Starting phenix.real_space_refine
on Fri Mar 14 00:34:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dw3_27750/03_2025/8dw3_27750.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dw3_27750/03_2025/8dw3_27750.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dw3_27750/03_2025/8dw3_27750.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dw3_27750/03_2025/8dw3_27750.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dw3_27750/03_2025/8dw3_27750.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dw3_27750/03_2025/8dw3_27750.cif"
  }
  resolution = 4.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    5897      2.51       5
     N    1564      2.21       5
     O    1857      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9351
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1140
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 3, 'TRANS': 151}
    Chain: "B"
      Number of atoms: 1521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1521
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 10, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1624
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201}
    Chain: "D"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1715
          Classifications: {'peptide': 228}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215}
    Chain: "H"
      Number of atoms: 1609
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 216, 1607
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 216, 1607
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1646
    Chain: "L"
      Number of atoms: 1703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1703
          Classifications: {'peptide': 219}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 6.84, per 1000 atoms: 0.73
  Number of scatterers: 9351
  At special positions: 0
  Unit cell: (82.062, 125.712, 174.6, 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      33     16.00
     O    1857      8.00
     N    1564      7.00
     C    5897      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  89 " distance=2.40
    Simple disulfide: pdb=" SG  CYS C 134 " - pdb=" SG  CYS C 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 154 " - pdb=" SG  CYS D 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG E   1 " - " ASN B 343 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.99
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2234

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 23 sheets defined
      15.3% alpha, 31.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 25
      removed outlier: 3.928A  pdb=" N   GLU A  20 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA A  24 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 49 through 58
      removed outlier: 4.283A  pdb=" N   LEU A  53 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 69
      removed outlier: 3.817A  pdb=" N   ASN A  69 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 91
      removed outlier: 3.930A  pdb=" N   LEU A  86 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 103
      removed outlier: 3.747A  pdb=" N   GLU A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 123
      removed outlier: 3.610A  pdb=" N   LEU A 119 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LEU A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 135
      removed outlier: 4.251A  pdb=" N   VAL A 129 " --> pdb=" O   HIS A 125 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLU A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN A 135 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 156
      removed outlier: 3.938A  pdb=" N   ILE A 152 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASN A 156 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 169
      removed outlier: 4.275A  pdb=" N   ALA A 162 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE A 164 " --> pdb=" O   ASP A 160 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 343
      removed outlier: 3.543A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.558A  pdb=" N   ALA B 352 " --> pdb=" O   SER B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 369
      removed outlier: 3.803A  pdb=" N   VAL B 367 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TYR B 369 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 408
      removed outlier: 3.789A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
      removed outlier: 3.869A  pdb=" N   TYR B 421 " --> pdb=" O   LYS B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
      removed outlier: 3.640A  pdb=" N   GLN B 506 " --> pdb=" O   VAL B 503 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 126
      removed outlier: 3.606A  pdb=" N   LEU C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.724A  pdb=" N   SER D  31 " --> pdb=" O   PRO D  28 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 28 through 32'
    Processing helix  chain 'D' and resid 170 through 172
      No H-bonds generated for 'chain 'D' and resid 170 through 172'
    Processing helix  chain 'D' and resid 199 through 203
      removed outlier: 3.715A  pdb=" N   SER D 202 " --> pdb=" O   PRO D 199 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.602A  pdb=" N   THR H  31 " --> pdb=" O   GLY H  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.947A  pdb=" N   GLN H  65 " --> pdb=" O   PRO H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 191 through 193
      No H-bonds generated for 'chain 'H' and resid 191 through 193'
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.989A  pdb=" N   VAL L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 127 through 134
    Processing helix  chain 'L' and resid 189 through 195
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356
      removed outlier: 3.761A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5
      removed outlier: 3.914A  pdb=" N   ARG C  24 " --> pdb=" O   THR C   5 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 39
    Processing sheet with id=AA6, first strand: chain 'C' and resid 34 through 39
    Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 50
    Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 118
    Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 150
    Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.498A  pdb=" N   GLU D  10 " --> pdb=" O   THR D 124 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLY D  33 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   ILE D  34 " --> pdb=" O   TRP D  50 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   TRP D  50 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   TRP D  36 " --> pdb=" O   MET D  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 138
    Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 138
    Processing sheet with id=AB5, first strand: chain 'D' and resid 165 through 168
      removed outlier: 4.150A  pdb=" N   TYR D 208 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 2 through 5
    Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.734A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.734A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL H 108 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 128
      removed outlier: 6.630A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL H 185 " --> pdb=" O   HIS H 168 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 155 through 158
      removed outlier: 4.121A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.570A  pdb=" N   THR L 108 " --> pdb=" O   TYR L  92 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 120 through 124
      removed outlier: 5.933A  pdb=" N   TYR L 179 " --> pdb=" O   ASN L 144 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 151 through 156

    336 hydrogen bonds defined for protein.
    864 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: 4.12

