Starting phenix.real_space_refine
on Wed Mar 12 02:34:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v4u_21048/03_2025/6v4u_21048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v4u_21048/03_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_21048/03_2025/6v4u_21048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v4u_21048/03_2025/6v4u_21048.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v4u_21048/03_2025/6v4u_21048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v4u_21048/03_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-5624/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: 4.77, per 1000 atoms: 0.67
  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: 1.58
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.67
  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: 1.66

  Time building geometry restraints manager: 1.91 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:             0.920
  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:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     19.720
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.910
-------------------------------------------------------------------------------
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  : 0.825 
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: 0.1868
  time to fit residues: 37.3945
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  : 0.828 
-------------------------------------------------------------------------------
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 = 0.4315 r_free = 0.4315 target = 0.133332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.116086 restraints weight = 23318.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.118979 restraints weight = 13845.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.121012 restraints weight = 9286.958|
|-----------------------------------------------------------------------------|
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 = 0.4112 r_free = 0.4112    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6543
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   8.509   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  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.7411 (tppt) cc_final: 0.7205 (tppt)
REVERT: A  385 PHE cc_start: 0.5349 (m-10) cc_final: 0.5128 (m-80)
REVERT: A  417 GLU cc_start: 0.6486 (mm-30) cc_final: 0.6129 (mm-30)
REVERT: A  479 MET cc_start: 0.8295 (mmt) cc_final: 0.8028 (mpp)
  outliers start: 16
  outliers final: 10
  residues processed: 116
  average time/residue: 0.1791
  time to fit residues: 28.5035
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  : 0.785 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 59 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0770
   chunk 26 optimal weight:    0.0570
   chunk 73 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 39 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.3472

-------------------------------------------------------------------------------
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 = 0.4353 r_free = 0.4353 target = 0.136387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.118337 restraints weight = 23086.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.121313 restraints weight = 13677.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.123469 restraints weight = 9231.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4152 r_free = 0.4152    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4152 r_free = 0.4152    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6461
moved from start:          0.2758

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= 0.139
  Angle     :  0.523   8.809   9817  Z= 0.261
  Chirality :  0.042   0.146   1226
  Planarity :  0.004   0.067   1294
  Dihedral  :  3.134  16.255   1110
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 22.00 %
    Favored  : 75.15 %
  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: -2.03 (0.26), residues: 1050
  helix:  2.00 (0.26), residues: 413
  sheet: -3.78 (0.39), residues: 113
  loop : -3.82 (0.23), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 148 
 HIS   0.003   0.001   HIS C 426 
 PHE   0.027   0.001   PHE C 132 
 TYR   0.022   0.001   TYR C 413 
 ARG   0.007   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
  110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: C   43 HIS cc_start: 0.8628 (p90) cc_final: 0.8415 (p-80)
REVERT: C  119 ASP cc_start: 0.7799 (t0) cc_final: 0.7502 (t0)
REVERT: A   32 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.7490 (t80)
REVERT: A  124 TYR cc_start: 0.8221 (t80) cc_final: 0.7969 (t80)
REVERT: A  385 PHE cc_start: 0.5373 (m-10) cc_final: 0.5125 (m-80)
REVERT: A  417 GLU cc_start: 0.6342 (mm-30) cc_final: 0.5997 (mm-30)
REVERT: A  479 MET cc_start: 0.8197 (mmt) cc_final: 0.7959 (mpp)
REVERT: B  911 LEU cc_start: 0.9118 (mt) cc_final: 0.8843 (mt)
  outliers start: 14
  outliers final: 6
  residues processed: 104
  average time/residue: 0.1627
  time to fit residues: 23.8010
Evaluate side-chains
  95 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 63 optimal weight:    0.0980
   chunk 38 optimal weight:    0.3980
   chunk 4 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    0.4980
   chunk 52 optimal weight:   10.0000
   chunk 105 optimal weight:    0.0470
   chunk 26 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.3278

-------------------------------------------------------------------------------
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 = 0.4349 r_free = 0.4349 target = 0.136277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.118631 restraints weight = 23358.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.121507 restraints weight = 13957.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.123594 restraints weight = 9484.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4149 r_free = 0.4149    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4149 r_free = 0.4149    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6473
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7167  Z= 0.135
  Angle     :  0.522   8.364   9817  Z= 0.260
  Chirality :  0.043   0.138   1226
  Planarity :  0.003   0.063   1294
  Dihedral  :  3.077  14.036   1110
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 23.22 %
    Favored  : 73.73 %
  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: -1.78 (0.27), residues: 1050
  helix:  2.20 (0.26), residues: 417
  sheet: -3.55 (0.40), residues: 118
  loop : -3.74 (0.23), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 148 
 HIS   0.003   0.000   HIS C 426 
 PHE   0.017   0.001   PHE C  93 
 TYR   0.020   0.002   TYR A 415 
 ARG   0.005   0.001   ARG C 160 

