Starting phenix.real_space_refine
on Fri Mar 15 14:09:51 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/03_2024/8hdz_34684.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/03_2024/8hdz_34684.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/03_2024/8hdz_34684.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/03_2024/8hdz_34684.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/03_2024/8hdz_34684.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/03_2024/8hdz_34684.pdb"
  }
  resolution = 3.05
  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=   0.000 sd=   0.020
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      62      5.16       5
     C    7619      2.51       5
     N    1951      2.21       5
     O    2229      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  125": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  156": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  176": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  181": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 11861
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 813, 6622
          Classifications: {'peptide': 813}
          Link IDs: {'PTRANS': 30, 'TRANS': 782}
    Chain: "C"
      Number of atoms: 3467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3467
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 10, 'TRANS': 415}
    Chain: "B"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1772
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 13, 'TRANS': 204}
  Time building chain proxies: 6.28, per 1000 atoms: 0.53
  Number of scatterers: 11861
  At special positions: 0
  Unit cell: (92.4, 124.32, 141.96, 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      62     16.00
     O    2229      8.00
     N    1951      7.00
     C    7619      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.37
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2782

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 17 sheets defined
      36.5% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 3.670A  pdb=" N   ASN A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 149
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 209 through 220
    Processing helix  chain 'A' and resid 226 through 230
    Processing helix  chain 'A' and resid 240 through 253
    Processing helix  chain 'A' and resid 267 through 281
    Processing helix  chain 'A' and resid 331 through 339
    Processing helix  chain 'A' and resid 345 through 354
      removed outlier: 3.830A  pdb=" N   PHE A 354 " --> pdb=" O   SER A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 391
      removed outlier: 3.939A  pdb=" N   THR A 384 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   THR A 391 " --> pdb=" O   LYS A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 445
    Processing helix  chain 'A' and resid 448 through 473
      removed outlier: 3.668A  pdb=" N   CYS A 466 " --> pdb=" O   ASP A 462 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLN A 467 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 487
    Processing helix  chain 'A' and resid 497 through 514
      removed outlier: 3.872A  pdb=" N   GLY A 504 " --> pdb=" O   THR A 500 " (cutoff:3.500A)
      Proline residue:  A 505  - end of helix
    Processing helix  chain 'A' and resid 552 through 562
    Processing helix  chain 'A' and resid 576 through 591
      removed outlier: 3.787A  pdb=" N   GLN A 589 " --> pdb=" O   GLN A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 642
    Processing helix  chain 'A' and resid 646 through 665
    Processing helix  chain 'A' and resid 666 through 672
      removed outlier: 3.880A  pdb=" N   GLY A 672 " --> pdb=" O   TYR A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 703
    Processing helix  chain 'A' and resid 763 through 781
    Processing helix  chain 'C' and resid 8 through 11
    Processing helix  chain 'C' and resid 12 through 19
      removed outlier: 3.881A  pdb=" N   LYS C  18 " --> pdb=" O   LEU C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 4.484A  pdb=" N   LYS C  30 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 59
    Processing helix  chain 'C' and resid 107 through 121
    Processing helix  chain 'C' and resid 132 through 135
    Processing helix  chain 'C' and resid 147 through 159
      removed outlier: 3.661A  pdb=" N   ILE C 151 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR C 158 " --> pdb=" O   LEU C 154 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLY C 159 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 188
    Processing helix  chain 'C' and resid 249 through 257
      removed outlier: 4.123A  pdb=" N   LYS C 257 " --> pdb=" O   LEU C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 285 through 298
      removed outlier: 3.570A  pdb=" N   VAL C 289 " --> pdb=" O   THR C 285 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   THR C 296 " --> pdb=" O   ARG C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 323
      removed outlier: 3.621A  pdb=" N   THR C 320 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 341
    Processing helix  chain 'C' and resid 341 through 350
      removed outlier: 3.565A  pdb=" N   LYS C 349 " --> pdb=" O   LYS C 345 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ASN C 350 " --> pdb=" O   ARG C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 361
    Processing helix  chain 'C' and resid 367 through 374
      removed outlier: 3.538A  pdb=" N   ASN C 374 " --> pdb=" O   THR C 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 392 through 396
      removed outlier: 3.992A  pdb=" N   ASN C 396 " --> pdb=" O   ASN C 393 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 397 through 406
      removed outlier: 3.574A  pdb=" N   GLU C 401 " --> pdb=" O   ASN C 397 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 425
    Processing helix  chain 'B' and resid 16 through 18
      No H-bonds generated for 'chain 'B' and resid 16 through 18'
    Processing helix  chain 'B' and resid 19 through 32
      removed outlier: 4.212A  pdb=" N   SER B  24 " --> pdb=" O   GLU B  20 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   GLN B  25 " --> pdb=" O   PRO B  21 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 50
