Starting phenix.real_space_refine
on Fri Oct 10 21:00:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wvu_37869/10_2025/8wvu_37869.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wvu_37869/10_2025/8wvu_37869.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wvu_37869/10_2025/8wvu_37869.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wvu_37869/10_2025/8wvu_37869.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wvu_37869/10_2025/8wvu_37869.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wvu_37869/10_2025/8wvu_37869.cif"
  }
  resolution = 3.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2063 atoms to isotropic.
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      50      5.16       5
     C    4783      2.51       5
     N    1238      2.21       5
     O    1356      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7427
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 733, 5714
          Classifications: {'peptide': 733}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 37, 'TRANS': 695}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 771
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 7, 'TRANS': 94}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 942
          Classifications: {'peptide': 137}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 10, 'TRANS': 126}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 134
          Unresolved non-hydrogen angles: 165
          Unresolved non-hydrogen dihedrals: 126
          Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 4, 'TRP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 93
  Time building chain proxies: 1.99, per 1000 atoms: 0.27
  Number of scatterers: 7427
  At special positions: 0
  Unit cell: (75.65, 85.85, 160.65, 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      50     16.00
     O    1356      8.00
     N    1238      7.00
     C    4783      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  29 " - pdb=" SG  CYS A  35 " distance=2.12
    Simple disulfide: pdb=" SG  CYS A  33 " - pdb=" SG  CYS A  43 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 364 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 470 " - pdb=" SG  CYS A 522 " distance=1.67
    Simple disulfide: pdb=" SG  CYS A 471 " - pdb=" SG  CYS A 532 " distance=2.21
    Simple disulfide: pdb=" SG  CYS A 618 " - pdb=" SG  CYS A 693 " distance=2.14
    Simple disulfide: pdb=" SG  CYS B  40 " - pdb=" SG  CYS B  47 " distance=2.30
    Simple disulfide: pdb=" SG  CYS B  44 " - pdb=" SG  CYS B  53 " distance=1.94
    Simple disulfide: pdb=" SG  CYS B  56 " - pdb=" SG  CYS B  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  79 " - pdb=" SG  CYS B  94 " distance=1.91
    Simple disulfide: pdb=" SG  CYS B  97 " - pdb=" SG  CYS B 105 " distance=2.10
    Simple disulfide: pdb=" SG  CYS B 102 " - pdb=" SG  CYS B 111 " distance=1.88
    Simple disulfide: pdb=" SG  CYS B 114 " - pdb=" SG  CYS B 125 " distance=2.12
    Simple disulfide: pdb=" SG  CYS B 129 " - pdb=" SG  CYS B 142 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C  91 " - pdb=" SG  CYS C 119 " distance=2.38

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 369.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1834

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 12 sheets defined
      29.2% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 128
      removed outlier: 4.264A  pdb=" N   GLY A 127 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 174
    Processing helix  chain 'A' and resid 242 through 247
      removed outlier: 3.836A  pdb=" N   LYS A 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA A 246 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 247 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 242 through 247'
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 4.272A  pdb=" N   GLN A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 472
      removed outlier: 3.559A  pdb=" N   GLN A 469 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   CYS A 471 " --> pdb=" O   TYR A 468 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ALA A 472 " --> pdb=" O   GLN A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 564
      removed outlier: 3.946A  pdb=" N   ARG A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU A 543 " --> pdb=" O   TRP A 539 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE A 554 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 601
      removed outlier: 3.589A  pdb=" N   SER A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 614
    Processing helix  chain 'A' and resid 617 through 646
    Processing helix  chain 'A' and resid 661 through 683
      removed outlier: 3.608A  pdb=" N   LEU A 671 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA A 673 " --> pdb=" O   ALA A 669 " (cutoff:3.500A)
      Proline residue:  A 680  - end of helix
    Processing helix  chain 'A' and resid 703 through 731
      removed outlier: 4.175A  pdb=" N   THR A 707 " --> pdb=" O   SER A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 759
      removed outlier: 4.366A  pdb=" N   MET A 745 " --> pdb=" O   SER A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 768
      removed outlier: 3.618A  pdb=" N   PHE A 768 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 773
      removed outlier: 3.673A  pdb=" N   ILE A 772 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 790
      removed outlier: 3.581A  pdb=" N   MET A 782 " --> pdb=" O   SER A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 804
      removed outlier: 3.726A  pdb=" N   CYS A 795 " --> pdb=" O   PRO A 791 " (cutoff:3.500A)
      Proline residue:  A 798  - end of helix
      removed outlier: 3.665A  pdb=" N   TYR A 801 " --> pdb=" O   ASN A 797 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 818