  Time building geometry restraints manager: 3.08 seconds

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

  Histogram of bond lengths:
        0.50 -     0.77: 1
        0.77 -     1.04: 0
        1.04 -     1.31: 1548
        1.31 -     1.58: 7967
        1.58 -     1.84: 46
  Bond restraints: 9562
  Sorted by residual:
  bond pdb=" CG  PRO D  28 "
       pdb=" CD  PRO D  28 "
    ideal  model  delta    sigma   weight residual
    1.503  0.505  0.998 3.40e-02 8.65e+02 8.62e+02
  bond pdb=" CG  PRO C 204 "
       pdb=" CD  PRO C 204 "
    ideal  model  delta    sigma   weight residual
    1.503  1.060  0.443 3.40e-02 8.65e+02 1.70e+02
  bond pdb=" N   PRO D  28 "
       pdb=" CD  PRO D  28 "
    ideal  model  delta    sigma   weight residual
    1.473  1.589 -0.116 1.40e-02 5.10e+03 6.84e+01
  bond pdb=" CB  PRO D  28 "
       pdb=" CG  PRO D  28 "
    ideal  model  delta    sigma   weight residual
    1.492  1.844 -0.352 5.00e-02 4.00e+02 4.95e+01
  bond pdb=" N   PRO C 204 "
       pdb=" CD  PRO C 204 "
    ideal  model  delta    sigma   weight residual
    1.473  1.569 -0.096 1.40e-02 5.10e+03 4.73e+01
  ... (remaining 9557 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.56: 12984
        7.56 -    15.11: 14
       15.11 -    22.67: 5
       22.67 -    30.23: 0
       30.23 -    37.79: 1
  Bond angle restraints: 13004
  Sorted by residual:
  angle pdb=" N   PRO D  28 "
        pdb=" CD  PRO D  28 "
        pdb=" CG  PRO D  28 "
      ideal   model   delta    sigma   weight residual
     103.20   65.41   37.79 1.50e+00 4.44e-01 6.35e+02
  angle pdb=" N   PRO C 204 "
        pdb=" CD  PRO C 204 "
        pdb=" CG  PRO C 204 "
      ideal   model   delta    sigma   weight residual
     103.20   81.48   21.72 1.50e+00 4.44e-01 2.10e+02
  angle pdb=" CA  PRO C 204 "
        pdb=" N   PRO C 204 "
        pdb=" CD  PRO C 204 "
      ideal   model   delta    sigma   weight residual
     112.00   94.26   17.74 1.40e+00 5.10e-01 1.61e+02
  angle pdb=" CA  PRO D  28 "
        pdb=" CB  PRO D  28 "
        pdb=" CG  PRO D  28 "
      ideal   model   delta    sigma   weight residual
     104.50   81.83   22.67 1.90e+00 2.77e-01 1.42e+02
  angle pdb=" CA  PRO C  81 "
        pdb=" N   PRO C  81 "
        pdb=" CD  PRO C  81 "
      ideal   model   delta    sigma   weight residual
     112.00   96.12   15.88 1.40e+00 5.10e-01 1.29e+02
  ... (remaining 12999 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.00: 5008
       21.00 -    42.01: 607
       42.01 -    63.01: 88
       63.01 -    84.01: 20
       84.01 -   105.02: 6
  Dihedral angle restraints: 5729
    sinusoidal: 2221
      harmonic: 3508
  Sorted by residual:
  dihedral pdb=" CB  CYS D 154 "
           pdb=" SG  CYS D 154 "
           pdb=" SG  CYS D 210 "
           pdb=" CB  CYS D 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.97   81.97     1      1.00e+01 1.00e-02 8.26e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   16.91   76.09     1      1.00e+01 1.00e-02 7.29e+01
  dihedral pdb=" CB  CYS C 134 "
           pdb=" SG  CYS C 134 "
           pdb=" SG  CYS C 194 "
           pdb=" CB  CYS C 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.05   75.05     1      1.00e+01 1.00e-02 7.12e+01
  ... (remaining 5726 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1453
       0.131 -    0.263: 12
       0.263 -    0.394: 2
       0.394 -    0.525: 0
       0.525 -    0.657: 1
  Chirality restraints: 1468
  Sorted by residual:
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-02 2.50e+03 1.77e+02
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 343 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.74   -0.66 2.00e-01 2.50e+01 1.08e+01
  chirality pdb=" CA  TRP D  50 "
            pdb=" N   TRP D  50 "
            pdb=" C   TRP D  50 "
            pdb=" CB  TRP D  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.08e+00
  ... (remaining 1465 not shown)