      removed outlier: 3.664A  pdb=" N   PHE B  50 " --> pdb=" O   ASP B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 101
      removed outlier: 3.647A  pdb=" N   LYS B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   ILE B  96 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ARG B  98 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   LEU B  99 " --> pdb=" O   SER B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 150
      removed outlier: 3.828A  pdb=" N   LEU B 145 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 170
    Processing helix  chain 'B' and resid 194 through 205
    Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126
      removed outlier: 5.604A  pdb=" N   CYS A   5 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   ARG A  23 " --> pdb=" O   CYS A   5 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASN A   7 " --> pdb=" O   LYS A  21 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   TYR A 140 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   PHE A  31 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   CYS A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43
      removed outlier: 6.070A  pdb=" N   LEU A  90 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   GLU A  92 " --> pdb=" O   ALA A  57 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ALA A  57 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73
      removed outlier: 6.654A  pdb=" N   SER A  73 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   LEU A 568 " --> pdb=" O   ASP A 616 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ASP A 616 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY A 570 " --> pdb=" O   ILE A 614 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER A 610 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU A 611 " --> pdb=" O   CYS A 601 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223
      removed outlier: 6.133A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   VAL A 237 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   THR A 201 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   CYS A 239 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   ILE A 203 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   SER A 184 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A 165 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 287
    Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 302
    Processing sheet with id=AA7, first strand: chain 'A' and resid 408 through 411
      removed outlier: 3.825A  pdb=" N   LEU A 411 " --> pdb=" O   GLY A 414 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL A 417 " --> pdb=" O   PHE A 370 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 397
    Processing sheet with id=AA9, first strand: chain 'A' and resid 732 through 734
      removed outlier: 3.510A  pdb=" N   ARG A 713 " --> pdb=" O   GLU A 706 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLU A 706 " --> pdb=" O   ARG A 713 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   SER A 747 " --> pdb=" O   GLU A 758 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   GLU A 758 " --> pdb=" O   SER A 747 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   TYR A 749 " --> pdb=" O   PHE A 756 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 755 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE A 548 " --> pdb=" O   VAL A 755 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A 547 " --> pdb=" O   ALA A 793 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   ALA A 793 " --> pdb=" O   ILE A 547 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ASP A 549 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   PHE A 791 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   TYR A 795 " --> pdb=" O   TYR A 811 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   TYR A 811 " --> pdb=" O   TYR A 795 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   ASN A 797 " --> pdb=" O   MET A 809 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   MET A 809 " --> pdb=" O   ASN A 797 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   LYS A 805 " --> pdb=" O   GLN A 801 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 65
      removed outlier: 5.969A  pdb=" N   ARG C 207 " --> pdb=" O   TYR C  61 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLU C  63 " --> pdb=" O   ARG C 207 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 70
      removed outlier: 3.516A  pdb=" N   PHE C  69 " --> pdb=" O   PHE C 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 170
    Processing sheet with id=AB4, first strand: chain 'C' and resid 86 through 87
      removed outlier: 4.023A  pdb=" N   PHE C 126 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG C 128 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ASP C 140 " --> pdb=" O   ARG C 128 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   VAL C 130 " --> pdb=" O   MET C 138 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   MET C 138 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 220 through 223
      removed outlier: 5.352A  pdb=" N   ILE C 238 " --> pdb=" O   GLU C 221 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 267 through 268
      removed outlier: 3.597A  pdb=" N   LYS C 267 " --> pdb=" O   ILE C 274 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 375 through 380
      removed outlier: 5.996A  pdb=" N   GLU C 380 " --> pdb=" O   VAL C 384 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   VAL C 384 " --> pdb=" O   GLU C 380 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 116 through 120
      removed outlier: 5.731A  pdb=" N   CYS B  63 " --> pdb=" O   TYR B 156 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   LEU B 158 " --> pdb=" O   CYS B  63 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   CYS B  65 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   LEU B 155 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   GLY B 179 " --> pdb=" O   LEU B 155 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   CYS B 157 " --> pdb=" O   GLY B 179 " (cutoff:3.500A)

