Starting phenix.real_space_refine
on Thu Mar 13 06:20:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y1r_33571/03_2025/7y1r_33571.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y1r_33571/03_2025/7y1r_33571.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y1r_33571/03_2025/7y1r_33571.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y1r_33571/03_2025/7y1r_33571.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y1r_33571/03_2025/7y1r_33571.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y1r_33571/03_2025/7y1r_33571.cif"
  }
  resolution = 4.01
  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=   0.001 sd=   0.025
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      55      5.16       5
     C    5432      2.51       5
     N    1469      2.21       5
     O    1609      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-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8565
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 2474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2474
          Classifications: {'peptide': 305}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 283}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2494
          Classifications: {'peptide': 308}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 286}
          Chain breaks: 3
    Chain: "E"
      Number of atoms: 3332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3332
          Classifications: {'peptide': 428}
          Link IDs: {'PTRANS': 23, 'TRANS': 404}
          Chain breaks: 2
    Chain: "L"
      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
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      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
    Chain: "G"
      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
    Chain: "H"
      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
    Chain: "I"
      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
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.99, per 1000 atoms: 0.58
  Number of scatterers: 8565
  At special positions: 0
  Unit cell: (98.115, 99.17, 132.93, 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      55     16.00
     O    1609      8.00
     N    1469      7.00
     C    5432      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS E 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 194 " - pdb=" SG  CYS B 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 256 " - pdb=" SG  CYS A 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 264 " - pdb=" SG  CYS A 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 293 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 297 " - pdb=" SG  CYS A 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS B 326 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS E 345 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 256 " - pdb=" SG  CYS B 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 264 " - pdb=" SG  CYS B 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 293 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 297 " - pdb=" SG  CYS B 360 " 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=0, symmetry=0
  Links applied
    BETA1-3
      " NAG D   1 " - " NAG D   2 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG L   1 " - " NAG L   2 "
      " NAG L   2 " - " BMA L   3 "
    NAG-ASN
      " NAG B 401 " - " ASN B  53 "
      " NAG C   1 " - " ASN A  53 "
      " NAG D   1 " - " ASN B 107 "
      " NAG F   1 " - " ASN E  56 "
      " NAG G   1 " - " ASN E 137 "
      " NAG H   1 " - " ASN E 390 "
      " NAG I   1 " - " ASN E 214 "
      " NAG L   1 " - " ASN A 107 "
  Time building additional restraints: 2.27
  Conformation dependent library (CDL) restraints added in 918.2 milliseconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1986

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 19 sheets defined
      16.8% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 29
    Processing helix  chain 'A' and resid 45 through 57
      removed outlier: 3.687A  pdb=" N   ASP A  57 " --> pdb=" O   ASN A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 95
      removed outlier: 3.518A  pdb=" N   TYR A  92 " --> pdb=" O   ASN A  89 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASP A  93 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 115
    Processing helix  chain 'A' and resid 170 through 174
      removed outlier: 3.908A  pdb=" N   GLY A 173 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 259
      removed outlier: 4.394A  pdb=" N   CYS A 256 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER A 259 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.507A  pdb=" N   ALA A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 323
    Processing helix  chain 'B' and resid 5 through 28
      removed outlier: 4.101A  pdb=" N   MET B   9 " --> pdb=" O   LYS B   5 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU B  10 " --> pdb=" O   THR B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 57
      removed outlier: 3.714A  pdb=" N   ASP B  57 " --> pdb=" O   ASN B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 95