      removed outlier: 3.719A  pdb=" N   LYS A 809 " --> pdb=" O   ASN A 805 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   TRP A 812 " --> pdb=" O   PHE A 808 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   LYS A 813 " --> pdb=" O   LYS A 809 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   LEU A 814 " --> pdb=" O   GLU A 810 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A 815 " --> pdb=" O   ASP A 811 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ARG A 817 " --> pdb=" O   LYS A 813 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.519A  pdb=" N   LEU C  90 " --> pdb=" O   PRO C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 132
      removed outlier: 3.779A  pdb=" N   GLU C 131 " --> pdb=" O   ARG C 127 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG C 132 " --> pdb=" O   MET C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 150
      removed outlier: 3.658A  pdb=" N   ALA C 148 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 178
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42
      removed outlier: 6.855A  pdb=" N   VAL A  41 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN A  87 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 159
      removed outlier: 7.232A  pdb=" N   LEU A 158 " --> pdb=" O   THR A 183 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   LEU A 182 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLY A 254 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192
      removed outlier: 4.211A  pdb=" N   ILE A 192 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263
    Processing sheet with id=AA6, first strand: chain 'A' and resid 302 through 303
      removed outlier: 3.841A  pdb=" N   LEU A 324 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   LEU A 348 " --> pdb=" O   SER A 371 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   LEU A 394 " --> pdb=" O   ASP A 419 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LEU A 439 " --> pdb=" O   SER A 463 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 46
      removed outlier: 6.624A  pdb=" N   LYS B  55 " --> pdb=" O   GLU B  45 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 66
    Processing sheet with id=AA9, first strand: chain 'B' and resid 83 through 84
    Processing sheet with id=AB1, first strand: chain 'B' and resid 102 through 104
      removed outlier: 6.879A  pdb=" N   LYS B 113 " --> pdb=" O   GLU B 103 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 119 through 121
    Processing sheet with id=AB3, first strand: chain 'C' and resid 81 through 84
      removed outlier: 7.169A  pdb=" N   PHE C 103 " --> pdb=" O   SER C 135 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL C 137 " --> pdb=" O   PHE C 103 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   SER C 105 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   PHE C 139 " --> pdb=" O   SER C 105 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL C 107 " --> pdb=" O   PHE C 139 " (cutoff:3.500A)
      removed outlier: 9.470A  pdb=" N   VAL C 162 " --> pdb=" O   SER C 135 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL C 137 " --> pdb=" O   VAL C 162 " (cutoff:3.500A)

    198 hydrogen bonds defined for protein.
    573 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: 1.25

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1298
        1.31 -     1.44: 1844
        1.44 -     1.56: 4386
        1.56 -     1.69: 0
        1.69 -     1.82: 63
  Bond restraints: 7591
  Sorted by residual:
  bond pdb=" C   ARG C 117 "
       pdb=" N   PRO C 118 "
    ideal  model  delta    sigma   weight residual
    1.330  1.534 -0.204 1.22e-02 6.72e+03 2.79e+02
  bond pdb=" C   ALA B  86 "
       pdb=" N   ARG B  87 "
    ideal  model  delta    sigma   weight residual
    1.330  1.543 -0.213 1.31e-02 5.83e+03 2.65e+02
  bond pdb=" C   PRO C 112 "
       pdb=" N   ARG C 113 "
    ideal  model  delta    sigma   weight residual
    1.334  1.540 -0.205 1.33e-02 5.65e+03 2.39e+02
  bond pdb=" C   LEU A 694 "
       pdb=" N   PRO A 695 "
    ideal  model  delta    sigma   weight residual
    1.336  1.486 -0.151 1.25e-02 6.40e+03 1.45e+02
  bond pdb=" C   HIS C  86 "
       pdb=" N   PRO C  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.495 -0.160 1.36e-02 5.41e+03 1.38e+02
  ... (remaining 7586 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.03: 10207
        5.03 -    10.07: 94
       10.07 -    15.10: 15
       15.10 -    20.13: 0
       20.13 -    25.16: 4
  Bond angle restraints: 10320
  Sorted by residual:
  angle pdb=" C   ILE C  51 "
        pdb=" N   PRO C  52 "
        pdb=" CA  PRO C  52 "
      ideal   model   delta    sigma   weight residual
     119.92  145.08  -25.16 1.07e+00 8.73e-01 5.53e+02
  angle pdb=" O   ILE C  51 "
        pdb=" C   ILE C  51 "
        pdb=" N   PRO C  52 "
      ideal   model   delta    sigma   weight residual
     121.10   96.64   24.46 1.14e+00 7.69e-01 4.60e+02
  angle pdb=" CA  ILE C  51 "
        pdb=" C   ILE C  51 "
        pdb=" N   PRO C  52 "
      ideal   model   delta    sigma   weight residual
     118.88  142.68  -23.80 1.54e+00 4.22e-01 2.39e+02
  angle pdb=" O   LYS C  81 "
        pdb=" C   LYS C  81 "
        pdb=" N   LEU C  82 "
      ideal   model   delta    sigma   weight residual
     122.96  110.40   12.56 1.13e+00 7.83e-01 1.23e+02
  angle pdb=" O   GLY C  80 "
        pdb=" C   GLY C  80 "
        pdb=" N   LYS C  81 "
      ideal   model   delta    sigma   weight residual
     123.55  111.31   12.24 1.19e+00 7.06e-01 1.06e+02
  ... (remaining 10315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.34: 4313
       12.34 -    24.69: 203
       24.69 -    37.03: 52
       37.03 -    49.37: 15
       49.37 -    61.71: 10
  Dihedral angle restraints: 4593
    sinusoidal: 1779
      harmonic: 2814
  Sorted by residual:
  dihedral pdb=" C   ARG A 460 "
           pdb=" N   ARG A 460 "