    443 hydrogen bonds defined for protein.
    1269 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.54

  Time building geometry restraints manager: 4.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3780
        1.34 -     1.46: 2569
        1.46 -     1.58: 5678
        1.58 -     1.69: 0
        1.69 -     1.81: 93
  Bond restraints: 12120
  Sorted by residual:
  bond pdb=" C   GLU A  93 "
       pdb=" O   GLU A  93 "
    ideal  model  delta    sigma   weight residual
    1.238  1.249 -0.011 1.28e-02 6.10e+03 7.83e-01
  bond pdb=" C   PRO A 593 "
       pdb=" N   PRO A 594 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.28e-02 6.10e+03 6.19e-01
  bond pdb=" CA  ILE A 153 "
       pdb=" CB  ILE A 153 "
    ideal  model  delta    sigma   weight residual
    1.537  1.547 -0.010 1.29e-02 6.01e+03 6.11e-01
  bond pdb=" CA  LEU C  10 "
       pdb=" CB  LEU C  10 "
    ideal  model  delta    sigma   weight residual
    1.533  1.545 -0.012 1.66e-02 3.63e+03 5.28e-01
  bond pdb=" CB  PRO B  82 "
       pdb=" CG  PRO B  82 "
    ideal  model  delta    sigma   weight residual
    1.492  1.525 -0.033 5.00e-02 4.00e+02 4.31e-01
  ... (remaining 12115 not shown)