      removed outlier: 4.183A  pdb=" N   LYS B  94 " --> pdb=" O   GLU B  90 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   PHE B  95 " --> pdb=" O   ILE B  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 90 through 95'
    Processing helix  chain 'B' and resid 108 through 115
    Processing helix  chain 'B' and resid 171 through 181
    Processing helix  chain 'B' and resid 235 through 239
    Processing helix  chain 'B' and resid 308 through 318
      removed outlier: 4.264A  pdb=" N   ALA B 312 " --> pdb=" O   SER B 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 81 through 86
      removed outlier: 3.751A  pdb=" N   GLN E  84 " --> pdb=" O   GLY E  81 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   GLU E  85 " --> pdb=" O   ALA E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 127 through 135
    Processing helix  chain 'E' and resid 326 through 332
      removed outlier: 3.885A  pdb=" N   LEU E 330 " --> pdb=" O   PRO E 326 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78
      removed outlier: 4.180A  pdb=" N   LYS A  77 " --> pdb=" O   GLN B 349 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LYS B 344 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   VAL B 341 " --> pdb=" O   LYS B 344 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LYS B 346 " --> pdb=" O   TYR B 339 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   TYR B 339 " --> pdb=" O   LYS B 346 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ASN B 352 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   GLU B 333 " --> pdb=" O   ASN B 352 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82
      removed outlier: 3.579A  pdb=" N   MET A 232 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ARG A 123 " --> pdb=" O   MET A 232 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 143
      removed outlier: 4.557A  pdb=" N   SER A 154 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   GLN A 143 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   TYR A 152 " --> pdb=" O   GLN A 143 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267
      removed outlier: 4.297A  pdb=" N   CYS A 265 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   PHE A 292 " --> pdb=" O   ARG A 267 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 272
      removed outlier: 3.627A  pdb=" N   ILE A 271 " --> pdb=" O   TYR A 288 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR A 288 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 338
      removed outlier: 8.038A  pdb=" N   CYS A 327 " --> pdb=" O   CYS A 358 " (cutoff:3.500A)
      removed outlier: 8.447A  pdb=" N   CYS A 358 " --> pdb=" O   CYS A 327 " (cutoff:3.500A)
      removed outlier: 8.286A  pdb=" N   ARG A 356 " --> pdb=" O   PRO A 329 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ALA A 331 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ILE A 354 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   GLU A 333 " --> pdb=" O   ASN A 352 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASN A 352 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 78 through 81
      removed outlier: 3.642A  pdb=" N   LEU B 231 " --> pdb=" O   THR B  80 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU B 128 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU B 167 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107
      removed outlier: 4.038A  pdb=" N   PHE B 106 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   GLU B 186 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 267
      removed outlier: 3.906A  pdb=" N   CYS B 265 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU B 294 " --> pdb=" O   CYS B 265 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG B 267 " --> pdb=" O   PHE B 292 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   PHE B 292 " --> pdb=" O   ARG B 267 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 271 through 272
      removed outlier: 3.835A  pdb=" N   ILE B 271 " --> pdb=" O   TYR B 288 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TYR B 288 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 328 through 329
      removed outlier: 3.905A  pdb=" N   VAL B 328 " --> pdb=" O   LYS B 359 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 46 through 47
      removed outlier: 6.494A  pdb=" N   LEU E  46 " --> pdb=" O   HIS E  71 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'E' and resid 93 through 94
      removed outlier: 6.992A  pdb=" N   VAL E 144 " --> pdb=" O   ASP E 169 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 153 through 154
      removed outlier: 3.862A  pdb=" N   LEU E 154 " --> pdb=" O   GLU E 177 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'E' and resid 189 through 192
      removed outlier: 6.698A  pdb=" N   ARG E 190 " --> pdb=" O   VAL E 212 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   LEU E 237 " --> pdb=" O   LEU E 260 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 202
      removed outlier: 4.176A  pdb=" N   ILE E 202 " --> pdb=" O   TRP E 222 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'E' and resid 349 through 350
      removed outlier: 7.387A  pdb=" N   LEU E 349 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'E' and resid 364 through 366
