Starting phenix.real_space_refine
on Sat Dec 28 23:56:09 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dw3_27750/12_2024/8dw3_27750.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dw3_27750/12_2024/8dw3_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_27750/12_2024/8dw3_27750.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dw3_27750/12_2024/8dw3_27750.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dw3_27750/12_2024/8dw3_27750.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dw3_27750/12_2024/8dw3_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.61, per 1000 atoms: 0.71
  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: 2.76
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.30
  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: 3.05

  Time building geometry restraints manager: 3.07 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:             0.830
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.820
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.170
-------------------------------------------------------------------------------
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  : 1.042 
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: 0.2253
  time to fit residues: 63.0283
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  : 1.113 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
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  : 1.110 
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: B  389 ASP cc_start: 0.7529 (t70) cc_final: 0.7324 (t0)
REVERT: B  460 ASN cc_start: 0.8737 (t0) cc_final: 0.8531 (m-40)
REVERT: C  118 PHE cc_start: 0.7178 (m-80) cc_final: 0.6588 (m-80)
REVERT: D   30 THR cc_start: 0.8140 (p) cc_final: 0.7886 (t)
REVERT: D   48 MET cc_start: 0.6644 (mmm) cc_final: 0.5517 (tpp)
REVERT: D   70 MET cc_start: 0.7853 (mtp) cc_final: 0.7539 (mtm)
REVERT: D  168 TRP cc_start: 0.7388 (m100) cc_final: 0.6656 (m100)
REVERT: D  210 CYS cc_start: 0.4003 (t) cc_final: 0.2281 (t)
REVERT: H  158 TRP cc_start: 0.7028 (m100) cc_final: 0.6808 (m100)
  outliers start: 4
  outliers final: 1
  residues processed: 183
  average time/residue: 0.2031
  time to fit residues: 52.3845
Evaluate side-chains
  105 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 89 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 108 optimal weight:    5.9990
   chunk 116 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 107 optimal weight:    7.9990
   chunk 36 optimal weight:    0.6980
   chunk 86 optimal weight:    8.9990
   overall best weight:    3.3388

