP C 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  VAL C 231 "
            pdb=" N   VAL C 231 "
            pdb=" C   VAL C 231 "
            pdb=" CB  VAL C 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE C 402 "
            pdb=" N   ILE C 402 "
            pdb=" C   ILE C 402 "
            pdb=" CB  ILE C 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 1223 not shown)

  Planarity restraints: 1294
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 466 "    0.019 5.00e-02 4.00e+02   2.92e-02 1.36e+00
        pdb=" N   PRO A 467 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 467 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 467 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 332 "    0.018 5.00e-02 4.00e+02   2.76e-02 1.22e+00
        pdb=" N   PRO C 333 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO C 333 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 333 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 182 "   -0.016 5.00e-02 4.00e+02   2.44e-02 9.54e-01
        pdb=" N   PRO C 183 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO C 183 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C 183 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1291 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1966
        2.80 -     3.32: 6433
        3.32 -     3.85: 11052
        3.85 -     4.37: 11027
        4.37 -     4.90: 19623
  Nonbonded interactions: 50101
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 750 "
            pdb=" OH  TYR B 760 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD1 ASP C 233 "
            pdb=" OG  SER C 235 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" OD1 ASN C 232 "
            pdb=" OG1 THR C 290 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" N   GLU C 409 "
            pdb=" O   CYS C 422 "
     model   vdw
     2.345 3.120
  nonbonded pdb=" O   ALA B 706 "
            pdb=" OG1 THR B 748 "
     model   vdw
     2.356 3.040
  ... (remaining 50096 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.370
  Find NCS groups from input model:        0.090
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6157
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      :  0.002   0.021   7167  Z= 0.106
  Angle     :  0.471   8.209   9817  Z= 0.237
  Chirality :  0.041   0.140   1226
  Planarity :  0.003   0.029   1294
  Dihedral  :  9.643  58.703   2096
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.58 (0.23), residues: 1050
  helix:  0.19 (0.23), residues: 411
  sheet: -4.40 (0.39), residues: 76
  loop : -4.35 (0.19), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP C 148 
 HIS   0.002   0.000   HIS C 404 
 PHE   0.008   0.001   PHE B 372 
 TYR   0.004   0.000   TYR B  99 
 ARG   0.001   0.000   ARG C 160 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.6796 (tppt) cc_final: 0.6446 (tppt)
REVERT: C  211 ASP cc_start: 0.4780 (m-30) cc_final: 0.3466 (m-30)
REVERT: A  385 PHE cc_start: 0.4738 (m-10) cc_final: 0.4289 (m-80)
REVERT: A  417 GLU cc_start: 0.5917 (mm-30) cc_final: 0.5697 (mm-30)
REVERT: A  479 MET cc_start: 0.8090 (mmt) cc_final: 0.7830 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1841
  time to fit residues: 36.9647
Evaluate side-chains
  94 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.0060
   chunk 82 optimal weight:   20.0000
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0050
   chunk 51 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   chunk 98 optimal weight:    9.9990
   overall best weight:    1.4014

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

Flipped N/Q/H residues before XYZ refinement:
C 125 GLN
** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 328 HIS
B 337 GLN
B 356 GLN
B 708 GLN
B 721 HIS
B 848 GLN
B 903 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.133211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.115840 restraints weight = 23233.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.118777 restraints weight = 13714.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.120831 restraints weight = 9212.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4117 r_free = 0.4117    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4113 r_free = 0.4113    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6538
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7167  Z= 0.242
  Angle     :  0.619   8.510   9817  Z= 0.317
  Chirality :  0.044   0.207   1226
  Planarity :  0.004   0.079   1294
  Dihedral  :  3.673  16.954   1110
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.72 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.25), residues: 1050
  helix:  1.36 (0.25), residues: 411
  sheet: -3.78 (0.38), residues: 112
  loop : -4.11 (0.22), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 431 
 HIS   0.010   0.001   HIS C 417 
 PHE   0.025   0.002   PHE B 345 
 TYR   0.022   0.002   TYR A 124 
 ARG   0.007   0.001   ARG C 199 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.7426 (tppt) cc_final: 0.7221 (tppt)
REVERT: A  385 PHE cc_start: 0.5363 (m-10) cc_final: 0.5147 (m-80)
REVERT: A  417 GLU cc_start: 0.6481 (mm-30) cc_final: 0.6126 (mm-30)
REVERT: A  479 MET cc_start: 0.8316 (mmt) cc_final: 0.8035 (mpp)
  outliers start: 16
  outliers final: 10
  residues processed: 116
  average time/residue: 0.1811
  time to fit residues: 28.6349
Evaluate side-chains
  97 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  429 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  380 ASP
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  901 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0570
   chunk 26 optimal weight:    0.0000
   chunk 73 optimal weight:    2.9990
   chunk 55 optimal weight:    0.4980
   chunk 14 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.4102