*********************** 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
  112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7503 (t80)
REVERT: A  385 PHE cc_start: 0.5331 (m-10) cc_final: 0.5041 (m-80)
REVERT: A  417 GLU cc_start: 0.6358 (mm-30) cc_final: 0.6007 (mm-30)
REVERT: A  479 MET cc_start: 0.8245 (mmt) cc_final: 0.7910 (mpp)
  outliers start: 15
  outliers final: 11
  residues processed: 105
  average time/residue: 0.1662
  time to fit residues: 24.6374
Evaluate side-chains
  98 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  736 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 7 optimal weight:    0.4980
   chunk 106 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 80 optimal weight:   30.0000
   chunk 67 optimal weight:    8.9990
   chunk 69 optimal weight:    0.0010
   chunk 59 optimal weight:    4.9990
   chunk 54 optimal weight:   20.0000
   chunk 53 optimal weight:    0.9990
   overall best weight:    1.2992

-------------------------------------------------------------------------------
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 = 0.4249 r_free = 0.4249 target = 0.128375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.111023 restraints weight = 23448.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.113809 restraints weight = 14170.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.115798 restraints weight = 9712.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4039 r_free = 0.4039    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4039 r_free = 0.4039    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.4039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7167  Z= 0.217
  Angle     :  0.606  10.767   9817  Z= 0.308
  Chirality :  0.044   0.149   1226
  Planarity :  0.004   0.070   1294
  Dihedral  :  3.824  20.465   1110
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.24 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 22.61 %
    Favored  : 71.28 %
  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: -1.85 (0.27), residues: 1050
  helix:  2.11 (0.27), residues: 413
  sheet: -3.71 (0.39), residues: 113
  loop : -3.68 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 431 
 HIS   0.007   0.001   HIS C 426 
 PHE   0.023   0.002   PHE C 132 
 TYR   0.020   0.002   TYR A 415 
 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
  122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 92
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: C  119 ASP cc_start: 0.7864 (t0) cc_final: 0.7632 (t0)
REVERT: C  211 ASP cc_start: 0.4749 (m-30) cc_final: 0.4526 (m-30)
REVERT: C  255 MET cc_start: 0.5035 (tpt) cc_final: 0.4835 (tpt)
REVERT: C  322 HIS cc_start: 0.5164 (OUTLIER) cc_final: 0.3903 (m90)
REVERT: A   32 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7688 (t80)
REVERT: A  417 GLU cc_start: 0.6061 (mm-30) cc_final: 0.5759 (mm-30)
REVERT: A  479 MET cc_start: 0.8242 (mmt) cc_final: 0.7874 (mpp)
  outliers start: 30
  outliers final: 17
  residues processed: 110
  average time/residue: 0.1513
  time to fit residues: 23.8802
Evaluate side-chains
  105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 HIS
Chi-restraints excluded: chain C residue   90 ILE
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  138 ILE
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  356 GLN
Chi-restraints excluded: chain B residue  368 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 105 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 93 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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**
** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.121546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.105359 restraints weight = 24872.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.107897 restraints weight = 15137.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.109738 restraints weight = 10460.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3945 r_free = 0.3945    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 = 0.3945 r_free = 0.3945    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6791
moved from start:          0.5122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7167  Z= 0.316
  Angle     :  0.697  10.683   9817  Z= 0.362
  Chirality :  0.047   0.167   1226
  Planarity :  0.005   0.073   1294
  Dihedral  :  4.709  22.471   1110
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.48 %
    Favored  : 87.52 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 25.05 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.20 (0.27), residues: 1050
  helix:  1.56 (0.27), residues: 423
  sheet: -3.69 (0.41), residues: 123
  loop : -3.77 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP C 431 
 HIS   0.007   0.001   HIS B 846 
 PHE   0.016   0.002   PHE C  93 
 TYR   0.026   0.002   TYR B 904 
 ARG   0.003   0.001   ARG C 331 