      removed outlier: 3.519A  pdb=" N   SER E 392 " --> pdb=" O   LEU E 365 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   ASP E 414 " --> pdb=" O   PHE E 389 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU E 391 " --> pdb=" O   ASP E 414 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER E 450 " --> pdb=" O   LEU E 413 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   MET E 415 " --> pdb=" O   SER E 450 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 471 through 473
      removed outlier: 6.279A  pdb=" N   LEU E 472 " --> pdb=" O   SER E 499 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1

    130 hydrogen bonds defined for protein.
    351 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.95

  Time building geometry restraints manager: 2.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2757
        1.35 -     1.46: 2003
        1.46 -     1.58: 3917
        1.58 -     1.70: 0
        1.70 -     1.82: 77
  Bond restraints: 8754
  Sorted by residual:
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.482 -0.076 2.00e-02 2.50e+03 1.43e+01
  bond pdb=" C1  NAG B 401 "
       pdb=" O5  NAG B 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.45e+00
  bond pdb=" C1  BMA F   3 "
       pdb=" C2  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.550 -0.031 2.00e-02 2.50e+03 2.41e+00
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.36e+00
  bond pdb=" C1  BMA G   3 "
       pdb=" C2  BMA G   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.549 -0.030 2.00e-02 2.50e+03 2.31e+00
  ... (remaining 8749 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 11381
        1.50 -     2.99: 358
        2.99 -     4.49: 80
        4.49 -     5.99: 43
        5.99 -     7.48: 12
  Bond angle restraints: 11874
  Sorted by residual:
  angle pdb=" C   LYS A 280 "
        pdb=" N   TRP A 281 "
        pdb=" CA  TRP A 281 "
      ideal   model   delta    sigma   weight residual
     121.58  115.05    6.53 1.95e+00 2.63e-01 1.12e+01
  angle pdb=" CA  ARG A  29 "
        pdb=" CB  ARG A  29 "
        pdb=" CG  ARG A  29 "
      ideal   model   delta    sigma   weight residual
     114.10  119.80   -5.70 2.00e+00 2.50e-01 8.11e+00
  angle pdb=" CA  MET E 443 "
        pdb=" CB  MET E 443 "
        pdb=" CG  MET E 443 "
      ideal   model   delta    sigma   weight residual
     114.10  119.43   -5.33 2.00e+00 2.50e-01 7.11e+00
  angle pdb=" CA  TRP A 281 "
        pdb=" CB  TRP A 281 "
        pdb=" CG  TRP A 281 "
      ideal   model   delta    sigma   weight residual
     113.60  118.60   -5.00 1.90e+00 2.77e-01 6.92e+00
  angle pdb=" CB  LYS B  15 "
        pdb=" CG  LYS B  15 "
        pdb=" CD  LYS B  15 "
      ideal   model   delta    sigma   weight residual
     111.30  117.18   -5.88 2.30e+00 1.89e-01 6.54e+00
  ... (remaining 11869 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.59: 5162
       22.59 -    45.17: 352
       45.17 -    67.76: 26
       67.76 -    90.34: 54
       90.34 -   112.93: 23
  Dihedral angle restraints: 5617
    sinusoidal: 2562
      harmonic: 3055
  Sorted by residual:
  dihedral pdb=" CB  CYS A   4 "
           pdb=" SG  CYS A   4 "
           pdb=" SG  CYS E 201 "
           pdb=" CB  CYS E 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.78  -84.78     1      1.00e+01 1.00e-02 8.73e+01
  dihedral pdb=" CB  CYS A 264 "
           pdb=" SG  CYS A 264 "
           pdb=" SG  CYS A 327 "
           pdb=" CB  CYS A 327 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  170.99  -77.99     1      1.00e+01 1.00e-02 7.60e+01
  dihedral pdb=" CB  CYS B 293 "
           pdb=" SG  CYS B 293 "
           pdb=" SG  CYS B 358 "
           pdb=" CB  CYS B 358 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.93  -60.93     1      1.00e+01 1.00e-02 4.94e+01
  ... (remaining 5614 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1161
       0.054 -    0.109: 195
       0.109 -    0.163: 20
       0.163 -    0.217: 2
       0.217 -    0.272: 6
  Chirality restraints: 1384
  Sorted by residual:
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" C5  BMA I   3 "
            pdb=" C4  BMA I   3 "
            pdb=" C6  BMA I   3 "
            pdb=" O5  BMA I   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" C5  BMA H   3 "
            pdb=" C4  BMA H   3 "
            pdb=" C6  BMA H   3 "
            pdb=" O5  BMA H   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.84e+00
  ... (remaining 1381 not shown)

  Planarity restraints: 1505
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 159 "   -0.064 5.00e-02 4.00e+02   9.88e-02 1.56e+01
        pdb=" N   PRO B 160 "    0.171 5.00e-02 4.00e+02
        pdb=" CA  PRO B 160 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 160 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 281 "   -0.020 2.00e-02 2.50e+03   1.93e-02 9.31e+00
        pdb=" CG  TRP A 281 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 281 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 281 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 281 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 281 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 281 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 281 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 281 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 281 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 279 "   -0.016 2.00e-02 2.50e+03   1.27e-02 4.03e+00