  Planarity restraints: 1671
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "   -0.081 2.00e-02 2.50e+03   6.71e-02 5.62e+01
        pdb=" C7  NAG E   1 "    0.020 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "   -0.061 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "    0.108 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 160 "    0.085 5.00e-02 4.00e+02   1.22e-01 2.39e+01
        pdb=" N   PRO D 161 "   -0.211 5.00e-02 4.00e+02
        pdb=" CA  PRO D 161 "    0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO D 161 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  50 "    0.034 2.00e-02 2.50e+03   3.08e-02 2.37e+01
        pdb=" CG  TRP D  50 "   -0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  50 "    0.039 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  50 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  50 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  50 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1668 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 233
        2.66 -     3.22: 8587
        3.22 -     3.78: 13725
        3.78 -     4.34: 17656
        4.34 -     4.90: 29133
  Nonbonded interactions: 69334
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 345 "
            pdb=" OG  SER D 109 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   ILE C 106 "
            pdb=" OH  TYR C 140 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O   SER C 121 "
            pdb=" NE2 GLN C 124 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" OG  SER B 383 "
            pdb=" OG  SER H 100 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG  SER D 202 "
            pdb=" OE1 GLN D 206 "
     model   vdw
     2.204 3.040
  ... (remaining 69329 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
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ 
 through 20 or resid 23 or resid 26 through 27 or resid 29 through 31 or resid 3 \ 
4 through 43 or resid 45 or resid 47 through 50 or resid 52 through 53 or resid  \ 
55 or resid 58 or resid 60 through 77 or resid 79 or resid 82 through 83 or resi \ 
d 85 through 91 or resid 94 or resid 97 through 99 or resid 101 through 213))
  selection = (chain 'L' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ 
 through 20 or resid 23 or resid 26 through 27 or resid 29 or resid 32 through 3 \ 
3 or resid 39 through 48 or resid 50 or resid 52 through 55 or resid 57 through  \ 
58 or resid 60 or resid 63 or resid 65 through 82 or resid 84 or resid 87 throug \ 
h 88 or resid 90 through 96 or resid 100 or resid 103 through 105 or resid 107 t \ 
hrough 219))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     29.030
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.090
  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:             0.020
  Load rotamer database and sin/cos tables:4.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
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      :  0.013   0.998   9562  Z= 0.914
  Angle     :  0.949  37.787  13004  Z= 0.526
  Chirality :  0.051   0.657   1468
  Planarity :  0.008   0.122   1670
  Dihedral  : 17.592 105.017   3459
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.71 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 37.69 %
    Favored  : 62.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.24), residues: 1209
  helix: -0.33 (0.49), residues: 104
  sheet:  0.37 (0.27), residues: 418
  loop : -1.29 (0.24), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.082   0.003   TRP D  50 
 HIS   0.005   0.001   HIS A  52 
 PHE   0.025   0.001   PHE L 145 
 TYR   0.041   0.001   TYR L 102 
 ARG   0.003   0.000   ARG L 148 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 205
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8274 (mp) cc_final: 0.7734 (tp)
REVERT: B  489 TYR cc_start: 0.6882 (m-80) cc_final: 0.6449 (m-80)
REVERT: C  117 ILE cc_start: 0.9102 (tt) cc_final: 0.8880 (tt)
REVERT: C  154 LEU cc_start: 0.9124 (tp) cc_final: 0.8874 (pt)
REVERT: D   48 MET cc_start: 0.6484 (mmm) cc_final: 0.6169 (tpp)
REVERT: D  138 LEU cc_start: 0.7749 (tp) cc_final: 0.7006 (mp)
REVERT: D  168 TRP cc_start: 0.7187 (m100) cc_final: 0.6603 (m100)
REVERT: D  210 CYS cc_start: 0.4075 (t) cc_final: 0.2355 (t)
REVERT: H  158 TRP cc_start: 0.7154 (m100) cc_final: 0.6662 (m100)
  outliers start: 1
  outliers final: 1
  residues processed: 205
  average time/residue: 0.2144
  time to fit residues: 60.3335
Evaluate side-chains
  128 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 90 optimal weight:   20.0000
   chunk 50 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0060
   chunk 60 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 36 optimal weight:    0.2980
   chunk 56 optimal weight:   40.0000
   chunk 69 optimal weight:    4.9990
   chunk 108 optimal weight:   10.0000
   overall best weight:    2.4400