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

Flipped N/Q/H residues before XYZ refinement:
C 125 GLN
** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  65 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.135803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.117831 restraints weight = 23124.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.120798 restraints weight = 13667.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.122914 restraints weight = 9235.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4143 r_free = 0.4143    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4143 r_free = 0.4143    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6476
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7167  Z= 0.143
  Angle     :  0.524   8.797   9817  Z= 0.262
  Chirality :  0.042   0.145   1226
  Planarity :  0.004   0.065   1294
  Dihedral  :  3.177  16.755   1110
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 22.40 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.26), residues: 1050
  helix:  1.96 (0.26), residues: 413
  sheet: -3.81 (0.39), residues: 113
  loop : -3.83 (0.23), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 148 
 HIS   0.005   0.001   HIS C  83 
 PHE   0.022   0.001   PHE C 132 
 TYR   0.022   0.001   TYR C 413 
 ARG   0.006   0.001   ARG C 199 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 HIS cc_start: 0.8651 (p90) cc_final: 0.8438 (p-80)
REVERT: C  119 ASP cc_start: 0.7819 (t0) cc_final: 0.7524 (t0)
REVERT: A   32 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7527 (t80)
REVERT: A  124 TYR cc_start: 0.8198 (t80) cc_final: 0.7949 (t80)
REVERT: A  385 PHE cc_start: 0.5391 (m-10) cc_final: 0.5140 (m-80)
REVERT: A  417 GLU cc_start: 0.6369 (mm-30) cc_final: 0.6022 (mm-30)
REVERT: A  479 MET cc_start: 0.8214 (mmt) cc_final: 0.7965 (mpp)
REVERT: B  911 LEU cc_start: 0.9125 (mt) cc_final: 0.8840 (mt)
  outliers start: 14
  outliers final: 6
  residues processed: 105
  average time/residue: 0.1666
  time to fit residues: 24.5538
Evaluate side-chains
  94 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  155 LEU
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  411 PHE
Chi-restraints excluded: chain C residue  429 ILE
Chi-restraints excluded: chain A residue   32 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0040
   chunk 4 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 55 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 105 optimal weight:    0.0470
   chunk 26 optimal weight:    0.9980
   chunk 101 optimal weight:    0.6980
   overall best weight:    1.1492