-------------------------------------------------------------------------------
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**
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
H  39 GLN
H  82 GLN
L 130 GLN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9562  Z= 0.251
  Angle     :  0.633   9.160  13004  Z= 0.320
  Chirality :  0.044   0.139   1468
  Planarity :  0.005   0.049   1670
  Dihedral  :  5.406  32.406   1372
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.53 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.46 %
    Favored  : 95.25 %
  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: -0.83 (0.25), residues: 1209
  helix: -0.23 (0.48), residues: 113
  sheet:  0.37 (0.26), residues: 419
  loop : -1.24 (0.24), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  50 
 HIS   0.005   0.001   HIS H 168 
 PHE   0.014   0.002   PHE B 429 
 TYR   0.019   0.002   TYR H 149 
 ARG   0.007   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
  158 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 155
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.8804 (pp20) cc_final: 0.8396 (pm20)
REVERT: B  414 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: C  118 PHE cc_start: 0.7310 (m-80) cc_final: 0.6709 (m-80)
REVERT: D   48 MET cc_start: 0.6362 (mmm) cc_final: 0.5983 (mmt)
REVERT: D  168 TRP cc_start: 0.7410 (m100) cc_final: 0.6706 (m100)
REVERT: D  210 CYS cc_start: 0.4309 (t) cc_final: 0.2697 (t)
  outliers start: 3
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2045
  time to fit residues: 46.0859
Evaluate side-chains
  99 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    5.9990
   chunk 81 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 51 optimal weight:   30.0000
   chunk 72 optimal weight:   20.0000
   chunk 108 optimal weight:    3.9990
   chunk 115 optimal weight:   10.0000
   chunk 102 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 95 optimal weight:    9.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081   9562  Z= 0.415
  Angle     :  0.774   9.883  13004  Z= 0.394
  Chirality :  0.047   0.239   1468
  Planarity :  0.005   0.049   1670
  Dihedral  :  5.868  35.703   1372
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 19.62
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.68 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  5.14 %
    Favored  : 94.77 %
  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: -1.24 (0.24), residues: 1209
  helix: -0.44 (0.45), residues: 118
  sheet:  0.02 (0.25), residues: 428
  loop : -1.49 (0.24), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  36 
 HIS   0.012   0.002   HIS H 168 
 PHE   0.024   0.003   PHE C  98 
 TYR   0.034   0.003   TYR H  32 
 ARG   0.005   0.001   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
  123 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8307 (p0) cc_final: 0.8036 (p0)
REVERT: B  386 LYS cc_start: 0.8171 (ptpt) cc_final: 0.7819 (pttt)
REVERT: B  390 LEU cc_start: 0.8092 (pp) cc_final: 0.7697 (pp)
REVERT: B  414 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7823 (tm-30)
REVERT: B  456 PHE cc_start: 0.6719 (t80) cc_final: 0.6461 (t80)
REVERT: D   48 MET cc_start: 0.6633 (mmm) cc_final: 0.5761 (tpp)
REVERT: D   94 TYR cc_start: 0.7694 (m-80) cc_final: 0.7487 (m-80)
REVERT: D  168 TRP cc_start: 0.7551 (m100) cc_final: 0.6516 (m100)
REVERT: D  210 CYS cc_start: 0.4716 (t) cc_final: 0.3871 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1977
  time to fit residues: 35.1800
Evaluate side-chains
  79 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9990
   chunk 47 optimal weight:    7.9990
   chunk 98 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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**
B 422 ASN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 116 ASN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.4442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9562  Z= 0.236
  Angle     :  0.647   9.938  13004  Z= 0.324
  Chirality :  0.045   0.213   1468
  Planarity :  0.004   0.044   1670
  Dihedral  :  5.388  32.644   1372
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.53 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.20 %
    Favored  : 96.71 %
  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: -1.02 (0.25), residues: 1209
  helix: -0.32 (0.46), residues: 119
  sheet:  0.10 (0.26), residues: 425
  loop : -1.28 (0.25), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H  33 
 HIS   0.005   0.001   HIS H 168 
 PHE   0.014   0.002   PHE B 456 
 TYR   0.024   0.002   TYR H 180 
 ARG   0.004   0.001   ARG C  24 

*********************** 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
  130 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8206 (p0) cc_final: 0.7792 (p0)
REVERT: B  386 LYS cc_start: 0.8316 (ptpt) cc_final: 0.8052 (pttt)
REVERT: B  390 LEU cc_start: 0.8024 (pp) cc_final: 0.7654 (pp)
REVERT: B  414 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: D  168 TRP cc_start: 0.7568 (m100) cc_final: 0.6630 (m100)
REVERT: D  210 CYS cc_start: 0.4642 (t) cc_final: 0.3694 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2068
  time to fit residues: 38.0775
Evaluate side-chains
  89 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 67 optimal weight:   20.0000
   chunk 28 optimal weight:    9.9990
   chunk 115 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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**
D 116 ASN
D 206 GLN
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
L 153 GLN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.4650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9562  Z= 0.271
  Angle     :  0.652  10.405  13004  Z= 0.327
  Chirality :  0.045   0.177   1468
  Planarity :  0.004   0.043   1670
  Dihedral  :  5.193  26.497   1372
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.44 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.81 %
    Favored  : 97.09 %
  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: -1.07 (0.24), residues: 1209
  helix: -0.28 (0.46), residues: 121
  sheet:  0.16 (0.26), residues: 413
  loop : -1.38 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  33 
 HIS   0.006   0.001   HIS H 168 
 PHE   0.021   0.002   PHE D 114 
 TYR   0.026   0.002   TYR H 180 
 ARG   0.004   0.001   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
  122 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8360 (p0) cc_final: 0.7905 (p0)
REVERT: B  386 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8141 (pttt)
REVERT: B  390 LEU cc_start: 0.8079 (pp) cc_final: 0.7695 (pp)
REVERT: B  414 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: D  168 TRP cc_start: 0.7603 (m100) cc_final: 0.6647 (m100)
REVERT: D  210 CYS cc_start: 0.4708 (t) cc_final: 0.3712 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.2122
  time to fit residues: 37.4593
Evaluate side-chains
  85 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 84 optimal weight:    8.9990
   chunk 96 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 114 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0670
   chunk 52 optimal weight:    8.9990
   chunk 70 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    6.2126