           pdb=" CA  ARG A 460 "
           pdb=" CB  ARG A 460 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.88   12.28     0      2.50e+00 1.60e-01 2.41e+01
  dihedral pdb=" N   SER A 461 "
           pdb=" C   SER A 461 "
           pdb=" CA  SER A 461 "
           pdb=" CB  SER A 461 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  111.76   11.04     0      2.50e+00 1.60e-01 1.95e+01
  dihedral pdb=" C   THR C  58 "
           pdb=" N   THR C  58 "
           pdb=" CA  THR C  58 "
           pdb=" CB  THR C  58 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -111.39  -10.61     0      2.50e+00 1.60e-01 1.80e+01
  ... (remaining 4590 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1028
       0.073 -    0.146: 146
       0.146 -    0.219: 35
       0.219 -    0.292: 3
       0.292 -    0.365: 4
  Chirality restraints: 1216
  Sorted by residual:
  chirality pdb=" CA  LEU C 163 "
            pdb=" N   LEU C 163 "
            pdb=" C   LEU C 163 "
            pdb=" CB  LEU C 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" CA  ARG A 460 "
            pdb=" N   ARG A 460 "
            pdb=" C   ARG A 460 "
            pdb=" CB  ARG A 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.08e+00
  chirality pdb=" CA  THR C  58 "
            pdb=" N   THR C  58 "
            pdb=" C   THR C  58 "
            pdb=" CB  THR C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.84   -0.31 2.00e-01 2.50e+01 2.47e+00
  ... (remaining 1213 not shown)

  Planarity restraints: 1315
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 184 "    0.024 2.00e-02 2.50e+03   4.85e-02 2.35e+01
        pdb=" C   VAL C 184 "   -0.084 2.00e-02 2.50e+03
        pdb=" O   VAL C 184 "    0.032 2.00e-02 2.50e+03
        pdb=" N   ARG C 185 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  50 "   -0.023 2.00e-02 2.50e+03   4.44e-02 1.97e+01
        pdb=" C   VAL C  50 "    0.077 2.00e-02 2.50e+03
        pdb=" O   VAL C  50 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ILE C  51 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  80 "   -0.022 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   GLY C  80 "    0.069 2.00e-02 2.50e+03
        pdb=" O   GLY C  80 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LYS C  81 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1312 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 74
        2.57 -     3.15: 6112
        3.15 -     3.74: 10735
        3.74 -     4.32: 14342
        4.32 -     4.90: 23687
  Nonbonded interactions: 54950
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B  51 "
            pdb=" CD  PRO C  87 "
     model   vdw
     1.989 3.520
  nonbonded pdb=" NH2 ARG B  66 "
            pdb=" CD1 LEU C  99 "
     model   vdw
     2.019 3.540
  nonbonded pdb=" O   VAL C  50 "
            pdb=" O   GLY C  59 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" ND1 HIS B 108 "
            pdb=" OD1 ASN B 109 "
     model   vdw
     2.153 3.120
  nonbonded pdb=" OH  TYR A 468 "
            pdb=" OE2 GLU A 613 "
     model   vdw
     2.193 3.040
  ... (remaining 54945 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.680
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6076
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      :  0.014   0.361   7606  Z= 0.937
  Angle     :  1.348  25.163  10350  Z= 0.966
  Chirality :  0.059   0.365   1216
  Planarity :  0.006   0.063   1315
  Dihedral  :  8.443  61.713   2714
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 17.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  :  5.11 %
    Favored  : 92.21 %
  Cbeta Deviations :  0.33 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.28), residues: 956
  helix:  0.71 (0.36), residues: 238
  sheet: -2.09 (0.50), residues: 134
  loop : -1.17 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  39 
 TYR   0.008   0.001   TYR A 687 
 PHE   0.007   0.001   PHE C 139 
 TRP   0.010   0.001   TRP A 812 
 HIS   0.002   0.000   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.01150 ( 7591)
  covalent geometry    : angle       1.31974 (10320)
  SS BOND              : bond        0.17132 (   15)
  SS BOND              : angle       5.22421 (   30)
  hydrogen bonds       : bond        0.26464 (  198)
  hydrogen bonds       : angle       6.48426 (  573)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 268
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 ILE cc_start: 0.8460 (mt) cc_final: 0.8217 (mt)
REVERT: A  178 THR cc_start: 0.7354 (p) cc_final: 0.6864 (p)
REVERT: A  265 ASP cc_start: 0.6958 (m-30) cc_final: 0.6471 (m-30)
REVERT: A  309 VAL cc_start: 0.7898 (t) cc_final: 0.7627 (p)
REVERT: A  373 GLN cc_start: 0.7545 (mt0) cc_final: 0.6999 (mt0)
REVERT: A  379 GLN cc_start: 0.7974 (pt0) cc_final: 0.7633 (pm20)
REVERT: A  402 HIS cc_start: 0.6791 (t70) cc_final: 0.6456 (t70)
REVERT: A  582 VAL cc_start: 0.7540 (t) cc_final: 0.7325 (p)
REVERT: A  587 MET cc_start: 0.7613 (tpp) cc_final: 0.7342 (tpp)
REVERT: A  589 ILE cc_start: 0.7470 (mm) cc_final: 0.7174 (tt)
REVERT: A  667 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7639 (tp)
REVERT: A  799 VAL cc_start: 0.8431 (m) cc_final: 0.8222 (p)
REVERT: B  113 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7547 (tmtm)
REVERT: C  163 LEU cc_start: 0.7639 (mt) cc_final: 0.7403 (mt)
  outliers start: 22
  outliers final: 5
  residues processed: 281
  average time/residue: 0.0787
  time to fit residues: 30.3266
Evaluate side-chains
  238 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 231
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  167 ASN
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  176 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0020
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0670
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.6528

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