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 450 ASN
C   6 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 206 GLN
D 218 ASN
H 204 HIS
H 208 ASN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 172 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.072636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.057341 restraints weight = 56120.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.058969 restraints weight = 33002.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.060046 restraints weight = 22196.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9562  Z= 0.244
  Angle     :  0.688   8.068  13004  Z= 0.348
  Chirality :  0.046   0.168   1468
  Planarity :  0.006   0.079   1670
  Dihedral  :  6.437  58.632   1372
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.96 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  5.04 %
    Favored  : 94.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.25), residues: 1209
  helix: -0.40 (0.46), residues: 119
  sheet:  0.46 (0.27), residues: 415
  loop : -1.26 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D  50 
 HIS   0.006   0.001   HIS H 168 
 PHE   0.021   0.002   PHE B 429 
 TYR   0.019   0.002   TYR L 102 
 ARG   0.010   0.001   ARG L  60 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 179
  time to evaluate  : 1.097 
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   53 LEU cc_start: 0.9466 (mp) cc_final: 0.9104 (tp)
REVERT: B  386 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8693 (mtmt)
REVERT: B  389 ASP cc_start: 0.8326 (t70) cc_final: 0.8038 (t0)
REVERT: B  406 GLU cc_start: 0.8427 (pm20) cc_final: 0.8171 (pm20)
REVERT: B  414 GLN cc_start: 0.7936 (tt0) cc_final: 0.7673 (tm-30)
REVERT: B  442 ASP cc_start: 0.8693 (m-30) cc_final: 0.8436 (m-30)
REVERT: B  489 TYR cc_start: 0.7332 (m-80) cc_final: 0.6773 (m-80)
REVERT: C  118 PHE cc_start: 0.8319 (m-80) cc_final: 0.7536 (m-80)
REVERT: D   30 THR cc_start: 0.9179 (p) cc_final: 0.8951 (t)
REVERT: D   46 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8506 (pm20)
REVERT: D   48 MET cc_start: 0.8869 (mmm) cc_final: 0.8288 (tpp)
REVERT: D   87 ARG cc_start: 0.8648 (mpp-170) cc_final: 0.8323 (mtt90)
REVERT: D   94 TYR cc_start: 0.8999 (m-10) cc_final: 0.8597 (m-80)
REVERT: D  108 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8125 (mp0)
REVERT: D  168 TRP cc_start: 0.7722 (m100) cc_final: 0.6871 (m100)
REVERT: D  210 CYS cc_start: 0.7811 (t) cc_final: 0.5172 (t)
REVERT: H  149 TYR cc_start: 0.5491 (p90) cc_final: 0.5251 (p90)
REVERT: H  158 TRP cc_start: 0.7457 (m100) cc_final: 0.7098 (m100)
REVERT: L  142 LEU cc_start: 0.8504 (tp) cc_final: 0.8291 (tp)
  outliers start: 4
  outliers final: 1
  residues processed: 183
  average time/residue: 0.1964
  time to fit residues: 51.2009
Evaluate side-chains
  109 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 17 optimal weight:   20.0000
   chunk 93 optimal weight:    0.6980
   chunk 114 optimal weight:    9.9990
   chunk 75 optimal weight:    8.9990
   chunk 2 optimal weight:    0.2980
   chunk 91 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0070
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.1800

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
H  39 GLN
H  82 GLN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.072735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.055897 restraints weight = 92151.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.058042 restraints weight = 45244.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.059492 restraints weight = 27661.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9562  Z= 0.169
  Angle     :  0.607   8.794  13004  Z= 0.303
  Chirality :  0.044   0.144   1468
  Planarity :  0.004   0.045   1670
  Dihedral  :  5.271  35.093   1372
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.13 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.78 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.25), residues: 1209
  helix:  0.01 (0.50), residues: 105
  sheet:  0.55 (0.27), residues: 407
  loop : -1.20 (0.24), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  50 
 HIS   0.003   0.001   HIS A 118 
 PHE   0.013   0.001   PHE B 429 
 TYR   0.020   0.001   TYR H  52 
 ARG   0.009   0.001   ARG L  60 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9470 (mp) cc_final: 0.9194 (pp)
REVERT: A   56 GLU cc_start: 0.9353 (tp30) cc_final: 0.8704 (pt0)
REVERT: B  386 LYS cc_start: 0.9028 (mtpp) cc_final: 0.8805 (mtmt)
REVERT: B  406 GLU cc_start: 0.8419 (pm20) cc_final: 0.8054 (pm20)
REVERT: B  414 GLN cc_start: 0.8793 (tt0) cc_final: 0.8176 (tt0)
REVERT: B  420 ASP cc_start: 0.9006 (t70) cc_final: 0.8775 (t0)
REVERT: B  442 ASP cc_start: 0.8741 (m-30) cc_final: 0.8454 (m-30)
REVERT: B  489 TYR cc_start: 0.7514 (m-80) cc_final: 0.6738 (m-80)
REVERT: C  118 PHE cc_start: 0.8332 (m-80) cc_final: 0.7399 (m-80)
REVERT: D   48 MET cc_start: 0.8924 (mmm) cc_final: 0.8676 (mmt)
REVERT: D   81 MET cc_start: 0.8994 (tmm) cc_final: 0.8636 (tmm)
REVERT: D  108 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8248 (mp0)
REVERT: D  168 TRP cc_start: 0.7747 (m100) cc_final: 0.6927 (m100)
REVERT: D  180 PHE cc_start: 0.8436 (m-80) cc_final: 0.8125 (m-10)
REVERT: D  210 CYS cc_start: 0.7918 (t) cc_final: 0.5247 (t)
REVERT: H  149 TYR cc_start: 0.5706 (p90) cc_final: 0.5350 (p90)
REVERT: H  158 TRP cc_start: 0.7497 (m100) cc_final: 0.7150 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 171
  average time/residue: 0.1974
  time to fit residues: 48.0573
Evaluate side-chains
  108 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0060
   chunk 25 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 94 optimal weight:    9.9990
   chunk 57 optimal weight:    0.0980
   chunk 63 optimal weight:   20.0000
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:   20.0000
   chunk 78 optimal weight:    0.0980
   overall best weight:    0.8398