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.5061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   9562  Z= 0.393
  Angle     :  0.755  14.890  13004  Z= 0.382
  Chirality :  0.046   0.176   1468
  Planarity :  0.005   0.054   1670
  Dihedral  :  5.980  41.086   1372
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 18.92
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.11 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  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: -1.36 (0.24), residues: 1209
  helix: -0.59 (0.43), residues: 127
  sheet: -0.18 (0.25), residues: 422
  loop : -1.47 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  50 
 HIS   0.010   0.002   HIS H 168 
 PHE   0.019   0.003   PHE H 170 
 TYR   0.032   0.002   TYR H 180 
 ARG   0.005   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
  112 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8352 (p0) cc_final: 0.7932 (p0)
REVERT: B  390 LEU cc_start: 0.8048 (pp) cc_final: 0.7643 (pp)
REVERT: B  414 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7822 (tm-30)
REVERT: D  168 TRP cc_start: 0.7627 (m100) cc_final: 0.6657 (m100)
REVERT: D  210 CYS cc_start: 0.4903 (t) cc_final: 0.4266 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1945
  time to fit residues: 32.1185
Evaluate side-chains
  76 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    0.3980
   chunk 72 optimal weight:    8.9990
   chunk 78 optimal weight:    7.9990
   chunk 56 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 90 optimal weight:    7.9990
   chunk 104 optimal weight:    7.9990
   chunk 109 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    3.2788

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9562  Z= 0.249
  Angle     :  0.673  13.976  13004  Z= 0.336
  Chirality :  0.045   0.156   1468
  Planarity :  0.004   0.040   1670
  Dihedral  :  5.448  33.024   1372
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.03 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  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: -1.19 (0.24), residues: 1209
  helix: -0.24 (0.46), residues: 119
  sheet: -0.15 (0.25), residues: 431
  loop : -1.33 (0.25), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  50 
 HIS   0.005   0.001   HIS H 168 
 PHE   0.017   0.002   PHE C  72 
 TYR   0.029   0.002   TYR L 102 
 ARG   0.004   0.001   ARG C  24 

*********************** 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
  122 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8281 (p0) cc_final: 0.7826 (p0)
REVERT: B  386 LYS cc_start: 0.8333 (ptpt) cc_final: 0.8064 (pttt)
REVERT: B  414 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7746 (tm-30)
REVERT: D  168 TRP cc_start: 0.7580 (m100) cc_final: 0.6763 (m100)
REVERT: D  210 CYS cc_start: 0.4777 (t) cc_final: 0.3960 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1953
  time to fit residues: 34.9190
Evaluate side-chains
  84 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 109 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 46 optimal weight:    0.1980
   chunk 83 optimal weight:    0.0370
   chunk 32 optimal weight:    7.9990
   chunk 96 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 70 optimal weight:   20.0000
   chunk 113 optimal weight:    4.9990
   chunk 68 optimal weight:    8.9990
   overall best weight:    3.0464

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 214 HIS
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.5217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9562  Z= 0.237
  Angle     :  0.667  14.111  13004  Z= 0.332
  Chirality :  0.045   0.154   1468
  Planarity :  0.004   0.040   1670
  Dihedral  :  5.214  31.080   1372
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.36 %
    Favored  : 92.56 %
  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 : 0.09 %