A 140 HIS
A 154 GLN
A 210 ASN
A 218 GLN
A 282 ASN
A 310 GLN
A 320 HIS
A 354 ASN
A 375 ASN
A 417 ASN
A 740 ASN
** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  67 ASN
B  71 GLN
C  62 ASN
C 167 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.145977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.120945 restraints weight = 12021.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.124714 restraints weight = 6156.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127339 restraints weight = 3830.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.129091 restraints weight = 2701.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.130316 restraints weight = 2096.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7606  Z= 0.149
  Angle     :  0.654   7.291  10350  Z= 0.323
  Chirality :  0.045   0.152   1216
  Planarity :  0.004   0.045   1315
  Dihedral  :  5.116  44.557   1027
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 13.26 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.28), residues: 956
  helix:  1.29 (0.35), residues: 234
  sheet: -2.15 (0.47), residues: 127
  loop : -1.13 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  39 
 TYR   0.014   0.001   TYR B  83 
 PHE   0.021   0.001   PHE A 768 
 TRP   0.014   0.001   TRP A 159 
 HIS   0.009   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7591)
  covalent geometry    : angle       0.65010 (10320)
  SS BOND              : bond        0.00384 (   15)
  SS BOND              : angle       1.47344 (   30)
  hydrogen bonds       : bond        0.06159 (  198)
  hydrogen bonds       : angle       4.93308 (  573)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 236
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7838 (tm-30)
REVERT: A   85 GLU cc_start: 0.6351 (tt0) cc_final: 0.6140 (tt0)
REVERT: A  113 GLN cc_start: 0.7397 (tt0) cc_final: 0.7182 (tt0)
REVERT: A  178 THR cc_start: 0.8041 (p) cc_final: 0.7792 (p)
REVERT: A  309 VAL cc_start: 0.8415 (t) cc_final: 0.8185 (p)
REVERT: A  354 ASN cc_start: 0.7964 (m-40) cc_final: 0.7642 (m-40)
REVERT: A  376 GLN cc_start: 0.7836 (mt0) cc_final: 0.7190 (mt0)
REVERT: A  468 TYR cc_start: 0.8324 (m-80) cc_final: 0.8086 (m-80)
REVERT: A  587 MET cc_start: 0.7802 (tpp) cc_final: 0.7380 (tpp)
REVERT: A  598 ASP cc_start: 0.7840 (t70) cc_final: 0.7611 (t70)
REVERT: A  613 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6666 (mt-10)
REVERT: A  630 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6671 (mm-30)
REVERT: A  667 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7759 (tp)
REVERT: A  674 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7449 (t)
REVERT: A  682 PHE cc_start: 0.7116 (t80) cc_final: 0.6887 (t80)
REVERT: A  745 MET cc_start: 0.6220 (tpp) cc_final: 0.5987 (tpp)
REVERT: B  113 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7130 (tmtm)
  outliers start: 24
  outliers final: 12
  residues processed: 250
  average time/residue: 0.0772
  time to fit residues: 26.4038
Evaluate side-chains
  235 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 220
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  602 TRP
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  740 ASN
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  176 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 33 optimal weight:    0.0870
   chunk 40 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0980
   chunk 6 optimal weight:    3.9990
   chunk 57 optimal weight:    0.1980
   chunk 87 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.3960

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
A 373 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.146459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.121244 restraints weight = 11905.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.125065 restraints weight = 6147.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.127645 restraints weight = 3814.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.129365 restraints weight = 2697.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.130515 restraints weight = 2109.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7606  Z= 0.110
  Angle     :  0.579   8.182  10350  Z= 0.287
  Chirality :  0.043   0.148   1216
  Planarity :  0.004   0.047   1315
  Dihedral  :  4.704  43.925   1023
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.40 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.28), residues: 956
  helix:  1.71 (0.36), residues: 233
  sheet: -1.87 (0.46), residues: 133
  loop : -0.96 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 407 
 TYR   0.008   0.001   TYR B 119 
 PHE   0.018   0.001   PHE A 768 
 TRP   0.012   0.001   TRP A 159 
 HIS   0.005   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7591)
  covalent geometry    : angle       0.57306 (10320)
  SS BOND              : bond        0.00356 (   15)
  SS BOND              : angle       1.67891 (   30)
  hydrogen bonds       : bond        0.05039 (  198)
  hydrogen bonds       : angle       4.48388 (  573)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 223
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7740 (pp30)
REVERT: A   88 LEU cc_start: 0.8078 (mm) cc_final: 0.7876 (mt)
REVERT: A   96 ILE cc_start: 0.8677 (mt) cc_final: 0.8456 (mt)
REVERT: A   99 LYS cc_start: 0.7594 (mptt) cc_final: 0.7382 (mppt)
REVERT: A  113 GLN cc_start: 0.7404 (tt0) cc_final: 0.6981 (tt0)
REVERT: A  178 THR cc_start: 0.8000 (p) cc_final: 0.7790 (p)
REVERT: A  309 VAL cc_start: 0.8394 (t) cc_final: 0.8180 (p)
REVERT: A  376 GLN cc_start: 0.7821 (mt0) cc_final: 0.6582 (mt0)
REVERT: A  468 TYR cc_start: 0.8318 (m-80) cc_final: 0.8080 (m-80)
REVERT: A  534 TYR cc_start: 0.8019 (m-10) cc_final: 0.7731 (m-10)
REVERT: A  587 MET cc_start: 0.7742 (tpp) cc_final: 0.7255 (tpp)
REVERT: A  613 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6636 (mt-10)