*********************** 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
  121 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
REVERT: C  105 LEU cc_start: 0.7826 (pp) cc_final: 0.7144 (mp)
REVERT: C  211 ASP cc_start: 0.5621 (m-30) cc_final: 0.5401 (m-30)
REVERT: C  322 HIS cc_start: 0.5520 (OUTLIER) cc_final: 0.4144 (m90)
REVERT: A   61 PHE cc_start: 0.9197 (t80) cc_final: 0.8827 (t80)
REVERT: A  417 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5950 (mm-30)
REVERT: A  479 MET cc_start: 0.8220 (mmt) cc_final: 0.7887 (mpp)
  outliers start: 28
  outliers final: 18
  residues processed: 111
  average time/residue: 0.1733
  time to fit residues: 26.5304
Evaluate side-chains
  103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 HIS
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  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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 90 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   chunk 54 optimal weight:   20.0000
   chunk 93 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 70 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
B 848 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.122497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.106517 restraints weight = 24439.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.109184 restraints weight = 14777.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.110689 restraints weight = 10092.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3964 r_free = 0.3964    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 = 0.3964 r_free = 0.3964    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6767
moved from start:          0.5368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7167  Z= 0.237
  Angle     :  0.654  10.282   9817  Z= 0.330
  Chirality :  0.045   0.166   1226
  Planarity :  0.004   0.078   1294
  Dihedral  :  4.409  20.085   1110
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.24 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 26.68 %
    Favored  : 67.21 %
  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: -2.02 (0.27), residues: 1050
  helix:  1.74 (0.27), residues: 424
  sheet: -3.84 (0.40), residues: 109
  loop : -3.67 (0.24), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 253 
 HIS   0.006   0.001   HIS B 846 
 PHE   0.026   0.002   PHE C 132 
 TYR   0.020   0.002   TYR A 415 
 ARG   0.003   0.001   ARG C 302 

*********************** 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
  118 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
REVERT: C   56 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6988 (mtm180)
REVERT: C  322 HIS cc_start: 0.5562 (OUTLIER) cc_final: 0.4040 (m90)
REVERT: A   61 PHE cc_start: 0.9153 (t80) cc_final: 0.8805 (t80)
REVERT: A   97 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8566 (mp)
REVERT: A  385 PHE cc_start: 0.6857 (m-80) cc_final: 0.6625 (m-80)
REVERT: A  417 GLU cc_start: 0.6527 (mm-30) cc_final: 0.6255 (mm-30)
REVERT: A  479 MET cc_start: 0.8177 (mmt) cc_final: 0.7683 (mpp)
REVERT: B  850 MET cc_start: 0.7823 (mpp) cc_final: 0.7303 (mpp)
  outliers start: 30
  outliers final: 20
  residues processed: 109
  average time/residue: 0.1667
  time to fit residues: 25.5130
Evaluate side-chains
  108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ARG
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  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  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  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:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9980
   chunk 11 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.2584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.122125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.105961 restraints weight = 24551.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.108644 restraints weight = 14685.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.110238 restraints weight = 9992.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
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: 0.6783
moved from start:          0.5623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7167  Z= 0.219
  Angle     :  0.646  10.720   9817  Z= 0.325
  Chirality :  0.045   0.171   1226
  Planarity :  0.004   0.079   1294
  Dihedral  :  4.324  19.868   1110
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.57 %
    Favored  : 87.43 %
  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: -1.92 (0.27), residues: 1050
  helix:  1.82 (0.27), residues: 423
  sheet: -3.75 (0.41), residues: 109
  loop : -3.61 (0.24), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 431 
 HIS   0.005   0.001   HIS B 846 
 PHE   0.025   0.002   PHE A 397 
 TYR   0.027   0.002   TYR B 904 
 ARG   0.002   0.001   ARG C 352 