        pdb=" CG  TRP A 279 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 279 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 279 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 279 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 279 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 279 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 279 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 279 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 279 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1502 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1126
        2.76 -     3.30: 7937
        3.30 -     3.83: 13107
        3.83 -     4.37: 14297
        4.37 -     4.90: 24519
  Nonbonded interactions: 60986
  Sorted by model distance:
  nonbonded pdb=" OG  SER E 100 "
            pdb=" OE1 GLU E 101 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   ALA B  76 "
            pdb=" OG1 THR B 234 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OE1 GLU B 125 "
            pdb=" OG  SER B 168 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   SER E 337 "
            pdb=" OG1 THR E 361 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" ND2 ASN A 155 "
            pdb=" OH  TYR B 152 "
     model   vdw
     2.322 3.120
  ... (remaining 60981 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 'A' and (resid 4 through 196 or resid 225 through 240 or resid 255 throug \ 
h 361))
  selection = (chain 'B' and (resid 4 through 60 or resid 73 through 180 or resid 188 through  \ 
196 or resid 225 through 240 or resid 255 through 361))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     20.950
  Find NCS groups from input model:        0.250
  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:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5420
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      :  0.003   0.076   8754  Z= 0.206
  Angle     :  0.704   7.482  11874  Z= 0.303
  Chirality :  0.044   0.272   1384
  Planarity :  0.005   0.099   1497
  Dihedral  : 17.910 112.926   3592
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.24), residues: 1017
  helix:  0.25 (0.46), residues: 130
  sheet: -1.23 (0.49), residues: 125
  loop : -2.57 (0.19), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP A 281 
 HIS   0.006   0.001   HIS A 138 
 PHE   0.012   0.001   PHE A 257 
 TYR   0.023   0.001   TYR B  74 
 ARG   0.006   0.000   ARG A 189 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.7826 (tp40) cc_final: 0.7563 (tp-100)
REVERT: A  228 PHE cc_start: 0.7472 (p90) cc_final: 0.7257 (p90)
REVERT: B   18 GLU cc_start: 0.7836 (tp30) cc_final: 0.7597 (tp30)
REVERT: B  314 TYR cc_start: 0.6555 (t80) cc_final: 0.6184 (t80)
REVERT: B  333 GLU cc_start: 0.6760 (mp0) cc_final: 0.6530 (mp0)
REVERT: E  414 ASP cc_start: 0.5281 (p0) cc_final: 0.4900 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2302
  time to fit residues: 51.5539
Evaluate side-chains
  157 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0060
   chunk 26 optimal weight:    6.9990
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 320 ASN
E 394 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.199840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.178825 restraints weight = 15426.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.182922 restraints weight = 9462.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.185785 restraints weight = 6609.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5661
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8754  Z= 0.192
  Angle     :  0.679   8.976  11874  Z= 0.305
  Chirality :  0.045   0.305   1384
  Planarity :  0.005   0.080   1497
  Dihedral  : 11.756  94.643   1549
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.24), residues: 1017
  helix:  0.17 (0.45), residues: 128
  sheet: -1.65 (0.44), residues: 148
  loop : -2.48 (0.20), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 281 
 HIS   0.007   0.001   HIS B 138 
 PHE   0.012   0.001   PHE A 106 
 TYR   0.011   0.001   TYR B  52 
 ARG   0.005   0.001   ARG E 153 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.7874 (tp40) cc_final: 0.7531 (tp-100)
REVERT: A   77 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7837 (mtpp)
REVERT: A   84 MET cc_start: 0.4831 (tpt) cc_final: 0.4435 (tpt)
REVERT: A  111 LEU cc_start: 0.6747 (mm) cc_final: 0.6497 (mt)
REVERT: A  151 ARG cc_start: 0.6837 (ptp90) cc_final: 0.6586 (ptp90)
REVERT: A  346 LYS cc_start: 0.8342 (pttm) cc_final: 0.7959 (pttm)
REVERT: B   15 LYS cc_start: 0.8255 (tppt) cc_final: 0.7604 (tppt)
REVERT: B   18 GLU cc_start: 0.7729 (tp30) cc_final: 0.7498 (tp30)
REVERT: B   74 TYR cc_start: 0.6531 (t80) cc_final: 0.6272 (t80)
REVERT: B  302 SER cc_start: 0.6854 (t) cc_final: 0.6422 (t)
REVERT: B  314 TYR cc_start: 0.6936 (t80) cc_final: 0.6730 (t80)
REVERT: B  353 MET cc_start: 0.7931 (mmp) cc_final: 0.7527 (mmp)