REVERT: A  614 THR cc_start: 0.8327 (m) cc_final: 0.7997 (t)
REVERT: A  630 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6537 (mm-30)
REVERT: A  667 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7740 (tp)
REVERT: A  682 PHE cc_start: 0.7123 (t80) cc_final: 0.6901 (t80)
REVERT: A  745 MET cc_start: 0.6104 (tpp) cc_final: 0.5858 (tpp)
REVERT: B  113 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6999 (tmtm)
  outliers start: 20
  outliers final: 13
  residues processed: 233
  average time/residue: 0.0844
  time to fit residues: 26.8800
Evaluate side-chains
  224 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 209
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  281 ASP
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  555 PHE
Chi-restraints excluded: chain A residue  602 TRP
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue  113 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0050
   chunk 47 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
A 438 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.146807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.120303 restraints weight = 12052.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.124275 restraints weight = 6153.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.126915 restraints weight = 3814.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.128719 restraints weight = 2702.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.129632 restraints weight = 2101.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.3929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7606  Z= 0.167
  Angle     :  0.624   6.444  10350  Z= 0.317
  Chirality :  0.045   0.147   1216
  Planarity :  0.004   0.046   1315
  Dihedral  :  4.963  44.291   1020
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.40 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.27), residues: 956
  helix:  1.22 (0.35), residues: 241
  sheet: -1.94 (0.44), residues: 139
  loop : -1.24 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 407 
 TYR   0.010   0.001   TYR B 119 
 PHE   0.024   0.002   PHE A 790 
 TRP   0.017   0.001   TRP A 159 
 HIS   0.007   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 7591)
  covalent geometry    : angle       0.61954 (10320)
  SS BOND              : bond        0.00323 (   15)
  SS BOND              : angle       1.53011 (   30)
  hydrogen bonds       : bond        0.06584 (  198)
  hydrogen bonds       : angle       4.65741 (  573)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 227
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6554 (mt-10)
REVERT: A  178 THR cc_start: 0.8070 (p) cc_final: 0.7750 (p)
REVERT: A  309 VAL cc_start: 0.8518 (t) cc_final: 0.8299 (p)
REVERT: A  376 GLN cc_start: 0.7945 (mt0) cc_final: 0.7588 (mt0)
REVERT: A  468 TYR cc_start: 0.8411 (m-80) cc_final: 0.8135 (m-80)
REVERT: A  534 TYR cc_start: 0.8071 (m-10) cc_final: 0.7870 (m-10)
REVERT: A  587 MET cc_start: 0.7805 (tpp) cc_final: 0.7196 (tpp)
REVERT: A  613 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6685 (mt-10)
REVERT: A  667 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7688 (tp)
REVERT: A  682 PHE cc_start: 0.7119 (t80) cc_final: 0.6918 (t80)
REVERT: A  745 MET cc_start: 0.6141 (tpp) cc_final: 0.5893 (tpp)
REVERT: B  113 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7129 (tmtm)
  outliers start: 31
  outliers final: 17
  residues processed: 241
  average time/residue: 0.0821
  time to fit residues: 27.0608
Evaluate side-chains
  239 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 220
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0770
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.7342

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 373 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.143225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.117850 restraints weight = 11940.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.121636 restraints weight = 6205.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.124189 restraints weight = 3863.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.125894 restraints weight = 2728.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.127034 restraints weight = 2128.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7606  Z= 0.143
  Angle     :  0.600   7.139  10350  Z= 0.301
  Chirality :  0.044   0.151   1216
  Planarity :  0.004   0.045   1315
  Dihedral  :  4.803  44.514   1020
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 19.22 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.27), residues: 956
  helix:  1.46 (0.35), residues: 234
  sheet: -1.87 (0.44), residues: 139
  loop : -1.22 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 392 
 TYR   0.009   0.001   TYR B  83 
 PHE   0.024   0.001   PHE A 790 
 TRP   0.015   0.001   TRP A 159 
 HIS   0.005   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7591)
  covalent geometry    : angle       0.59611 (10320)
  SS BOND              : bond        0.00316 (   15)
  SS BOND              : angle       1.36331 (   30)
  hydrogen bonds       : bond        0.05773 (  198)
  hydrogen bonds       : angle       4.49911 (  573)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 223
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7793 (pp30)
REVERT: A   84 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6527 (mt-10)
REVERT: A  106 GLU cc_start: 0.7932 (mp0) cc_final: 0.7611 (mp0)
REVERT: A  113 GLN cc_start: 0.7498 (tt0) cc_final: 0.7168 (tt0)
REVERT: A  307 SER cc_start: 0.8141 (p) cc_final: 0.7698 (p)
REVERT: A  309 VAL cc_start: 0.8493 (t) cc_final: 0.8241 (p)
REVERT: A  376 GLN cc_start: 0.7855 (mt0) cc_final: 0.7441 (mt0)
REVERT: A  446 LYS cc_start: 0.8338 (mmmm) cc_final: 0.8132 (mmmm)
REVERT: A  468 TYR cc_start: 0.8419 (m-80) cc_final: 0.8148 (m-80)