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 155 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 206 GLN
D 218 ASN
L 130 GLN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.073159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.057298 restraints weight = 64702.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.059138 restraints weight = 35042.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.060378 restraints weight = 22695.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9562  Z= 0.157
  Angle     :  0.604   8.649  13004  Z= 0.299
  Chirality :  0.044   0.140   1468
  Planarity :  0.004   0.042   1670
  Dihedral  :  4.746  30.006   1372
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.79 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.20 %
    Favored  : 96.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.25), residues: 1209
  helix: -0.13 (0.50), residues: 105
  sheet:  0.57 (0.27), residues: 420
  loop : -1.17 (0.24), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 105 
 HIS   0.006   0.001   HIS A 118 
 PHE   0.016   0.001   PHE L  77 
 TYR   0.026   0.001   TYR H  32 
 ARG   0.004   0.000   ARG L  60 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 1.009 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9493 (mp) cc_final: 0.9053 (tp)
REVERT: B  386 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8819 (mtmt)
REVERT: B  390 LEU cc_start: 0.8585 (pp) cc_final: 0.8235 (pp)
REVERT: B  414 GLN cc_start: 0.8723 (tt0) cc_final: 0.8013 (tm-30)
REVERT: B  442 ASP cc_start: 0.8741 (m-30) cc_final: 0.8425 (m-30)
REVERT: B  489 TYR cc_start: 0.7331 (m-80) cc_final: 0.6709 (m-80)
REVERT: C  118 PHE cc_start: 0.8260 (m-80) cc_final: 0.7421 (m-80)
REVERT: D  108 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8319 (mp0)
REVERT: D  168 TRP cc_start: 0.7719 (m100) cc_final: 0.6908 (m100)
REVERT: D  180 PHE cc_start: 0.8532 (m-80) cc_final: 0.8129 (m-10)
REVERT: D  206 GLN cc_start: 0.4836 (OUTLIER) cc_final: 0.4526 (pp30)
REVERT: D  210 CYS cc_start: 0.7757 (t) cc_final: 0.4870 (t)
REVERT: H   83 TRP cc_start: 0.7523 (m100) cc_final: 0.6764 (m100)
REVERT: H  149 TYR cc_start: 0.5657 (p90) cc_final: 0.5421 (p90)
REVERT: H  158 TRP cc_start: 0.7509 (m100) cc_final: 0.7150 (m100)
  outliers start: 2
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2114
  time to fit residues: 49.1443
Evaluate side-chains
  107 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 29 optimal weight:   30.0000
   chunk 83 optimal weight:    0.0470
   chunk 26 optimal weight:    5.9990
   chunk 93 optimal weight:    7.9990
   chunk 66 optimal weight:    9.9990
   chunk 102 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0870
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:   30.0000
   chunk 46 optimal weight:    0.0070
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.9676

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.072985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.057165 restraints weight = 65408.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.058974 restraints weight = 35771.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.060188 restraints weight = 23247.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.3774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9562  Z= 0.158
  Angle     :  0.597   9.069  13004  Z= 0.294
  Chirality :  0.043   0.172   1468
  Planarity :  0.004   0.040   1670
  Dihedral  :  4.603  31.986   1372
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.87 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.25), residues: 1209
  helix: -0.06 (0.51), residues: 107
  sheet:  0.67 (0.27), residues: 408
  loop : -1.19 (0.24), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  33 
 HIS   0.003   0.001   HIS A 118 
 PHE   0.015   0.001   PHE B 377 
 TYR   0.020   0.001   TYR H  52 
 ARG   0.007   0.001   ARG B 509 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9458 (mp) cc_final: 0.9191 (pp)
REVERT: A   56 GLU cc_start: 0.9192 (tp30) cc_final: 0.8627 (pt0)
REVERT: B  386 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8770 (mtmt)
REVERT: B  390 LEU cc_start: 0.8706 (pp) cc_final: 0.8359 (pp)
REVERT: B  414 GLN cc_start: 0.8699 (tt0) cc_final: 0.8042 (tm-30)
REVERT: B  442 ASP cc_start: 0.8713 (m-30) cc_final: 0.8341 (m-30)
REVERT: B  489 TYR cc_start: 0.7529 (m-80) cc_final: 0.6697 (m-80)
REVERT: C  118 PHE cc_start: 0.8283 (m-80) cc_final: 0.7503 (m-80)
REVERT: D   81 MET cc_start: 0.8985 (tmm) cc_final: 0.8752 (tmm)
REVERT: D  108 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8390 (mp0)
REVERT: D  168 TRP cc_start: 0.7774 (m100) cc_final: 0.7097 (m100)
REVERT: D  180 PHE cc_start: 0.8534 (m-80) cc_final: 0.8202 (m-10)
REVERT: D  210 CYS cc_start: 0.7745 (t) cc_final: 0.4819 (t)
REVERT: H   29 PHE cc_start: 0.8887 (t80) cc_final: 0.7890 (t80)
REVERT: H   83 TRP cc_start: 0.7597 (m100) cc_final: 0.6765 (m100)
REVERT: H  149 TYR cc_start: 0.5627 (p90) cc_final: 0.5393 (p90)
REVERT: H  158 TRP cc_start: 0.7551 (m100) cc_final: 0.7190 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1751
  time to fit residues: 40.2050
Evaluate side-chains
  109 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 67 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   chunk 4 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0470
   chunk 36 optimal weight:    8.9990
   overall best weight:    1.8084