  Histogram of bond angle deviations from ideal:
      100.34 -   107.07: 281
      107.07 -   113.80: 6645
      113.80 -   120.53: 4720
      120.53 -   127.26: 4650
      127.26 -   133.99: 91
  Bond angle restraints: 16387
  Sorted by residual:
  angle pdb=" CA  LEU C  10 "
        pdb=" CB  LEU C  10 "
        pdb=" CG  LEU C  10 "
      ideal   model   delta    sigma   weight residual
     116.30  126.94  -10.64 3.50e+00 8.16e-02 9.25e+00
  angle pdb=" CA  LEU C 202 "
        pdb=" CB  LEU C 202 "
        pdb=" CG  LEU C 202 "
      ideal   model   delta    sigma   weight residual
     116.30  124.50   -8.20 3.50e+00 8.16e-02 5.49e+00
  angle pdb=" C   GLU C  36 "
        pdb=" N   TRP C  37 "
        pdb=" CA  TRP C  37 "
      ideal   model   delta    sigma   weight residual
     122.62  118.74    3.88 1.78e+00 3.16e-01 4.76e+00
  angle pdb=" N   ILE A 180 "
        pdb=" CA  ILE A 180 "
        pdb=" C   ILE A 180 "
      ideal   model   delta    sigma   weight residual
     112.12  110.42    1.70 8.40e-01 1.42e+00 4.08e+00
  angle pdb=" CA  LEU A 517 "
        pdb=" CB  LEU A 517 "
        pdb=" CG  LEU A 517 "
      ideal   model   delta    sigma   weight residual
     116.30  123.33   -7.03 3.50e+00 8.16e-02 4.03e+00
  ... (remaining 16382 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.15: 6437
       16.15 -    32.29: 704
       32.29 -    48.44: 143
       48.44 -    64.58: 27
       64.58 -    80.73: 9
  Dihedral angle restraints: 7320
    sinusoidal: 3002
      harmonic: 4318
  Sorted by residual:
  dihedral pdb=" CA  TYR B  70 "
           pdb=" C   TYR B  70 "
           pdb=" N   PRO B  71 "
           pdb=" CA  PRO B  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.76  -17.24     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  ASP C 178 "
           pdb=" CB  ASP C 178 "
           pdb=" CG  ASP C 178 "
           pdb=" OD1 ASP C 178 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.04   59.04     1      2.00e+01 2.50e-03 1.17e+01
  dihedral pdb=" CA  ASP A 728 "
           pdb=" CB  ASP A 728 "
           pdb=" CG  ASP A 728 "
           pdb=" OD1 ASP A 728 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.00   59.00     1      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 7317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1098
       0.027 -    0.054: 417
       0.054 -    0.080: 160
       0.080 -    0.107: 95
       0.107 -    0.134: 47
  Chirality restraints: 1817
  Sorted by residual:
  chirality pdb=" CA  ILE A 158 "
            pdb=" N   ILE A 158 "
            pdb=" C   ILE A 158 "
            pdb=" CB  ILE A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality pdb=" CA  ILE A 516 "
            pdb=" N   ILE A 516 "
            pdb=" C   ILE A 516 "
            pdb=" CB  ILE A 516 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.09e-01
  chirality pdb=" CA  ILE C  77 "
            pdb=" N   ILE C  77 "
            pdb=" C   ILE C  77 "
            pdb=" CB  ILE C  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 1814 not shown)

  Planarity restraints: 2085
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 592 "    0.032 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO A 593 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 593 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 593 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  45 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO B  46 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B  46 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  46 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  43 "    0.025 5.00e-02 4.00e+02   3.69e-02 2.17e+00
        pdb=" N   PRO B  44 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B  44 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  44 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2082 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 407
        2.72 -     3.26: 11714
        3.26 -     3.81: 19147
        3.81 -     4.35: 23103
        4.35 -     4.90: 39529
  Nonbonded interactions: 93900
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 302 "
            pdb=" O   LEU C 361 "
     model   vdw
     2.174 2.440
  nonbonded pdb=" OH  TYR A 190 "
            pdb=" OD2 ASP A 192 "
     model   vdw
     2.229 2.440
  nonbonded pdb=" O   LYS C 310 "
            pdb=" NE2 GLN C 318 "
     model   vdw
     2.232 2.520
  nonbonded pdb=" ND2 ASN C 304 "
            pdb=" O   GLY C 362 "
     model   vdw
     2.239 2.520
  nonbonded pdb=" OG  SER A 564 "
            pdb=" OE1 GLU A 566 "
     model   vdw
     2.239 2.440
  ... (remaining 93895 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          7.660
  Check model and map are aligned:         0.170
  Set scattering table:                    0.110
  Process input model:                     33.050
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4673
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12120  Z= 0.109
  Angle     :  0.437  10.643  16387  Z= 0.228
  Chirality :  0.040   0.134   1817
  Planarity :  0.003   0.049   2085
  Dihedral  : 13.939  80.731   4538
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.27 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.23), residues: 1451
  helix:  1.26 (0.25), residues: 474
  sheet:  0.88 (0.34), residues: 258
  loop : -0.96 (0.24), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 137 
 HIS   0.001   0.000   HIS A  36 
 PHE   0.007   0.001   PHE A 200 
 TYR   0.013   0.001   TYR B  70 
 ARG   0.003   0.000   ARG A  23 