REVERT: A  587 MET cc_start: 0.7834 (tpp) cc_final: 0.7242 (tpp)
REVERT: A  613 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6710 (mt-10)
REVERT: A  667 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7655 (tp)
REVERT: A  745 MET cc_start: 0.5896 (tpp) cc_final: 0.5667 (tpp)
REVERT: B  113 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7100 (tmtm)
REVERT: C  100 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6928 (pp20)
  outliers start: 31
  outliers final: 20
  residues processed: 236
  average time/residue: 0.0819
  time to fit residues: 26.3248
Evaluate side-chains
  239 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 215
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  310 GLN
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  100 GLU
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 47 optimal weight:    0.3980
   chunk 63 optimal weight:    0.6980
   chunk 72 optimal weight:    0.4980
   chunk 23 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0060
   chunk 25 optimal weight:    0.3980
   chunk 67 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 218 GLN
A 373 GLN
A 405 HIS
A 740 ASN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.144516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.119162 restraints weight = 11893.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.122985 restraints weight = 6164.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.125573 restraints weight = 3829.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.127359 restraints weight = 2695.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.128393 restraints weight = 2082.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.4439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7606  Z= 0.109
  Angle     :  0.576   6.867  10350  Z= 0.287
  Chirality :  0.043   0.166   1216
  Planarity :  0.004   0.044   1315
  Dihedral  :  4.576  45.366   1020
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.68 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.28), residues: 956
  helix:  1.81 (0.36), residues: 222
  sheet: -2.00 (0.42), residues: 151
  loop : -1.06 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 407 
 TYR   0.010   0.001   TYR A 687 
 PHE   0.025   0.001   PHE A 623 
 TRP   0.012   0.001   TRP A 159 
 HIS   0.004   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7591)
  covalent geometry    : angle       0.57242 (10320)
  SS BOND              : bond        0.00293 (   15)
  SS BOND              : angle       1.28744 (   30)
  hydrogen bonds       : bond        0.04790 (  198)
  hydrogen bonds       : angle       4.30459 (  573)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 221
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8166 (mmpt) cc_final: 0.7876 (mmpt)
REVERT: A   71 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7806 (pp30)
REVERT: A   84 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6537 (mt-10)
REVERT: A  113 GLN cc_start: 0.7489 (tt0) cc_final: 0.7184 (tt0)
REVERT: A  180 GLN cc_start: 0.8401 (mt0) cc_final: 0.8171 (mt0)
REVERT: A  307 SER cc_start: 0.8162 (p) cc_final: 0.7785 (p)
REVERT: A  309 VAL cc_start: 0.8461 (t) cc_final: 0.8193 (p)
REVERT: A  376 GLN cc_start: 0.7875 (mt0) cc_final: 0.7621 (mt0)
REVERT: A  468 TYR cc_start: 0.8401 (m-80) cc_final: 0.8122 (m-80)
REVERT: A  587 MET cc_start: 0.7828 (tpp) cc_final: 0.7191 (tpp)
REVERT: A  613 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6694 (mt-10)
REVERT: A  667 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7632 (tp)
REVERT: A  745 MET cc_start: 0.5805 (tpp) cc_final: 0.5555 (tpp)
REVERT: B  108 HIS cc_start: 0.6828 (p90) cc_final: 0.6525 (p-80)
REVERT: B  113 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7019 (tmtm)
  outliers start: 24
  outliers final: 18
  residues processed: 232
  average time/residue: 0.0831
  time to fit residues: 26.3762
Evaluate side-chains
  232 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 211
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  682 PHE
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  740 ASN
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 282 ASN
A 373 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.142183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.116563 restraints weight = 11981.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.120416 restraints weight = 6235.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.122997 restraints weight = 3870.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.124736 restraints weight = 2728.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.125755 restraints weight = 2129.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.4621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7606  Z= 0.161
  Angle     :  0.620   6.981  10350  Z= 0.313
  Chirality :  0.045   0.166   1216
  Planarity :  0.004   0.048   1315
  Dihedral  :  4.852  46.023   1020
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 21.41 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.27), residues: 956
  helix:  1.47 (0.35), residues: 234
  sheet: -1.87 (0.44), residues: 141
  loop : -1.25 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 460 
 TYR   0.009   0.001   TYR A 590 
 PHE   0.025   0.002   PHE A 790 
 TRP   0.015   0.001   TRP A 159 
 HIS   0.005   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 7591)
  covalent geometry    : angle       0.61378 (10320)
  SS BOND              : bond        0.00303 (   15)
  SS BOND              : angle       1.69224 (   30)
  hydrogen bonds       : bond        0.05940 (  198)
  hydrogen bonds       : angle       4.46772 (  573)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 225
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8230 (mmpt) cc_final: 0.7933 (mmpt)
REVERT: A   71 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7705 (pp30)