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.071530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.055527 restraints weight = 66832.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.057349 restraints weight = 36041.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.058549 restraints weight = 23326.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9562  Z= 0.171
  Angle     :  0.592  12.054  13004  Z= 0.291
  Chirality :  0.043   0.176   1468
  Planarity :  0.004   0.038   1670
  Dihedral  :  4.424  25.643   1372
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.29 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.25), residues: 1209
  helix:  0.04 (0.51), residues: 107
  sheet:  0.62 (0.26), residues: 421
  loop : -1.14 (0.24), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  33 
 HIS   0.003   0.001   HIS H 168 
 PHE   0.015   0.001   PHE B 377 
 TYR   0.020   0.001   TYR D  95 
 ARG   0.004   0.000   ARG C  24 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9468 (mp) cc_final: 0.9195 (pp)
REVERT: A   56 GLU cc_start: 0.9239 (tp30) cc_final: 0.8669 (pt0)
REVERT: A  102 ASN cc_start: 0.8841 (p0) cc_final: 0.8613 (p0)
REVERT: B  386 LYS cc_start: 0.9110 (mtpp) cc_final: 0.8703 (mtmt)
REVERT: B  390 LEU cc_start: 0.8564 (pp) cc_final: 0.8210 (pp)
REVERT: B  414 GLN cc_start: 0.8695 (tt0) cc_final: 0.8128 (tm-30)
REVERT: C  118 PHE cc_start: 0.8267 (m-80) cc_final: 0.7540 (m-80)
REVERT: D   32 TYR cc_start: 0.8518 (m-10) cc_final: 0.8262 (m-10)
REVERT: D   55 ASN cc_start: 0.9367 (p0) cc_final: 0.9135 (p0)
REVERT: D   73 ASP cc_start: 0.9087 (t0) cc_final: 0.8868 (t0)
REVERT: D   81 MET cc_start: 0.8988 (tmm) cc_final: 0.8732 (tmm)
REVERT: D  108 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8523 (mp0)
REVERT: D  168 TRP cc_start: 0.7785 (m100) cc_final: 0.6935 (m100)
REVERT: D  180 PHE cc_start: 0.8536 (m-80) cc_final: 0.8249 (m-10)
REVERT: D  210 CYS cc_start: 0.7501 (t) cc_final: 0.5256 (t)
REVERT: H   48 MET cc_start: 0.8857 (mpp) cc_final: 0.8567 (mpp)
REVERT: H   83 TRP cc_start: 0.7646 (m100) cc_final: 0.6785 (m100)
REVERT: H  149 TYR cc_start: 0.5591 (p90) cc_final: 0.5382 (p90)
REVERT: H  158 TRP cc_start: 0.7601 (m100) cc_final: 0.7253 (m100)
REVERT: L    9 ASP cc_start: 0.8946 (p0) cc_final: 0.8670 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1860
  time to fit residues: 42.2504
Evaluate side-chains
  112 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 86 optimal weight:    9.9990
   chunk 83 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 99 optimal weight:   10.0000
   chunk 111 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0070
   chunk 75 optimal weight:    0.3980
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.8804

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.069812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.054101 restraints weight = 68529.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.055869 restraints weight = 37125.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.057041 restraints weight = 24097.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9562  Z= 0.216
  Angle     :  0.611  11.459  13004  Z= 0.306
  Chirality :  0.043   0.161   1468
  Planarity :  0.004   0.078   1670
  Dihedral  :  4.776  33.986   1372
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.12 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.25), residues: 1209
  helix:  0.05 (0.51), residues: 107
  sheet:  0.65 (0.27), residues: 413
  loop : -1.14 (0.24), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  33 
 HIS   0.004   0.001   HIS H 168 
 PHE   0.022   0.001   PHE C  72 
 TYR   0.017   0.001   TYR H  52 
 ARG   0.006   0.001   ARG C  24 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9479 (mp) cc_final: 0.9203 (pp)
REVERT: A   56 GLU cc_start: 0.9227 (tp30) cc_final: 0.8672 (pt0)
REVERT: A  102 ASN cc_start: 0.8839 (p0) cc_final: 0.8625 (p0)
REVERT: B  386 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8924 (mtmt)
REVERT: B  390 LEU cc_start: 0.8595 (pp) cc_final: 0.8258 (pp)
REVERT: B  414 GLN cc_start: 0.8769 (tt0) cc_final: 0.8146 (tm-30)
REVERT: B  420 ASP cc_start: 0.9050 (t0) cc_final: 0.8818 (t0)
REVERT: C   50 TYR cc_start: 0.8403 (p90) cc_final: 0.8123 (p90)
REVERT: C  118 PHE cc_start: 0.8313 (m-80) cc_final: 0.7635 (m-80)
REVERT: D   73 ASP cc_start: 0.8999 (t0) cc_final: 0.8664 (t0)
REVERT: D   81 MET cc_start: 0.9008 (tmm) cc_final: 0.8735 (tmm)
REVERT: D  108 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8771 (mp0)
REVERT: D  168 TRP cc_start: 0.7704 (m100) cc_final: 0.7022 (m100)
REVERT: D  210 CYS cc_start: 0.7949 (t) cc_final: 0.5161 (t)
REVERT: H   83 TRP cc_start: 0.7883 (m100) cc_final: 0.7588 (m100)
REVERT: H  149 TYR cc_start: 0.5480 (p90) cc_final: 0.5250 (p90)
REVERT: H  158 TRP cc_start: 0.7676 (m100) cc_final: 0.7300 (m100)
REVERT: L    9 ASP cc_start: 0.8988 (p0) cc_final: 0.8710 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1911
  time to fit residues: 41.0773
Evaluate side-chains
  100 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 114 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   chunk 95 optimal weight:   20.0000
   chunk 104 optimal weight:    0.0060
   chunk 116 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 118 optimal weight:    8.9990
   chunk 107 optimal weight:   20.0000
   chunk 106 optimal weight:    8.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    3.0004