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.336 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.5299 (mm-30) cc_final: 0.4629 (tm-30)
REVERT: B  212 TRP cc_start: 0.3241 (m100) cc_final: 0.2938 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2450
  time to fit residues: 51.5074
Evaluate side-chains
  109 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    7.9990
   chunk 109 optimal weight:    9.9990
   chunk 60 optimal weight:    0.3980
   chunk 37 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 130 optimal weight:    0.0970
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4936
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12120  Z= 0.268
  Angle     :  0.603  11.285  16387  Z= 0.312
  Chirality :  0.045   0.168   1817
  Planarity :  0.004   0.050   2085
  Dihedral  :  4.126  19.542   1604
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.10 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.22 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.23), residues: 1451
  helix:  0.88 (0.24), residues: 472
  sheet:  0.88 (0.35), residues: 235
  loop : -1.08 (0.23), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  37 
 HIS   0.013   0.002   HIS A 170 
 PHE   0.016   0.002   PHE A 560 
 TYR   0.031   0.002   TYR A 190 
 ARG   0.006   0.001   ARG A 604 

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  455 MET cc_start: 0.2880 (mtt) cc_final: 0.2579 (mtt)
  outliers start: 11
  outliers final: 9
  residues processed: 113
  average time/residue: 0.2374
  time to fit residues: 39.9606
Evaluate side-chains
  107 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 131 optimal weight:    4.9990
   chunk 141 optimal weight:   10.0000
   chunk 116 optimal weight:    0.4980
   chunk 129 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 105 optimal weight:    6.9990
   overall best weight:    2.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
A 657 GLN
** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   8 HIS
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5143
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.094  12120  Z= 0.398
  Angle     :  0.740  11.079  16387  Z= 0.388
  Chirality :  0.049   0.211   1817
  Planarity :  0.006   0.080   2085
  Dihedral  :  5.117  22.912   1604
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 19.97
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.27 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 14.55 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.22), residues: 1451
  helix:  0.02 (0.24), residues: 457
  sheet:  0.15 (0.35), residues: 239
  loop : -1.47 (0.22), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C  37 
 HIS   0.009   0.002   HIS A 319 
 PHE   0.022   0.002   PHE A 113 
 TYR   0.034   0.003   TYR A 190 
 ARG   0.009   0.001   ARG A 604 

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 114
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.5187 (OUTLIER) cc_final: 0.4974 (mt)
REVERT: A  334 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.5985 (t80)
REVERT: A  455 MET cc_start: 0.3409 (mtt) cc_final: 0.3070 (mtt)
REVERT: C  339 ASN cc_start: 0.4292 (t0) cc_final: 0.4042 (t0)
REVERT: B   23 MET cc_start: 0.3544 (tpp) cc_final: 0.3215 (ptm)
REVERT: B   29 PHE cc_start: 0.5758 (m-80) cc_final: 0.4203 (t80)
REVERT: B  186 ASP cc_start: 0.2538 (OUTLIER) cc_final: 0.2025 (t70)
  outliers start: 41
  outliers final: 27
  residues processed: 143
  average time/residue: 0.2194
  time to fit residues: 47.3569
Evaluate side-chains
  135 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  324 ASN
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  436 ASP
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  125 CYS
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 129 optimal weight:    0.9990
   chunk 98 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 87 optimal weight:   10.0000
   chunk 131 optimal weight:    4.9990
   chunk 139 optimal weight:    0.0020
   chunk 68 optimal weight:    0.7980
   chunk 124 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
A 657 GLN
C 374 ASN
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4978
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12120  Z= 0.168
  Angle     :  0.535   9.348  16387  Z= 0.277
  Chirality :  0.043   0.189   1817
  Planarity :  0.004   0.060   2085
  Dihedral  :  4.302  19.481   1604
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.58 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 17.61 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.23), residues: 1451
  helix:  0.52 (0.24), residues: 474
  sheet:  0.14 (0.34), residues: 251
  loop : -1.24 (0.24), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 137 
 HIS   0.007   0.001   HIS A 170 
 PHE   0.022   0.001   PHE A 267 
 TYR   0.018   0.001   TYR A 190 
 ARG   0.005   0.000   ARG A 160 