REVERT: A   84 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6525 (mt-10)
REVERT: A  106 GLU cc_start: 0.7957 (mp0) cc_final: 0.7629 (mp0)
REVERT: A  113 GLN cc_start: 0.7511 (tt0) cc_final: 0.7192 (tt0)
REVERT: A  307 SER cc_start: 0.8149 (p) cc_final: 0.7725 (p)
REVERT: A  309 VAL cc_start: 0.8501 (t) cc_final: 0.8222 (p)
REVERT: A  376 GLN cc_start: 0.7887 (mt0) cc_final: 0.7461 (mt0)
REVERT: A  468 TYR cc_start: 0.8433 (m-80) cc_final: 0.8151 (m-80)
REVERT: A  587 MET cc_start: 0.7837 (tpp) cc_final: 0.7098 (tpp)
REVERT: A  613 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6713 (mt-10)
REVERT: A  667 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7478 (tp)
REVERT: A  745 MET cc_start: 0.5881 (tpp) cc_final: 0.5620 (tpp)
REVERT: B  113 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7064 (tmtm)
  outliers start: 29
  outliers final: 25
  residues processed: 235
  average time/residue: 0.0818
  time to fit residues: 26.1832
Evaluate side-chains
  247 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 219
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  299 HIS
Chi-restraints excluded: chain A residue  310 GLN
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  379 GLN
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0770
   chunk 3 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 94 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 373 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.142769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.117221 restraints weight = 12006.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.121061 restraints weight = 6227.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.123650 restraints weight = 3869.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.125405 restraints weight = 2738.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.126634 restraints weight = 2128.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.4748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7606  Z= 0.132
  Angle     :  0.612   6.758  10350  Z= 0.306
  Chirality :  0.044   0.178   1216
  Planarity :  0.005   0.055   1315
  Dihedral  :  4.720  45.884   1020
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 22.26 %
    Favored  : 74.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.28), residues: 956
  helix:  1.53 (0.35), residues: 231
  sheet: -1.94 (0.42), residues: 151
  loop : -1.15 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 214 
 TYR   0.012   0.001   TYR A 534 
 PHE   0.024   0.001   PHE A 790 
 TRP   0.018   0.001   TRP A 602 
 HIS   0.007   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7591)
  covalent geometry    : angle       0.60623 (10320)
  SS BOND              : bond        0.00300 (   15)
  SS BOND              : angle       1.62284 (   30)
  hydrogen bonds       : bond        0.05414 (  198)
  hydrogen bonds       : angle       4.35944 (  573)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8210 (mmpt) cc_final: 0.7913 (mmpt)
REVERT: A   71 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7769 (pp30)
REVERT: A   84 GLU cc_start: 0.6351 (mt-10) cc_final: 0.5978 (mt-10)
REVERT: A  113 GLN cc_start: 0.7473 (tt0) cc_final: 0.7209 (tt0)
REVERT: A  307 SER cc_start: 0.8167 (p) cc_final: 0.7831 (p)
REVERT: A  309 VAL cc_start: 0.8476 (t) cc_final: 0.8153 (p)
REVERT: A  376 GLN cc_start: 0.7856 (mt0) cc_final: 0.7396 (mt0)
REVERT: A  468 TYR cc_start: 0.8424 (m-80) cc_final: 0.8120 (m-80)
REVERT: A  587 MET cc_start: 0.7834 (tpp) cc_final: 0.7099 (tpp)
REVERT: A  613 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6680 (mt-10)
REVERT: A  667 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7370 (tp)
REVERT: A  745 MET cc_start: 0.5814 (tpp) cc_final: 0.5573 (tpp)
REVERT: B  113 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7044 (tmtm)
  outliers start: 29
  outliers final: 23
  residues processed: 227
  average time/residue: 0.0854
  time to fit residues: 26.3529
Evaluate side-chains
  238 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 212
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  379 GLN
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 87 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 373 GLN
A 376 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN
B 108 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.142703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.117108 restraints weight = 11918.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.120976 restraints weight = 6127.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.123587 restraints weight = 3786.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.125362 restraints weight = 2654.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.126244 restraints weight = 2047.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.5040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7606  Z= 0.267
  Angle     :  0.730   7.589  10350  Z= 0.376
  Chirality :  0.049   0.167   1216
  Planarity :  0.006   0.076   1315
  Dihedral  :  5.523  46.047   1020
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 22.51 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.64 (0.26), residues: 956
  helix:  0.64 (0.34), residues: 249
  sheet: -1.99 (0.45), residues: 124
  loop : -1.73 (0.24), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 214 
 TYR   0.017   0.002   TYR A 534 
 PHE   0.028   0.002   PHE A 790 
 TRP   0.019   0.002   TRP A 159 
 HIS   0.010   0.002   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 7591)
  covalent geometry    : angle       0.72376 (10320)
  SS BOND              : bond        0.00602 (   15)
  SS BOND              : angle       1.95981 (   30)
  hydrogen bonds       : bond        0.08154 (  198)
  hydrogen bonds       : angle       4.94089 (  573)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 228