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.068817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.053758 restraints weight = 57606.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.055316 restraints weight = 33131.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.056353 restraints weight = 22240.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.4404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9562  Z= 0.224
  Angle     :  0.627  11.878  13004  Z= 0.315
  Chirality :  0.043   0.167   1468
  Planarity :  0.004   0.040   1670
  Dihedral  :  4.714  30.752   1372
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.96 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.25), residues: 1209
  helix: -0.16 (0.49), residues: 113
  sheet:  0.56 (0.26), residues: 424
  loop : -1.10 (0.25), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  33 
 HIS   0.005   0.001   HIS H 168 
 PHE   0.015   0.002   PHE C  72 
 TYR   0.022   0.002   TYR B 453 
 ARG   0.004   0.001   ARG B 466 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9481 (mp) cc_final: 0.9223 (pp)
REVERT: A   56 GLU cc_start: 0.9231 (tp30) cc_final: 0.8711 (pt0)
REVERT: B  386 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8886 (mtmt)
REVERT: B  390 LEU cc_start: 0.8567 (pp) cc_final: 0.8230 (pp)
REVERT: B  414 GLN cc_start: 0.8830 (tt0) cc_final: 0.8348 (tt0)
REVERT: B  420 ASP cc_start: 0.9063 (t0) cc_final: 0.8742 (t0)
REVERT: C  118 PHE cc_start: 0.8234 (m-80) cc_final: 0.7354 (m-80)
REVERT: D   81 MET cc_start: 0.9038 (tmm) cc_final: 0.8699 (tmm)
REVERT: D  108 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8851 (mp0)
REVERT: D  168 TRP cc_start: 0.7778 (m100) cc_final: 0.6978 (m100)
REVERT: D  210 CYS cc_start: 0.7996 (t) cc_final: 0.5351 (t)
REVERT: H    1 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7531 (tm-30)
REVERT: H   48 MET cc_start: 0.8841 (mpp) cc_final: 0.8586 (mpp)
REVERT: H   83 TRP cc_start: 0.7904 (m100) cc_final: 0.7658 (m100)
REVERT: H  149 TYR cc_start: 0.5390 (p90) cc_final: 0.5155 (p90)
REVERT: H  158 TRP cc_start: 0.7737 (m100) cc_final: 0.7390 (m100)
REVERT: L    9 ASP cc_start: 0.9034 (p0) cc_final: 0.8768 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1775
  time to fit residues: 37.6798
Evaluate side-chains
  102 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 95 optimal weight:   10.0000
   chunk 81 optimal weight:    0.8980
   chunk 90 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 63 optimal weight:   20.0000
   chunk 100 optimal weight:   30.0000
   chunk 96 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.066377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.051493 restraints weight = 58802.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.052997 restraints weight = 34325.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.053990 restraints weight = 23219.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.4687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9562  Z= 0.314
  Angle     :  0.674  12.240  13004  Z= 0.340
  Chirality :  0.045   0.237   1468
  Planarity :  0.004   0.040   1670
  Dihedral  :  5.090  29.729   1372
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.53 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.25), residues: 1209
  helix: -0.17 (0.49), residues: 113
  sheet:  0.35 (0.25), residues: 449
  loop : -1.17 (0.25), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 105 
 HIS   0.009   0.001   HIS H 168 
 PHE   0.023   0.002   PHE B 456 
 TYR   0.019   0.002   TYR D 190 
 ARG   0.004   0.001   ARG C  24 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9489 (mp) cc_final: 0.9235 (pp)
REVERT: A   56 GLU cc_start: 0.9259 (tp30) cc_final: 0.8691 (pt0)
REVERT: B  386 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8860 (mtmt)
REVERT: B  390 LEU cc_start: 0.8601 (pp) cc_final: 0.8260 (pp)
REVERT: B  414 GLN cc_start: 0.8854 (tt0) cc_final: 0.8454 (tt0)
REVERT: B  456 PHE cc_start: 0.6872 (t80) cc_final: 0.6541 (t80)
REVERT: C  165 GLU cc_start: 0.8812 (tp30) cc_final: 0.8400 (tp30)
REVERT: D    3 GLN cc_start: 0.8294 (tm-30) cc_final: 0.8092 (tm-30)
REVERT: D   81 MET cc_start: 0.8965 (tmm) cc_final: 0.8720 (tmm)
REVERT: D  108 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8923 (mp0)
REVERT: D  168 TRP cc_start: 0.7785 (m100) cc_final: 0.7045 (m100)
REVERT: D  210 CYS cc_start: 0.8077 (t) cc_final: 0.5583 (t)
REVERT: H   48 MET cc_start: 0.8786 (mpp) cc_final: 0.8537 (mpp)
REVERT: H   83 TRP cc_start: 0.8088 (m100) cc_final: 0.7852 (m100)
REVERT: H  149 TYR cc_start: 0.5303 (p90) cc_final: 0.5071 (p90)
REVERT: H  158 TRP cc_start: 0.7856 (m100) cc_final: 0.7515 (m100)
REVERT: L    9 ASP cc_start: 0.9082 (p0) cc_final: 0.8824 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1816
  time to fit residues: 33.4249
Evaluate side-chains
  91 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0270
   chunk 14 optimal weight:    5.9990
   chunk 102 optimal weight:    0.0470
   chunk 99 optimal weight:    7.9990
   chunk 56 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 98 optimal weight:   20.0000
   chunk 96 optimal weight:   10.0000
   overall best weight:    0.9740