*********************** 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
  117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  148 TRP cc_start: 0.7717 (p-90) cc_final: 0.7047 (p-90)
REVERT: C  322 HIS cc_start: 0.5333 (OUTLIER) cc_final: 0.3501 (m90)
REVERT: A   61 PHE cc_start: 0.9122 (t80) cc_final: 0.8758 (t80)
REVERT: A   97 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8564 (mp)
REVERT: A  417 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6166 (mm-30)
REVERT: A  479 MET cc_start: 0.8138 (mmt) cc_final: 0.7668 (mpp)
REVERT: B  850 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7460 (mpp)
  outliers start: 28
  outliers final: 20
  residues processed: 108
  average time/residue: 0.1709
  time to fit residues: 25.7843
Evaluate side-chains
  110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ARG
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   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  850 MET
Chi-restraints excluded: chain B residue  860 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:    0.9980
   chunk 51 optimal weight:    0.0070
   chunk 18 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 42 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
C 426 HIS
A 128 HIS
B 848 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.124006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.107675 restraints weight = 24295.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.110493 restraints weight = 14396.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.112180 restraints weight = 9676.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3996 r_free = 0.3996    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3996 r_free = 0.3996    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6724
moved from start:          0.5576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7167  Z= 0.181
  Angle     :  0.635  10.465   9817  Z= 0.314
  Chirality :  0.044   0.163   1226
  Planarity :  0.004   0.080   1294
  Dihedral  :  4.066  19.704   1110
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 27.90 %
    Favored  : 66.80 %
  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: -1.75 (0.27), residues: 1050
  helix:  2.00 (0.27), residues: 422
  sheet: -3.62 (0.42), residues: 109
  loop : -3.55 (0.24), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 118 
 HIS   0.003   0.001   HIS B 846 
 PHE   0.016   0.001   PHE C 132 
 TYR   0.028   0.002   TYR B 904 
 ARG   0.003   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
  111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: C  148 TRP cc_start: 0.7647 (p-90) cc_final: 0.7049 (p-90)
REVERT: C  322 HIS cc_start: 0.5500 (OUTLIER) cc_final: 0.3632 (m90)
REVERT: A   61 PHE cc_start: 0.9106 (t80) cc_final: 0.8746 (t80)
REVERT: A   97 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8534 (mp)
REVERT: A  417 GLU cc_start: 0.6368 (mm-30) cc_final: 0.6054 (mm-30)
REVERT: A  479 MET cc_start: 0.8121 (mmt) cc_final: 0.7695 (mpp)
REVERT: B  850 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7363 (mpp)
  outliers start: 26
  outliers final: 20
  residues processed: 102
  average time/residue: 0.1759
  time to fit residues: 25.0608
Evaluate side-chains
  106 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 83
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   49 LEU
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   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  850 MET
Chi-restraints excluded: chain B residue  860 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 2 optimal weight:    0.2980
   chunk 60 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0270
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.7640

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

Flipped N/Q/H residues before XYZ refinement:
C 426 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 = 0.4206 r_free = 0.4206 target = 0.124476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.107673 restraints weight = 24609.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.110327 restraints weight = 15031.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.112256 restraints weight = 10369.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4003 r_free = 0.4003    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4003 r_free = 0.4003    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.4003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6753
moved from start:          0.5662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7167  Z= 0.183
  Angle     :  0.631  10.291   9817  Z= 0.314
  Chirality :  0.044   0.161   1226
  Planarity :  0.004   0.081   1294
  Dihedral  :  4.012  19.090   1110
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.14 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 27.29 %
    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: -1.72 (0.27), residues: 1050
  helix:  1.98 (0.27), residues: 426
  sheet: -3.57 (0.42), residues: 117
  loop : -3.52 (0.24), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 118 
 HIS   0.005   0.001   HIS C 426 
 PHE   0.025   0.002   PHE A 385 
 TYR   0.026   0.002   TYR B 904 
 ARG   0.005   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
  108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
REVERT: C  322 HIS cc_start: 0.4956 (OUTLIER) cc_final: 0.3072 (m90)
REVERT: A   61 PHE cc_start: 0.9132 (t80) cc_final: 0.8776 (t80)
REVERT: A   97 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8544 (mp)
REVERT: A  417 GLU cc_start: 0.6359 (mm-30) cc_final: 0.6056 (mm-30)
REVERT: B  850 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7482 (mpp)
  outliers start: 24
  outliers final: 21
  residues processed: 99
  average time/residue: 0.1683
  time to fit residues: 23.9944
Evaluate side-chains
  107 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   49 LEU
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   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  353 LEU
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  850 MET
Chi-restraints excluded: chain B residue  860 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   chunk 67 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 106 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 343 HIS
B 848 GLN
B 884 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.116052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.100344 restraints weight = 25116.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.102804 restraints weight = 15159.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.104571 restraints weight = 10354.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    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 = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.6734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   7167  Z= 0.387
  Angle     :  0.800  11.877   9817  Z= 0.414
  Chirality :  0.049   0.194   1226
  Planarity :  0.006   0.130   1294
  Dihedral  :  5.463  28.843   1110
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.81 %
    Favored  : 84.19 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 26.68 %
    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: -2.32 (0.26), residues: 1050
  helix:  1.17 (0.26), residues: 429
  sheet: -3.35 (0.44), residues: 113
  loop : -3.74 (0.24), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 431 
 HIS   0.010   0.002   HIS C 404 
 PHE   0.032   0.003   PHE A 385 
 TYR   0.029   0.002   TYR B 904 
 ARG   0.005   0.001   ARG C 335 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3291.80 seconds
wall clock time: 57 minutes 15.48 seconds (3435.48 seconds total)