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

Flipped N/Q/H residues before XYZ refinement:
** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 848 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.129687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.112588 restraints weight = 23905.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.115368 restraints weight = 14373.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.117356 restraints weight = 9816.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4056 r_free = 0.4056    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4056 r_free = 0.4056    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.4056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6631
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7167  Z= 0.195
  Angle     :  0.563   8.556   9817  Z= 0.289
  Chirality :  0.044   0.172   1226
  Planarity :  0.004   0.069   1294
  Dihedral  :  3.622  16.453   1110
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 21.59 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.27), residues: 1050
  helix:  1.99 (0.26), residues: 417
  sheet: -3.83 (0.39), residues: 113
  loop : -3.76 (0.24), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 431 
 HIS   0.006   0.001   HIS C 426 
 PHE   0.013   0.002   PHE A  84 
 TYR   0.028   0.002   TYR C  55 
 ARG   0.003   0.001   ARG C 199 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
REVERT: C  211 ASP cc_start: 0.4595 (m-30) cc_final: 0.4356 (m-30)
REVERT: C  322 HIS cc_start: 0.5032 (OUTLIER) cc_final: 0.3922 (m90)
REVERT: A   32 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7607 (t80)
REVERT: A  417 GLU cc_start: 0.6126 (mm-30) cc_final: 0.5783 (mm-30)
REVERT: A  479 MET cc_start: 0.8288 (mmt) cc_final: 0.7975 (mpp)
  outliers start: 26
  outliers final: 13
  residues processed: 114
  average time/residue: 0.1661
  time to fit residues: 26.6322
Evaluate side-chains
  101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  155 LEU
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  322 HIS
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  411 PHE
Chi-restraints excluded: chain C residue  429 ILE
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  901 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 80 optimal weight:   40.0000
   chunk 67 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 54 optimal weight:   20.0000
   chunk 53 optimal weight:    5.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 343 HIS
B 884 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.116258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.100171 restraints weight = 24989.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.102671 restraints weight = 15351.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.104372 restraints weight = 10609.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3865 r_free = 0.3865    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3865 r_free = 0.3865    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.6036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   7167  Z= 0.459
  Angle     :  0.872  12.862   9817  Z= 0.458
  Chirality :  0.051   0.219   1226
  Planarity :  0.006   0.078   1294
  Dihedral  :  6.068  33.303   1110
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.71 %
    Favored  : 84.29 %
  Rotamer:
    Outliers :  7.74 %
    Allowed  : 22.20 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -2.88 (0.25), residues: 1050
  helix:  0.69 (0.26), residues: 424
  sheet: -3.82 (0.39), residues: 123
  loop : -3.92 (0.23), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP C 431 
 HIS   0.012   0.002   HIS C  83 
 PHE   0.022   0.003   PHE A 397 
 TYR   0.019   0.003   TYR C 413 
 ARG   0.005   0.001   ARG C 160 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 85
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5603 (tt)
REVERT: C  148 TRP cc_start: 0.7668 (p-90) cc_final: 0.6924 (p-90)
REVERT: C  255 MET cc_start: 0.5637 (tpt) cc_final: 0.5278 (tpt)
REVERT: C  322 HIS cc_start: 0.5235 (OUTLIER) cc_final: 0.3726 (m90)
REVERT: A   61 PHE cc_start: 0.9162 (t80) cc_final: 0.8784 (t80)
REVERT: A   97 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8634 (mp)
REVERT: A  417 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6535 (mm-30)
REVERT: A  479 MET cc_start: 0.8238 (mmt) cc_final: 0.7479 (mpp)
REVERT: B  911 LEU cc_start: 0.9407 (mt) cc_final: 0.9178 (mt)
REVERT: B  927 PHE cc_start: 0.4897 (m-80) cc_final: 0.4435 (m-80)
  outliers start: 38
  outliers final: 23
  residues processed: 117
  average time/residue: 0.1724
  time to fit residues: 28.2986
Evaluate side-chains
  104 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   56 ARG
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  155 LEU
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain C residue  322 HIS
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  411 PHE
Chi-restraints excluded: chain C residue  429 ILE
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  735 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 105 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 47 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 98 optimal weight:    0.1980
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 848 GLN