REVERT: E   90 ARG cc_start: 0.6707 (tpp-160) cc_final: 0.6371 (tpp-160)
REVERT: E  414 ASP cc_start: 0.5892 (p0) cc_final: 0.5622 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2225
  time to fit residues: 52.2154
Evaluate side-chains
  159 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0270
   chunk 82 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7440

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

Flipped N/Q/H residues before XYZ refinement:
A 193 HIS
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 143 GLN
E 320 ASN
E 343 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.191674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.170433 restraints weight = 15376.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.174486 restraints weight = 9522.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.177288 restraints weight = 6692.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5874
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8754  Z= 0.234
  Angle     :  0.711   9.430  11874  Z= 0.325
  Chirality :  0.045   0.254   1384
  Planarity :  0.005   0.070   1497
  Dihedral  :  9.926  89.515   1549
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.49 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.24), residues: 1017
  helix: -0.14 (0.43), residues: 141
  sheet: -1.71 (0.41), residues: 169
  loop : -2.50 (0.20), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 301 
 HIS   0.009   0.001   HIS B 138 
 PHE   0.010   0.001   PHE A 228 
 TYR   0.025   0.002   TYR A  52 
 ARG   0.008   0.001   ARG E 153 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 VAL cc_start: 0.8019 (t) cc_final: 0.7804 (p)
REVERT: A   84 MET cc_start: 0.4918 (tpt) cc_final: 0.4378 (tpt)
REVERT: A  151 ARG cc_start: 0.7646 (ptp90) cc_final: 0.7437 (ptp90)
REVERT: A  171 VAL cc_start: 0.7886 (m) cc_final: 0.7261 (t)
REVERT: A  333 GLU cc_start: 0.6765 (pt0) cc_final: 0.6453 (pt0)
REVERT: A  338 VAL cc_start: 0.7667 (t) cc_final: 0.7314 (p)
REVERT: A  346 LYS cc_start: 0.8440 (pttm) cc_final: 0.8080 (pttm)
REVERT: B  150 TRP cc_start: 0.5331 (p90) cc_final: 0.5098 (p90)
REVERT: B  353 MET cc_start: 0.8100 (mmp) cc_final: 0.7659 (mmm)
REVERT: E   90 ARG cc_start: 0.6717 (tpp-160) cc_final: 0.6442 (tpp-160)
REVERT: E  317 MET cc_start: 0.6956 (mtm) cc_final: 0.6498 (mtp)
REVERT: E  319 GLN cc_start: 0.7892 (mp10) cc_final: 0.7672 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.2267
  time to fit residues: 55.3846
Evaluate side-chains
  163 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 33 optimal weight:    0.0470
   chunk 93 optimal weight:    0.0980
   chunk 74 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0970
   chunk 26 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.2676

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 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 = 0.4414 r_free = 0.4414 target = 0.193040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.172043 restraints weight = 15450.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.176128 restraints weight = 9472.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.178959 restraints weight = 6590.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5826
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8754  Z= 0.151
  Angle     :  0.642   9.576  11874  Z= 0.285
  Chirality :  0.042   0.246   1384
  Planarity :  0.004   0.061   1497
  Dihedral  :  8.808  85.989   1549
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.19 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.24), residues: 1017
  helix:  0.15 (0.45), residues: 134
  sheet: -1.55 (0.44), residues: 156
  loop : -2.41 (0.20), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 279 
 HIS   0.005   0.001   HIS A 283 
 PHE   0.016   0.001   PHE E 322 
 TYR   0.017   0.001   TYR A 340 
 ARG   0.008   0.000   ARG E 166 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 VAL cc_start: 0.7989 (t) cc_final: 0.7785 (p)
REVERT: A   81 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7933 (ptt90)
REVERT: A   84 MET cc_start: 0.4820 (tpt) cc_final: 0.4387 (tpt)
REVERT: A  151 ARG cc_start: 0.7634 (ptp90) cc_final: 0.7249 (ptp90)
REVERT: A  152 TYR cc_start: 0.6711 (t80) cc_final: 0.6373 (t80)
REVERT: A  171 VAL cc_start: 0.7871 (m) cc_final: 0.7236 (t)
REVERT: A  333 GLU cc_start: 0.6802 (pt0) cc_final: 0.6519 (pt0)
REVERT: A  338 VAL cc_start: 0.7487 (t) cc_final: 0.7053 (p)
REVERT: A  346 LYS cc_start: 0.8360 (pttm) cc_final: 0.8003 (pttm)
REVERT: B  150 TRP cc_start: 0.5265 (p90) cc_final: 0.5059 (p90)
REVERT: B  299 TYR cc_start: 0.6970 (t80) cc_final: 0.6753 (t80)
REVERT: E   90 ARG cc_start: 0.6826 (tpp-160) cc_final: 0.6557 (tpp-160)
REVERT: E  319 GLN cc_start: 0.8237 (mp10) cc_final: 0.7623 (mp10)
REVERT: E  325 LEU cc_start: 0.6940 (tt) cc_final: 0.6274 (mp)
REVERT: E  339 LEU cc_start: 0.7788 (tp) cc_final: 0.7583 (tt)
REVERT: E  414 ASP cc_start: 0.6775 (p0) cc_final: 0.6493 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2236
  time to fit residues: 53.8799
Evaluate side-chains
  162 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 78 optimal weight:    0.3980