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8319 (mmpt) cc_final: 0.7968 (mmpt)
REVERT: A   84 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6059 (mt-10)
REVERT: A  113 GLN cc_start: 0.7587 (tt0) cc_final: 0.7296 (tt0)
REVERT: A  307 SER cc_start: 0.8176 (p) cc_final: 0.7706 (p)
REVERT: A  309 VAL cc_start: 0.8515 (t) cc_final: 0.8206 (p)
REVERT: A  376 GLN cc_start: 0.7930 (mt0) cc_final: 0.7432 (mt0)
REVERT: A  468 TYR cc_start: 0.8501 (m-80) cc_final: 0.8288 (m-80)
REVERT: A  598 ASP cc_start: 0.7849 (t0) cc_final: 0.6884 (t0)
REVERT: A  613 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6818 (mt-10)
REVERT: A  667 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7512 (tp)
REVERT: A  745 MET cc_start: 0.6095 (tpp) cc_final: 0.5847 (tpp)
REVERT: B   62 ILE cc_start: 0.8734 (tt) cc_final: 0.8436 (pt)
  outliers start: 30
  outliers final: 22
  residues processed: 239
  average time/residue: 0.0817
  time to fit residues: 26.7854
Evaluate side-chains
  245 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 222
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  299 HIS
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 29 optimal weight:    0.0570
   chunk 74 optimal weight:    0.4980
   chunk 57 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 94 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 55 optimal weight:    0.1980
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 373 GLN
A 714 ASN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.143393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.118177 restraints weight = 11881.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.121977 restraints weight = 6187.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.124545 restraints weight = 3868.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.126119 restraints weight = 2740.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.127356 restraints weight = 2155.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.5102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7606  Z= 0.120
  Angle     :  0.626   9.194  10350  Z= 0.311
  Chirality :  0.044   0.178   1216
  Planarity :  0.005   0.070   1315
  Dihedral  :  4.555  26.857   1016
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 23.60 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.27), residues: 956
  helix:  1.28 (0.35), residues: 236
  sheet: -1.99 (0.42), residues: 149
  loop : -1.31 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 214 
 TYR   0.010   0.001   TYR A 725 
 PHE   0.023   0.001   PHE A 790 
 TRP   0.020   0.001   TRP A 602 
 HIS   0.005   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7591)
  covalent geometry    : angle       0.62097 (10320)
  SS BOND              : bond        0.00235 (   15)
  SS BOND              : angle       1.52945 (   30)
  hydrogen bonds       : bond        0.04946 (  198)
  hydrogen bonds       : angle       4.30686 (  573)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 224
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8337 (mmpt) cc_final: 0.8070 (mmpt)
REVERT: A  180 GLN cc_start: 0.8470 (mt0) cc_final: 0.8208 (mt0)
REVERT: A  307 SER cc_start: 0.8231 (p) cc_final: 0.7945 (p)
REVERT: A  376 GLN cc_start: 0.7813 (mt0) cc_final: 0.7320 (mt0)
REVERT: A  468 TYR cc_start: 0.8355 (m-80) cc_final: 0.8079 (m-80)
REVERT: A  525 SER cc_start: 0.8651 (t) cc_final: 0.8175 (p)
REVERT: A  587 MET cc_start: 0.7810 (tpp) cc_final: 0.7056 (tpp)
REVERT: A  598 ASP cc_start: 0.7904 (t0) cc_final: 0.7095 (t0)
REVERT: A  613 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6656 (mt-10)
REVERT: A  667 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7335 (tp)
REVERT: A  745 MET cc_start: 0.5589 (tpp) cc_final: 0.5341 (tpp)
REVERT: C   55 MET cc_start: 0.4228 (ppp) cc_final: 0.3958 (ppp)
  outliers start: 19
  outliers final: 14
  residues processed: 233
  average time/residue: 0.0775
  time to fit residues: 25.0135
Evaluate side-chains
  233 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 218
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 82 optimal weight:    0.3980
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 373 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 108 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.146295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.120720 restraints weight = 11949.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.124623 restraints weight = 6135.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.127200 restraints weight = 3790.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.128944 restraints weight = 2670.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.130099 restraints weight = 2066.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.5195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7606  Z= 0.158
  Angle     :  0.651   9.494  10350  Z= 0.325
  Chirality :  0.044   0.169   1216
  Planarity :  0.005   0.068   1315
  Dihedral  :  4.674  25.880   1016
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.72 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.27), residues: 956
  helix:  1.01 (0.34), residues: 250
  sheet: -1.96 (0.42), residues: 148
  loop : -1.43 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 214 
 TYR   0.012   0.001   TYR A 534 
 PHE   0.029   0.002   PHE A 790 
 TRP   0.016   0.002   TRP A 602 
 HIS   0.010   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7591)
  covalent geometry    : angle       0.64576 (10320)
  SS BOND              : bond        0.00329 (   15)
  SS BOND              : angle       1.66009 (   30)
  hydrogen bonds       : bond        0.06021 (  198)
  hydrogen bonds       : angle       4.42644 (  573)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1602.66 seconds
wall clock time: 28 minutes 14.53 seconds (1694.53 seconds total)