B 884 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.121440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.105160 restraints weight = 24660.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.107861 restraints weight = 14974.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.109406 restraints weight = 10204.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3948 r_free = 0.3948    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3948 r_free = 0.3948    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.5795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7167  Z= 0.222
  Angle     :  0.675  10.553   9817  Z= 0.340
  Chirality :  0.045   0.165   1226
  Planarity :  0.004   0.074   1294
  Dihedral  :  4.665  19.225   1110
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 26.27 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.26), residues: 1050
  helix:  1.43 (0.27), residues: 418
  sheet: -3.98 (0.38), residues: 121
  loop : -3.78 (0.23), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 118 
 HIS   0.005   0.001   HIS B 846 
 PHE   0.023   0.002   PHE B 863 
 TYR   0.019   0.002   TYR B 904 
 ARG   0.007   0.001   ARG C 160 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.7442 (tppt) cc_final: 0.7167 (mmtm)
REVERT: C  146 ASP cc_start: 0.7575 (p0) cc_final: 0.6711 (t0)
REVERT: C  148 TRP cc_start: 0.7673 (p-90) cc_final: 0.6907 (p-90)
REVERT: C  322 HIS cc_start: 0.5320 (OUTLIER) cc_final: 0.3760 (m90)
REVERT: A   61 PHE cc_start: 0.9125 (t80) cc_final: 0.8795 (t80)
REVERT: A   62 LEU cc_start: 0.9786 (mm) cc_final: 0.9579 (mp)
REVERT: A  385 PHE cc_start: 0.6974 (m-10) cc_final: 0.6644 (m-10)
REVERT: A  417 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6234 (mm-30)
REVERT: A  479 MET cc_start: 0.8281 (mmt) cc_final: 0.7839 (mpp)
REVERT: B  850 MET cc_start: 0.7748 (mpp) cc_final: 0.7110 (mpp)
REVERT: B  927 PHE cc_start: 0.4897 (m-80) cc_final: 0.4453 (m-80)
  outliers start: 26
  outliers final: 18
  residues processed: 106
  average time/residue: 0.1593
  time to fit residues: 23.8300
Evaluate side-chains
  100 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 HIS
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  155 LEU
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain C residue  322 HIS
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  411 PHE
Chi-restraints excluded: chain C residue  429 ILE
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  860 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 90 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 93 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.121308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.105146 restraints weight = 24618.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.107739 restraints weight = 15071.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.109669 restraints weight = 10399.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
moved from start:          0.5875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7167  Z= 0.216
  Angle     :  0.656  10.689   9817  Z= 0.330
  Chirality :  0.045   0.167   1226
  Planarity :  0.004   0.078   1294
  Dihedral  :  4.474  21.244   1110
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.95 %
    Favored  : 87.05 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 26.07 %
    Favored  : 68.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.27), residues: 1050
  helix:  1.57 (0.27), residues: 422
  sheet: -3.70 (0.40), residues: 118
  loop : -3.76 (0.23), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 118 
 HIS   0.005   0.001   HIS B 866 
 PHE   0.023   0.002   PHE A 397 
 TYR   0.018   0.002   TYR B 904 
 ARG   0.005   0.001   ARG C 160 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: C  148 TRP cc_start: 0.7794 (p-90) cc_final: 0.6936 (p-90)
REVERT: C  149 LEU cc_start: 0.8510 (mt) cc_final: 0.8272 (mt)
REVERT: C  322 HIS cc_start: 0.5337 (OUTLIER) cc_final: 0.3559 (m90)
REVERT: A   61 PHE cc_start: 0.9123 (t80) cc_final: 0.8747 (t80)
REVERT: A  417 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6223 (mm-30)
REVERT: A  479 MET cc_start: 0.8253 (mmt) cc_final: 0.7695 (mpp)
REVERT: B  850 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7274 (mpp)
REVERT: B  927 PHE cc_start: 0.4934 (m-80) cc_final: 0.4483 (m-80)
  outliers start: 25
  outliers final: 22
  residues processed: 100
  average time/residue: 0.1670
  time to fit residues: 23.4538
Evaluate side-chains
  105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 HIS
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  155 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain C residue  322 HIS
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  411 PHE
Chi-restraints excluded: chain C residue  429 ILE
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 MET
Chi-restraints excluded: chain B residue  860 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 108 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 78 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 848 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.121990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.105648 restraints weight = 24307.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.108323 restraints weight = 14651.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.110253 restraints weight = 10010.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3959 r_free = 0.3959    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3959 r_free = 0.3959    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