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 HIS cc_start: 0.5651 (m170) cc_final: 0.5362 (m170)
REVERT: A  334 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.5739 (t80)
REVERT: B  212 TRP cc_start: 0.3881 (m100) cc_final: 0.3632 (m100)
  outliers start: 13
  outliers final: 11
  residues processed: 126
  average time/residue: 0.2381
  time to fit residues: 44.5327
Evaluate side-chains
  124 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 115 optimal weight:    5.9990
   chunk 79 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 96 optimal weight:   20.0000
   chunk 0 optimal weight:    1.9990
   chunk 71 optimal weight:    9.9990
   chunk 124 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 GLN
C 374 ASN
C 393 ASN
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5140
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  12120  Z= 0.346
  Angle     :  0.672  11.603  16387  Z= 0.348
  Chirality :  0.047   0.202   1817
  Planarity :  0.005   0.064   2085
  Dihedral  :  4.826  20.994   1604
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.96 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.06 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.22), residues: 1451
  helix:  0.14 (0.24), residues: 464
  sheet:  0.30 (0.36), residues: 220
  loop : -1.47 (0.23), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C  37 
 HIS   0.007   0.001   HIS A 319 
 PHE   0.022   0.002   PHE A 560 
 TYR   0.032   0.002   TYR A 190 
 ARG   0.009   0.001   ARG A 497 

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 1.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6521 (tm-30)
REVERT: A  334 PHE cc_start: 0.6423 (OUTLIER) cc_final: 0.5747 (t80)
REVERT: B   29 PHE cc_start: 0.5334 (m-80) cc_final: 0.4388 (t80)
REVERT: B  186 ASP cc_start: 0.2508 (OUTLIER) cc_final: 0.2282 (t70)
  outliers start: 41
  outliers final: 30
  residues processed: 142
  average time/residue: 0.2669
  time to fit residues: 56.2699
Evaluate side-chains
  140 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 1.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 ASP
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  693 ARG
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  108 ASP
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 125 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 139 optimal weight:    2.9990
   chunk 115 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 73 optimal weight:    8.9990
   chunk 134 optimal weight:    0.0980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 657 GLN
B   2 ASN
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5079
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12120  Z= 0.239
  Angle     :  0.589  11.172  16387  Z= 0.303
  Chirality :  0.044   0.184   1817
  Planarity :  0.005   0.065   2085
  Dihedral  :  4.572  19.805   1604
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.20 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.18 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.22), residues: 1451
  helix:  0.29 (0.24), residues: 469
  sheet:  0.16 (0.36), residues: 221
  loop : -1.33 (0.23), residues: 761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  37 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.018   0.002   PHE C 410 
 TYR   0.028   0.002   TYR B 108 
 ARG   0.007   0.000   ARG A 497 

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.6089 (OUTLIER) cc_final: 0.5853 (p0)
REVERT: A  334 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5795 (t80)
REVERT: A  416 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6761 (mmtm)
REVERT: B   29 PHE cc_start: 0.5226 (m-80) cc_final: 0.4488 (t80)
REVERT: B  212 TRP cc_start: 0.4186 (m100) cc_final: 0.3984 (m100)
  outliers start: 40
  outliers final: 30
  residues processed: 152
  average time/residue: 0.2287
  time to fit residues: 51.5123
Evaluate side-chains
  152 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 119
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  324 ASN
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  416 LYS
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain C residue  401 GLU
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 79 optimal weight:   10.0000
   chunk 101 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 117 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 138 optimal weight:    9.9990
   chunk 86 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5072
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12120  Z= 0.232
  Angle     :  0.603  15.166  16387  Z= 0.306
  Chirality :  0.044   0.204   1817
  Planarity :  0.005   0.066   2085
  Dihedral  :  4.523  20.368   1604
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.34 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 19.18 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.22), residues: 1451
  helix:  0.40 (0.24), residues: 470
  sheet:  0.27 (0.37), residues: 217
  loop : -1.32 (0.23), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  37 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.022   0.002   PHE C 410 
 TYR   0.022   0.001   TYR A 190 
 ARG   0.008   0.000   ARG A 497 