   chunk 75 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0770
   chunk 50 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 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 = 0.4380 r_free = 0.4380 target = 0.190353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.169600 restraints weight = 15245.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.173681 restraints weight = 9350.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.176464 restraints weight = 6522.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5886
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8754  Z= 0.172
  Angle     :  0.662   9.691  11874  Z= 0.298
  Chirality :  0.042   0.257   1384
  Planarity :  0.004   0.051   1497
  Dihedral  :  8.198  82.703   1549
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.59 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.24), residues: 1017
  helix:  0.16 (0.45), residues: 133
  sheet: -1.44 (0.45), residues: 151
  loop : -2.53 (0.20), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 279 
 HIS   0.005   0.001   HIS B 138 
 PHE   0.011   0.001   PHE E 322 
 TYR   0.014   0.001   TYR B  74 
 ARG   0.006   0.000   ARG E 153 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ARG cc_start: 0.8336 (ttp80) cc_final: 0.8097 (ptt90)
REVERT: A   84 MET cc_start: 0.5042 (tpt) cc_final: 0.4583 (tpt)
REVERT: A  151 ARG cc_start: 0.7756 (ptp90) cc_final: 0.7464 (ptp90)
REVERT: A  152 TYR cc_start: 0.6992 (t80) cc_final: 0.6568 (t80)
REVERT: A  171 VAL cc_start: 0.7850 (m) cc_final: 0.7214 (t)
REVERT: A  333 GLU cc_start: 0.6947 (pt0) cc_final: 0.6594 (pt0)
REVERT: A  338 VAL cc_start: 0.7639 (t) cc_final: 0.7248 (p)
REVERT: A  346 LYS cc_start: 0.8400 (pttm) cc_final: 0.8086 (pttm)
REVERT: B  224 MET cc_start: 0.4356 (mpp) cc_final: 0.3968 (mpp)
REVERT: E   90 ARG cc_start: 0.6815 (tpp-160) cc_final: 0.6492 (tpp-160)
REVERT: E  319 GLN cc_start: 0.8199 (mp10) cc_final: 0.7269 (mp10)
REVERT: E  339 LEU cc_start: 0.7921 (tp) cc_final: 0.7656 (tt)
REVERT: E  343 GLN cc_start: 0.7459 (mt0) cc_final: 0.7212 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2195
  time to fit residues: 53.9560
Evaluate side-chains
  166 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    0.0020
   chunk 48 optimal weight:    0.0020
   chunk 62 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0000
   chunk 2 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0870
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.1378

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.191887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.171112 restraints weight = 15245.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.175229 restraints weight = 9350.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.178048 restraints weight = 6490.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5842
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8754  Z= 0.140
  Angle     :  0.643   9.580  11874  Z= 0.284
  Chirality :  0.041   0.242   1384
  Planarity :  0.004   0.045   1497
  Dihedral  :  7.622  79.815   1549
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.24), residues: 1017
  helix:  0.36 (0.46), residues: 127
  sheet: -1.50 (0.46), residues: 147
  loop : -2.50 (0.20), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 301 
 HIS   0.004   0.001   HIS E  40 
 PHE   0.015   0.001   PHE A 228 
 TYR   0.014   0.001   TYR B  74 
 ARG   0.009   0.000   ARG E 153 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ARG cc_start: 0.8353 (ttp80) cc_final: 0.8104 (ptt90)
REVERT: A   84 MET cc_start: 0.5025 (tpt) cc_final: 0.4443 (tpt)
REVERT: A  151 ARG cc_start: 0.7681 (ptp90) cc_final: 0.7459 (ptp90)
REVERT: A  152 TYR cc_start: 0.6884 (t80) cc_final: 0.6542 (t80)
REVERT: A  171 VAL cc_start: 0.7810 (m) cc_final: 0.7154 (t)
REVERT: A  289 HIS cc_start: 0.6218 (m-70) cc_final: 0.5961 (m90)
REVERT: A  333 GLU cc_start: 0.6852 (pt0) cc_final: 0.6551 (pt0)
REVERT: A  338 VAL cc_start: 0.7489 (t) cc_final: 0.6982 (p)
REVERT: A  346 LYS cc_start: 0.8418 (pttm) cc_final: 0.8194 (pttp)
REVERT: B  224 MET cc_start: 0.4332 (mpp) cc_final: 0.3949 (mpp)
REVERT: B  292 PHE cc_start: 0.6887 (p90) cc_final: 0.6667 (p90)
REVERT: B  349 GLN cc_start: 0.7253 (tt0) cc_final: 0.6990 (tt0)
REVERT: E   90 ARG cc_start: 0.6839 (tpp-160) cc_final: 0.6532 (tpp-160)
REVERT: E  263 ASP cc_start: 0.7497 (m-30) cc_final: 0.7186 (m-30)
REVERT: E  319 GLN cc_start: 0.8183 (mp10) cc_final: 0.7186 (mp10)
REVERT: E  333 MET cc_start: 0.6525 (mmt) cc_final: 0.6259 (mmm)
REVERT: E  343 GLN cc_start: 0.7457 (mt0) cc_final: 0.7131 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2367
  time to fit residues: 56.6925
Evaluate side-chains
  162 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0770
   chunk 91 optimal weight:    0.0570
   chunk 35 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 75 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.3856

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.189166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.168219 restraints weight = 15430.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.172385 restraints weight = 9424.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.175194 restraints weight = 6538.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5909