moved from start:          0.5900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7167  Z= 0.195
  Angle     :  0.647  10.542   9817  Z= 0.322
  Chirality :  0.044   0.164   1226
  Planarity :  0.004   0.079   1294
  Dihedral  :  4.291  19.245   1110
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.86 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 25.87 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.27), residues: 1050
  helix:  1.70 (0.27), residues: 423
  sheet: -3.65 (0.40), residues: 121
  loop : -3.68 (0.24), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 118 
 HIS   0.007   0.001   HIS B 866 
 PHE   0.017   0.002   PHE A 385 
 TYR   0.027   0.002   TYR B 904 
 ARG   0.006   0.001   ARG C 335 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  119 ASP cc_start: 0.8008 (t0) cc_final: 0.7735 (t0)
REVERT: C  148 TRP cc_start: 0.7862 (p-90) cc_final: 0.7061 (p-90)
REVERT: C  149 LEU cc_start: 0.8547 (mt) cc_final: 0.8300 (mt)
REVERT: C  322 HIS cc_start: 0.5169 (OUTLIER) cc_final: 0.3203 (m90)
REVERT: A   61 PHE cc_start: 0.9156 (t80) cc_final: 0.8761 (t80)
REVERT: A   97 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: A  417 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6122 (mm-30)
REVERT: A  479 MET cc_start: 0.8269 (mmt) cc_final: 0.7729 (mpp)
REVERT: B  850 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7201 (mpp)
REVERT: B  927 PHE cc_start: 0.4899 (m-80) cc_final: 0.4434 (m-80)
  outliers start: 31
  outliers final: 25
  residues processed: 105
  average time/residue: 0.1771
  time to fit residues: 25.7687
Evaluate side-chains
  109 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 HIS
Chi-restraints excluded: chain C residue   56 ARG
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  138 CYS
Chi-restraints excluded: chain C residue  155 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  322 HIS
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  411 PHE
Chi-restraints excluded: chain C residue  429 ILE
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  356 GLN
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  850 MET
Chi-restraints excluded: chain B residue  860 LEU
Chi-restraints excluded: chain B residue  892 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 37 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 18 optimal weight:    0.4980
   chunk 83 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 42 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 128 HIS
B 848 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.118504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.102339 restraints weight = 24902.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.104946 restraints weight = 14975.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.106767 restraints weight = 10221.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3910 r_free = 0.3910    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3910 r_free = 0.3910    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.6416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7167  Z= 0.293
  Angle     :  0.701  11.139   9817  Z= 0.359
  Chirality :  0.046   0.175   1226
  Planarity :  0.005   0.085   1294
  Dihedral  :  4.843  21.718   1110
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.48 %
    Favored  : 85.52 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 25.87 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.30 (0.27), residues: 1050
  helix:  1.35 (0.27), residues: 429
  sheet: -3.52 (0.40), residues: 129
  loop : -3.82 (0.24), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 431 
 HIS   0.006   0.001   HIS B 846 
 PHE   0.026   0.002   PHE A 385 
 TYR   0.019   0.002   TYR B 904 
 ARG   0.006   0.001   ARG C 335 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 84
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: C  322 HIS cc_start: 0.5440 (OUTLIER) cc_final: 0.3399 (m90)
REVERT: A   61 PHE cc_start: 0.9136 (t80) cc_final: 0.8735 (t80)
REVERT: A   97 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8575 (mp)
REVERT: A  417 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6320 (mm-30)
REVERT: A  479 MET cc_start: 0.8322 (mmt) cc_final: 0.7871 (mpp)
REVERT: B  850 MET cc_start: 0.7856 (mpp) cc_final: 0.7186 (mpp)
REVERT: B  854 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8083 (mp)
REVERT: B  927 PHE cc_start: 0.5272 (m-80) cc_final: 0.4804 (m-80)
  outliers start: 31
  outliers final: 26
  residues processed: 106
  average time/residue: 0.1691
  time to fit residues: 24.9477
Evaluate side-chains
  109 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 HIS
Chi-restraints excluded: chain C residue   56 ARG
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  138 CYS
Chi-restraints excluded: chain C residue  155 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  322 HIS
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  411 PHE
Chi-restraints excluded: chain C residue  429 ILE
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  356 GLN
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  854 LEU
Chi-restraints excluded: chain B residue  860 LEU
Chi-restraints excluded: chain B residue  892 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 28 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0010
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.9190