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 116
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.5787 (t80)
REVERT: A  416 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6837 (mmtm)
REVERT: A  497 ARG cc_start: 0.5384 (mmm160) cc_final: 0.3615 (ttt-90)
REVERT: C  425 PHE cc_start: 0.4637 (m-80) cc_final: 0.4349 (m-10)
REVERT: B   29 PHE cc_start: 0.5269 (m-80) cc_final: 0.4536 (t80)
  outliers start: 51
  outliers final: 41
  residues processed: 154
  average time/residue: 0.2174
  time to fit residues: 50.3760
Evaluate side-chains
  154 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 111
  time to evaluate  : 1.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ASP
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  324 ASN
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  416 LYS
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 ASP
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain A residue  693 ARG
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue  108 ASP
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain C residue  401 GLU
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0270
   chunk 41 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 88 optimal weight:    8.9990
   chunk 94 optimal weight:    7.9990
   chunk 68 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 109 optimal weight:    0.0970
   chunk 126 optimal weight:    0.7980
   overall best weight:    0.4436

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

Flipped N/Q/H residues before XYZ refinement:
C 374 ASN
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4943
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12120  Z= 0.149
  Angle     :  0.531  10.585  16387  Z= 0.271
  Chirality :  0.043   0.209   1817
  Planarity :  0.004   0.064   2085
  Dihedral  :  4.121  19.102   1604
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.17 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.67 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.23), residues: 1451
  helix:  0.78 (0.24), residues: 476
  sheet:  0.31 (0.36), residues: 222
  loop : -1.15 (0.23), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 137 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.027   0.001   PHE A 267 
 TYR   0.033   0.001   TYR B 108 
 ARG   0.006   0.000   ARG A 497 

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  370 PHE cc_start: 0.6005 (m-80) cc_final: 0.5395 (m-80)
REVERT: A  416 LYS cc_start: 0.7325 (mmtm) cc_final: 0.6927 (mmtm)
REVERT: C   95 MET cc_start: 0.4589 (tpp) cc_final: 0.3097 (tpp)
REVERT: B   29 PHE cc_start: 0.5804 (m-80) cc_final: 0.4419 (t80)
REVERT: B  212 TRP cc_start: 0.3937 (m100) cc_final: 0.3731 (m100)
  outliers start: 32
  outliers final: 22
  residues processed: 144
  average time/residue: 0.2242
  time to fit residues: 48.3581
Evaluate side-chains
  141 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ASP
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 132 optimal weight:    8.9990
   chunk 121 optimal weight:    3.9990
   chunk 129 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 101 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 116 optimal weight:    0.0670
   chunk 122 optimal weight:    0.9980
   chunk 128 optimal weight:    0.3980
   chunk 84 optimal weight:    4.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4967
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12120  Z= 0.164
  Angle     :  0.548  11.460  16387  Z= 0.279
  Chirality :  0.043   0.195   1817
  Planarity :  0.004   0.062   2085
  Dihedral  :  4.096  18.839   1604
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.24 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.90 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.23), residues: 1451
  helix:  0.83 (0.25), residues: 477
  sheet:  0.40 (0.35), residues: 232
  loop : -1.13 (0.24), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  37 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.025   0.001   PHE A 267 
 TYR   0.017   0.001   TYR A 162 
 ARG   0.010   0.000   ARG A 497 