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 116 ASN
H  39 GLN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.068864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.053219 restraints weight = 69206.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.054979 restraints weight = 37360.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.056146 restraints weight = 24314.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9562  Z= 0.163
  Angle     :  0.637  11.912  13004  Z= 0.313
  Chirality :  0.045   0.166   1468
  Planarity :  0.004   0.043   1670
  Dihedral  :  4.691  28.808   1372
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.45 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.25), residues: 1209
  helix: -0.08 (0.49), residues: 114
  sheet:  0.51 (0.26), residues: 438
  loop : -1.08 (0.25), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP H  47 
 HIS   0.003   0.001   HIS A  52 
 PHE   0.016   0.001   PHE L  77 
 TYR   0.023   0.001   TYR L 102 
 ARG   0.003   0.001   ARG D  98 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.023 
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   53 LEU cc_start: 0.9488 (mp) cc_final: 0.9242 (pp)
REVERT: A   56 GLU cc_start: 0.9222 (tp30) cc_final: 0.8707 (pt0)
REVERT: B  390 LEU cc_start: 0.8672 (pp) cc_final: 0.8335 (pp)
REVERT: B  414 GLN cc_start: 0.8764 (tt0) cc_final: 0.8376 (tt0)
REVERT: B  456 PHE cc_start: 0.6852 (t80) cc_final: 0.6450 (t80)
REVERT: C  165 GLU cc_start: 0.8713 (tp30) cc_final: 0.8307 (tp30)
REVERT: D   81 MET cc_start: 0.8980 (tmm) cc_final: 0.8700 (tmm)
REVERT: D  168 TRP cc_start: 0.7808 (m100) cc_final: 0.7035 (m100)
REVERT: D  210 CYS cc_start: 0.7728 (t) cc_final: 0.5122 (t)
REVERT: H   40 MET cc_start: 0.8790 (mmm) cc_final: 0.8472 (mmt)
REVERT: H  149 TYR cc_start: 0.5299 (p90) cc_final: 0.5097 (p90)
REVERT: H  158 TRP cc_start: 0.7799 (m100) cc_final: 0.7464 (m100)
REVERT: L    9 ASP cc_start: 0.9041 (p0) cc_final: 0.8781 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1757
  time to fit residues: 36.8460
Evaluate side-chains
  107 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 96 optimal weight:   20.0000
   chunk 8 optimal weight:    0.0060
   chunk 87 optimal weight:    0.0970
   chunk 68 optimal weight:    0.0040
   chunk 105 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 64 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0060
   chunk 81 optimal weight:    0.6980
   chunk 43 optimal weight:   10.0000
   overall best weight:    0.1622

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

Flipped N/Q/H residues before XYZ refinement:
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.069846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.053268 restraints weight = 92633.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.055366 restraints weight = 45058.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.056728 restraints weight = 27515.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9562  Z= 0.152
  Angle     :  0.629  11.632  13004  Z= 0.306
  Chirality :  0.044   0.160   1468
  Planarity :  0.004   0.042   1670
  Dihedral  :  4.479  27.290   1372
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.25), residues: 1209
  helix: -0.11 (0.49), residues: 114
  sheet:  0.62 (0.26), residues: 439
  loop : -1.05 (0.25), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP H  47 
 HIS   0.004   0.001   HIS A 118 
 PHE   0.012   0.001   PHE L 122 
 TYR   0.025   0.001   TYR B 380 
 ARG   0.003   0.000   ARG H  59 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3428.47 seconds
wall clock time: 60 minutes 14.18 seconds (3614.18 seconds total)