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

Flipped N/Q/H residues before XYZ refinement:
C 295 ASN
B 848 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.121532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.105259 restraints weight = 24874.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.107846 restraints weight = 14755.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.109724 restraints weight = 10133.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3956 r_free = 0.3956    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3956 r_free = 0.3956    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.6365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7167  Z= 0.201
  Angle     :  0.671  10.592   9817  Z= 0.335
  Chirality :  0.045   0.170   1226
  Planarity :  0.004   0.082   1294
  Dihedral  :  4.448  18.440   1110
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.24 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 27.29 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.27), residues: 1050
  helix:  1.68 (0.27), residues: 422
  sheet: -3.63 (0.41), residues: 121
  loop : -3.71 (0.24), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP C 210 
 HIS   0.006   0.001   HIS B 866 
 PHE   0.016   0.001   PHE C 132 
 TYR   0.036   0.002   TYR B 904 
 ARG   0.007   0.001   ARG C 335 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 82
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  119 ASP cc_start: 0.8015 (t0) cc_final: 0.7756 (t0)
REVERT: C  148 TRP cc_start: 0.8031 (p-90) cc_final: 0.7425 (p-90)
REVERT: C  322 HIS cc_start: 0.5117 (OUTLIER) cc_final: 0.3186 (m90)
REVERT: A   61 PHE cc_start: 0.9093 (t80) cc_final: 0.8737 (t80)
REVERT: A   97 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8552 (mp)
REVERT: A  417 GLU cc_start: 0.6453 (mm-30) cc_final: 0.6236 (mm-30)
REVERT: A  479 MET cc_start: 0.8267 (mmt) cc_final: 0.7771 (mpp)
REVERT: B  850 MET cc_start: 0.7802 (mpp) cc_final: 0.7256 (mpp)
REVERT: B  866 HIS cc_start: 0.1292 (t-90) cc_final: 0.0492 (t-170)
REVERT: B  927 PHE cc_start: 0.5072 (m-80) cc_final: 0.4561 (m-80)
  outliers start: 28
  outliers final: 24
  residues processed: 101
  average time/residue: 0.1802
  time to fit residues: 25.2943
Evaluate side-chains
  105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 HIS
Chi-restraints excluded: chain C residue   56 ARG
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  138 CYS
Chi-restraints excluded: chain C residue  155 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  254 THR
Chi-restraints excluded: chain C residue  322 HIS
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  411 PHE
Chi-restraints excluded: chain C residue  429 ILE
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  356 GLN
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  860 LEU
Chi-restraints excluded: chain B residue  892 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0870
   chunk 67 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 106 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 97 optimal weight:    9.9990
   chunk 57 optimal weight:    8.9990
   chunk 48 optimal weight:    0.2980
   chunk 28 optimal weight:    9.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    3.0764

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

Flipped N/Q/H residues before XYZ refinement:
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 848 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.114128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.098543 restraints weight = 25276.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.100910 restraints weight = 15671.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.102287 restraints weight = 10892.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3837 r_free = 0.3837    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3837 r_free = 0.3837    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.7334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   7167  Z= 0.412
  Angle     :  0.828  11.233   9817  Z= 0.430
  Chirality :  0.049   0.193   1226
  Planarity :  0.006   0.092   1294
  Dihedral  :  5.749  31.347   1110
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.48 %
    Favored  : 83.52 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 27.70 %
    Favored  : 66.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.75 (0.26), residues: 1050
  helix:  0.84 (0.26), residues: 430
  sheet: -3.64 (0.39), residues: 138
  loop : -3.95 (0.23), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP C 210 
 HIS   0.012   0.002   HIS C 404 
 PHE   0.033   0.003   PHE A 385 
 TYR   0.038   0.003   TYR A  32 
 ARG   0.011   0.001   ARG C 335 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3259.79 seconds
wall clock time: 58 minutes 19.32 seconds (3499.32 seconds total)