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.5699 (ttt)
REVERT: A  370 PHE cc_start: 0.5938 (m-80) cc_final: 0.5341 (m-80)
REVERT: A  416 LYS cc_start: 0.7319 (mmtm) cc_final: 0.6922 (mmtm)
REVERT: A  497 ARG cc_start: 0.5255 (mmm160) cc_final: 0.3650 (ttt-90)
REVERT: C   10 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6883 (tt)
REVERT: C   95 MET cc_start: 0.4484 (tpp) cc_final: 0.3158 (tpp)
REVERT: C  425 PHE cc_start: 0.4793 (m-80) cc_final: 0.4484 (m-80)
REVERT: B   29 PHE cc_start: 0.5760 (m-80) cc_final: 0.4515 (t80)
REVERT: B  212 TRP cc_start: 0.4024 (m100) cc_final: 0.3693 (m100)
  outliers start: 32
  outliers final: 28
  residues processed: 141
  average time/residue: 0.2250
  time to fit residues: 47.6977
Evaluate side-chains
  146 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ASP
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue  108 ASP
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 136 optimal weight:    5.9990
   chunk 83 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 95 optimal weight:    9.9990
   chunk 143 optimal weight:    6.9990
   chunk 132 optimal weight:    9.9990
   chunk 114 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0570
   chunk 88 optimal weight:    7.9990
   chunk 70 optimal weight:    0.8980
   chunk 90 optimal weight:   10.0000
   overall best weight:    1.7100

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 351 GLN
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5103
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12120  Z= 0.276
  Angle     :  0.635  11.906  16387  Z= 0.326
  Chirality :  0.045   0.263   1817
  Planarity :  0.005   0.063   2085
  Dihedral  :  4.573  20.424   1604
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 16.97
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.48 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.75 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.23), residues: 1451
  helix:  0.48 (0.24), residues: 469
  sheet:  0.39 (0.37), residues: 215
  loop : -1.20 (0.23), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  37 
 HIS   0.006   0.001   HIS A 319 
 PHE   0.037   0.002   PHE C 410 
 TYR   0.027   0.002   TYR A 190 
 ARG   0.010   0.001   ARG A 497 

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 111
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  370 PHE cc_start: 0.5828 (m-80) cc_final: 0.5180 (m-80)
REVERT: A  416 LYS cc_start: 0.7334 (mmtm) cc_final: 0.6917 (mmtm)
REVERT: A  497 ARG cc_start: 0.5537 (mmm160) cc_final: 0.3759 (ttt-90)
REVERT: C   10 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6935 (tt)
REVERT: C  425 PHE cc_start: 0.4753 (m-80) cc_final: 0.4422 (m-80)
REVERT: B   29 PHE cc_start: 0.5702 (m-80) cc_final: 0.4535 (t80)
REVERT: B  212 TRP cc_start: 0.4024 (m100) cc_final: 0.3753 (m100)
  outliers start: 35
  outliers final: 30
  residues processed: 137
  average time/residue: 0.2282
  time to fit residues: 47.3353
Evaluate side-chains
  140 residues out of total 1340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ASP
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  108 ASP
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0050
   chunk 105 optimal weight:    0.0670
   chunk 16 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 114 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0040
   overall best weight:    0.3344

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5460 r_free = 0.5460 target = 0.301086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5176 r_free = 0.5176 target = 0.258996 restraints weight = 12188.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.5143 rms_B_bonded: 3.54
r_work: 0.4704 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.4704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5484
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12120  Z= 0.140
  Angle     :  0.537  11.053  16387  Z= 0.274
  Chirality :  0.043   0.192   1817
  Planarity :  0.004   0.062   2085
  Dihedral  :  4.090  18.913   1604
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.76 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.27 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.23), residues: 1451
  helix:  0.92 (0.25), residues: 467
  sheet:  0.43 (0.36), residues: 224
  loop : -1.07 (0.23), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 137 
 HIS   0.002   0.000   HIS A 265 
 PHE   0.049   0.001   PHE C 410 
 TYR   0.036   0.001   TYR B 108 
 ARG   0.008   0.000   ARG A 497 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2593.28 seconds
wall clock time: 47 minutes 48.14 seconds (2868.14 seconds total)