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: -1.10 (0.24), residues: 1209
  helix: -0.23 (0.46), residues: 119
  sheet: -0.03 (0.25), residues: 428
  loop : -1.30 (0.25), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D 105 
 HIS   0.005   0.001   HIS A 118 
 PHE   0.015   0.002   PHE C  72 
 TYR   0.023   0.002   TYR L 102 
 ARG   0.003   0.001   ARG H  38 

*********************** 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
  115 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8293 (p0) cc_final: 0.7812 (p0)
REVERT: B  386 LYS cc_start: 0.8328 (ptpt) cc_final: 0.7966 (ptpt)
REVERT: B  390 LEU cc_start: 0.8150 (pp) cc_final: 0.7896 (pp)
REVERT: B  414 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7699 (tm-30)
REVERT: D  168 TRP cc_start: 0.7496 (m100) cc_final: 0.6747 (m100)
REVERT: D  210 CYS cc_start: 0.4853 (t) cc_final: 0.3927 (t)
REVERT: H   40 MET cc_start: 0.7717 (mmm) cc_final: 0.7461 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1894
  time to fit residues: 32.3420
Evaluate side-chains
  82 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 118 optimal weight:    2.9990
   chunk 109 optimal weight:    8.9990
   chunk 94 optimal weight:    0.2980
   chunk 9 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 100 optimal weight:    8.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    3.8588

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

Flipped N/Q/H residues before XYZ refinement:
D 206 GLN
D 218 ASN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.5346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9562  Z= 0.271
  Angle     :  0.676  14.028  13004  Z= 0.338
  Chirality :  0.045   0.140   1468
  Planarity :  0.004   0.040   1670
  Dihedral  :  5.213  30.009   1372
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.61 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.48 %
    Favored  : 99.42 %
  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: -1.11 (0.24), residues: 1209
  helix: -0.10 (0.47), residues: 113
  sheet: -0.09 (0.25), residues: 428
  loop : -1.29 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 105 
 HIS   0.006   0.001   HIS A 118 
 PHE   0.017   0.002   PHE C  72 
 TYR   0.020   0.002   TYR H 180 
 ARG   0.002   0.000   ARG L 217 

********************** 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
  112 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8332 (p0) cc_final: 0.7904 (p0)
REVERT: B  386 LYS cc_start: 0.8313 (ptpt) cc_final: 0.7741 (ptpt)
REVERT: B  390 LEU cc_start: 0.8118 (pp) cc_final: 0.7847 (pp)
REVERT: B  414 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7697 (tm-30)
REVERT: D  168 TRP cc_start: 0.7554 (m100) cc_final: 0.6799 (m100)
REVERT: D  210 CYS cc_start: 0.4901 (t) cc_final: 0.3899 (t)
REVERT: H   40 MET cc_start: 0.7688 (mmm) cc_final: 0.7429 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1961
  time to fit residues: 32.3291
Evaluate side-chains
  82 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 26 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 97 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0870
   chunk 5 optimal weight:   20.0000
   chunk 68 optimal weight:   30.0000
   overall best weight:    1.7162

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
** 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 = 0.3460 r_free = 0.3460 target = 0.066685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.051695 restraints weight = 66829.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.053305 restraints weight = 36871.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.054405 restraints weight = 24202.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    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 = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.5370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9562  Z= 0.179
  Angle     :  0.663  13.597  13004  Z= 0.324
  Chirality :  0.045   0.257   1468
  Planarity :  0.004   0.042   1670
  Dihedral  :  5.203  35.273   1372
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.62 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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: -0.95 (0.25), residues: 1209
  helix:  0.27 (0.50), residues: 107
  sheet: -0.04 (0.25), residues: 439
  loop : -1.20 (0.25), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H  33 
 HIS   0.006   0.001   HIS A 118 
 PHE   0.014   0.001   PHE C  72 
 TYR   0.017   0.001   TYR H 180 
 ARG   0.003   0.001   ARG B 346 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1980.84 seconds
wall clock time: 37 minutes 22.80 seconds (2242.80 seconds total)