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8754  Z= 0.156
  Angle     :  0.658   9.650  11874  Z= 0.292
  Chirality :  0.042   0.264   1384
  Planarity :  0.004   0.040   1497
  Dihedral  :  7.270  76.583   1549
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.24), residues: 1017
  helix:  0.42 (0.45), residues: 133
  sheet: -1.44 (0.45), residues: 151
  loop : -2.53 (0.20), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 301 
 HIS   0.004   0.001   HIS E  40 
 PHE   0.015   0.001   PHE A 228 
 TYR   0.023   0.001   TYR A  52 
 ARG   0.007   0.000   ARG E 153 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8132 (ptt90)
REVERT: A  151 ARG cc_start: 0.7838 (ptp90) cc_final: 0.7551 (ptp90)
REVERT: A  152 TYR cc_start: 0.6961 (t80) cc_final: 0.6633 (t80)
REVERT: A  171 VAL cc_start: 0.7785 (m) cc_final: 0.7149 (t)
REVERT: A  289 HIS cc_start: 0.6263 (m-70) cc_final: 0.5981 (m90)
REVERT: A  333 GLU cc_start: 0.7049 (pt0) cc_final: 0.6661 (pt0)
REVERT: A  338 VAL cc_start: 0.7654 (t) cc_final: 0.7260 (p)
REVERT: B  224 MET cc_start: 0.4418 (mpp) cc_final: 0.3972 (mpp)
REVERT: B  333 GLU cc_start: 0.7146 (mp0) cc_final: 0.6924 (mp0)
REVERT: B  349 GLN cc_start: 0.7349 (tt0) cc_final: 0.7123 (tt0)
REVERT: E   90 ARG cc_start: 0.6845 (tpp-160) cc_final: 0.6511 (tpp-160)
REVERT: E  146 LEU cc_start: 0.8415 (mt) cc_final: 0.8211 (mt)
REVERT: E  212 VAL cc_start: 0.8624 (p) cc_final: 0.8384 (t)
REVERT: E  238 ASP cc_start: 0.7559 (t0) cc_final: 0.7169 (t0)
REVERT: E  263 ASP cc_start: 0.7396 (m-30) cc_final: 0.7135 (m-30)
REVERT: E  315 LEU cc_start: 0.7936 (tp) cc_final: 0.7425 (tt)
REVERT: E  319 GLN cc_start: 0.8151 (mp10) cc_final: 0.7139 (mp10)
REVERT: E  333 MET cc_start: 0.6544 (mmt) cc_final: 0.6234 (mmm)
REVERT: E  343 GLN cc_start: 0.7523 (mt0) cc_final: 0.7204 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.2191
  time to fit residues: 51.6219
Evaluate side-chains
  160 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 98 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 102 ASN
E 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.184209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.162915 restraints weight = 15343.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.167091 restraints weight = 9229.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.169947 restraints weight = 6374.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6023
moved from start:          0.4278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8754  Z= 0.212
  Angle     :  0.715  11.998  11874  Z= 0.326
  Chirality :  0.044   0.267   1384
  Planarity :  0.005   0.061   1497
  Dihedral  :  7.352  72.826   1549
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.24), residues: 1017
  helix:  0.33 (0.45), residues: 134
  sheet: -1.38 (0.42), residues: 168
  loop : -2.60 (0.20), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 301 
 HIS   0.005   0.001   HIS E  40 
 PHE   0.019   0.002   PHE E 389 
 TYR   0.016   0.002   TYR B  74 
 ARG   0.008   0.001   ARG E 153 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8105 (ptt90)
REVERT: A  151 ARG cc_start: 0.7843 (ptp90) cc_final: 0.7630 (ptp90)
REVERT: A  152 TYR cc_start: 0.7145 (t80) cc_final: 0.6808 (t80)
REVERT: A  171 VAL cc_start: 0.7947 (m) cc_final: 0.7357 (t)
REVERT: A  338 VAL cc_start: 0.7973 (t) cc_final: 0.7624 (p)
REVERT: A  346 LYS cc_start: 0.8390 (pttp) cc_final: 0.8124 (pttm)
REVERT: B  291 ASN cc_start: 0.7968 (m110) cc_final: 0.7753 (m-40)
REVERT: B  349 GLN cc_start: 0.7335 (tt0) cc_final: 0.7048 (tt0)
REVERT: E   90 ARG cc_start: 0.6858 (tpp-160) cc_final: 0.6475 (tpp-160)
REVERT: E  146 LEU cc_start: 0.8395 (mt) cc_final: 0.8130 (mt)
REVERT: E  212 VAL cc_start: 0.8735 (p) cc_final: 0.8525 (t)
REVERT: E  263 ASP cc_start: 0.7290 (m-30) cc_final: 0.6907 (m-30)
REVERT: E  319 GLN cc_start: 0.8022 (mp10) cc_final: 0.6972 (mp10)
REVERT: E  343 GLN cc_start: 0.7444 (mt0) cc_final: 0.7087 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.2548
  time to fit residues: 62.2965
Evaluate side-chains
  171 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 100 optimal weight:    0.1980
   chunk 69 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0970
   chunk 46 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
E 102 ASN
E 342 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.184248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.163217 restraints weight = 14954.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.167577 restraints weight = 8753.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.170579 restraints weight = 5897.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6000
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8754  Z= 0.178
  Angle     :  0.689  10.421  11874  Z= 0.314
  Chirality :  0.043   0.253   1384
  Planarity :  0.005   0.056   1497
  Dihedral  :  7.050  69.196   1549
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.40 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.24), residues: 1017
  helix:  0.49 (0.46), residues: 134
  sheet: -1.57 (0.43), residues: 151
  loop : -2.54 (0.20), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 279 
 HIS   0.006   0.001   HIS A 283 
 PHE   0.016   0.001   PHE A 228 
 TYR   0.027   0.001   TYR B 314 
 ARG   0.006   0.000   ARG B  81 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8168 (ptt90)
REVERT: A  151 ARG cc_start: 0.7941 (ptp90) cc_final: 0.7579 (ptp90)
REVERT: A  152 TYR cc_start: 0.7021 (t80) cc_final: 0.6755 (t80)
REVERT: A  171 VAL cc_start: 0.7853 (m) cc_final: 0.7294 (t)
REVERT: A  232 MET cc_start: 0.7286 (mtm) cc_final: 0.7030 (mtm)
REVERT: A  338 VAL cc_start: 0.7854 (t) cc_final: 0.7503 (p)
REVERT: A  346 LYS cc_start: 0.8397 (pttp) cc_final: 0.8127 (pttm)
REVERT: B   74 TYR cc_start: 0.7549 (t80) cc_final: 0.7289 (t80)
REVERT: B  349 GLN cc_start: 0.7319 (tt0) cc_final: 0.6993 (tt0)
REVERT: E   90 ARG cc_start: 0.6962 (tpp-160) cc_final: 0.6520 (tpp-160)
REVERT: E  146 LEU cc_start: 0.8319 (mt) cc_final: 0.8073 (mt)
REVERT: E  212 VAL cc_start: 0.8644 (p) cc_final: 0.8416 (t)
REVERT: E  315 LEU cc_start: 0.8088 (tp) cc_final: 0.7668 (tp)
REVERT: E  317 MET cc_start: 0.6642 (mtm) cc_final: 0.6240 (mtm)
REVERT: E  318 SER cc_start: 0.7503 (p) cc_final: 0.6915 (p)
REVERT: E  343 GLN cc_start: 0.7561 (mt0) cc_final: 0.7057 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 185
  average time/residue: 0.2253
  time to fit residues: 56.5574
Evaluate side-chains
  169 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 86 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 44 optimal weight:    0.1980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  88 HIS
E 102 ASN
E 342 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.183067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.162655 restraints weight = 15055.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.166819 restraints weight = 9188.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.169631 restraints weight = 6325.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6025
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8754  Z= 0.181
  Angle     :  0.701  10.577  11874  Z= 0.319
  Chirality :  0.043   0.259   1384
  Planarity :  0.005   0.057   1497
  Dihedral  :  6.931  65.282   1549
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.65 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.24), residues: 1017
  helix:  0.54 (0.46), residues: 134
  sheet: -1.50 (0.44), residues: 146
  loop : -2.54 (0.20), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 301 
 HIS   0.005   0.001   HIS A 283 
 PHE   0.016   0.001   PHE A 228 
 TYR   0.023   0.002   TYR A  52 
 ARG   0.004   0.000   ARG B 151 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ARG cc_start: 0.8412 (ttp80) cc_final: 0.8115 (ptt90)
REVERT: A  171 VAL cc_start: 0.7930 (m) cc_final: 0.7355 (t)
REVERT: A  232 MET cc_start: 0.7282 (mtm) cc_final: 0.7047 (mtm)
REVERT: A  338 VAL cc_start: 0.7975 (t) cc_final: 0.7614 (p)
REVERT: A  346 LYS cc_start: 0.8402 (pttp) cc_final: 0.8135 (pttp)
REVERT: B  175 VAL cc_start: 0.7867 (t) cc_final: 0.7624 (p)
REVERT: B  349 GLN cc_start: 0.7294 (tt0) cc_final: 0.6977 (tt0)
REVERT: E   90 ARG cc_start: 0.6943 (tpp-160) cc_final: 0.6520 (tpp-160)
REVERT: E  116 LEU cc_start: 0.7452 (mm) cc_final: 0.7172 (mm)
REVERT: E  146 LEU cc_start: 0.8292 (mt) cc_final: 0.8033 (mt)
REVERT: E  212 VAL cc_start: 0.8722 (p) cc_final: 0.8487 (t)
REVERT: E  315 LEU cc_start: 0.8083 (tp) cc_final: 0.7621 (tp)
REVERT: E  317 MET cc_start: 0.6676 (mtm) cc_final: 0.6213 (mtm)
REVERT: E  318 SER cc_start: 0.7477 (p) cc_final: 0.7079 (p)
REVERT: E  343 GLN cc_start: 0.7479 (mt0) cc_final: 0.7182 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2312
  time to fit residues: 56.1111
Evaluate side-chains
  173 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 70 optimal weight:    0.0060
   chunk 69 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 99 optimal weight:    0.5980
   chunk 86 optimal weight:    3.9990
   chunk 76 optimal weight:    0.2980
   chunk 4 optimal weight:    0.4980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 102 ASN
E 342 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.182668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.162310 restraints weight = 15150.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.166319 restraints weight = 9289.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.169138 restraints weight = 6466.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6028
moved from start:          0.4837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8754  Z= 0.175
  Angle     :  0.714  10.721  11874  Z= 0.323
  Chirality :  0.042   0.256   1384
  Planarity :  0.005   0.055   1497
  Dihedral  :  6.744  61.440   1549
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.24), residues: 1017
  helix:  0.60 (0.46), residues: 134
  sheet: -1.50 (0.42), residues: 153
  loop : -2.56 (0.20), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 279 
 HIS   0.005   0.001   HIS E  40 
 PHE   0.008   0.001   PHE B 228 
 TYR   0.041   0.002   TYR B  74 
 ARG   0.010   0.000   ARG A 151 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2859.41 seconds
wall clock time: 50 minutes 44.33 seconds (3044.33 seconds total)