Starting phenix.real_space_refine
on Mon May 12 00:36:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ubt_42102/05_2025/8ubt_42102.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ubt_42102/05_2025/8ubt_42102.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ubt_42102/05_2025/8ubt_42102.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ubt_42102/05_2025/8ubt_42102.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ubt_42102/05_2025/8ubt_42102.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ubt_42102/05_2025/8ubt_42102.cif"
  }
  resolution = 3.1
  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=   0.035
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      58      5.16       5
     C    5494      2.51       5
     N    1444      2.21       5
     O    1646      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8642
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3651
          Classifications: {'peptide': 448}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 442}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1163
          Classifications: {'peptide': 146}
          Link IDs: {'PTRANS': 8, 'TRANS': 137}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2937
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 6, 'TRANS': 368}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'ARG:plan': 14}
          Unresolved non-hydrogen planarities: 40
    Chain: "D"
      Number of atoms: 891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 891
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 2, 'TRANS': 110}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 5.16, per 1000 atoms: 0.60
  Number of scatterers: 8642
  At special positions: 0
  Unit cell: (76.529, 125.567, 150.829, 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      58     16.00
     O    1646      8.00
     N    1444      7.00
     C    5494      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 396 " - pdb=" SG  CYS C 422 " 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
  Time building additional restraints: 2.15
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2074

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 3 sheets defined
      58.2% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 26
    Processing helix  chain 'A' and resid 27 through 32
      removed outlier: 3.844A  pdb=" N   TYR A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 54
      removed outlier: 3.646A  pdb=" N   TYR A  42 " --> pdb=" O   ALA A  38 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   MET A  43 " --> pdb=" O   LYS A  39 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLU A  44 " --> pdb=" O   SER A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 104
    Processing helix  chain 'A' and resid 115 through 120
      removed outlier: 3.581A  pdb=" N   THR A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 128
      removed outlier: 3.729A  pdb=" N   GLU A 124 " --> pdb=" O   THR A 120 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASP A 125 " --> pdb=" O   GLN A 121 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   TYR A 126 " --> pdb=" O   GLN A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 133
      removed outlier: 3.764A  pdb=" N   VAL A 132 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU A 133 " --> pdb=" O   SER A 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 128 through 133'
    Processing helix  chain 'A' and resid 138 through 143
      removed outlier: 3.797A  pdb=" N   HIS A 143 " --> pdb=" O   TYR A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 167
    Processing helix  chain 'A' and resid 174 through 178
    Processing helix  chain 'A' and resid 179 through 188
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 3.824A  pdb=" N   ILE A 201 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 232
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.698A  pdb=" N   ALA A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASP A 239 " --> pdb=" O   GLN A 235 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ARG A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER A 248 " --> pdb=" O   TYR A 244 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   THR A 249 " --> pdb=" O   THR A 245 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLU A 250 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 274
      removed outlier: 3.637A  pdb=" N   GLU A 265 " --> pdb=" O   MET A 261 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLN A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ARG A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 288
    Processing helix  chain 'A' and resid 289 through 292
      removed outlier: 3.523A  pdb=" N   GLU A 292 " --> pdb=" O   ARG A 289 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 289 through 292'
    Processing helix  chain 'A' and resid 303 through 313
    Processing helix  chain 'A' and resid 316 through 328
      removed outlier: 3.709A  pdb=" N   ARG A 328 " --> pdb=" O   ASN A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 336
      No H-bonds generated for 'chain 'A' and resid 334 through 336'
    Processing helix  chain 'A' and resid 337 through 356
      removed outlier: 3.690A  pdb=" N   ILE A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLU A 353 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLY A 356 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 361
      removed outlier: 3.541A  pdb=" N   LEU A 360 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 384
      removed outlier: 3.583A  pdb=" N   VAL A 370 " --> pdb=" O   TYR A 366 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR A 377 " --> pdb=" O   VAL A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 400
      removed outlier: 3.584A  pdb=" N   ALA A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLY A 400 " --> pdb=" O   ASP A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 430
    Processing helix  chain 'A' and resid 440 through 454
      removed outlier: 4.448A  pdb=" N   LEU A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL A 452 " --> pdb=" O   GLN A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 476
      removed outlier: 3.693A  pdb=" N   LYS A 472 " --> pdb=" O   LYS A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 495
      removed outlier: 3.862A  pdb=" N   GLU A 485 " --> pdb=" O   SER A 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 22
    Processing helix  chain 'B' and resid 24 through 33
    Processing helix  chain 'B' and resid 51 through 65
    Processing helix  chain 'B' and resid 86 through 93
    Processing helix  chain 'B' and resid 96 through 111
    Processing helix  chain 'B' and resid 112 through 128
    Processing helix  chain 'B' and resid 131 through 140
    Processing helix  chain 'B' and resid 146 through 157
    Processing helix  chain 'C' and resid 320 through 324
    Processing helix  chain 'C' and resid 325 through 334
    Processing helix  chain 'C' and resid 337 through 343
    Processing helix  chain 'C' and resid 344 through 348
      removed outlier: 3.541A  pdb=" N   VAL C 348 " --> pdb=" O   ALA C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 349 through 357
    Processing helix  chain 'C' and resid 377 through 385
    Processing helix  chain 'C' and resid 400 through 404
      removed outlier: 3.608A  pdb=" N   GLY C 403 " --> pdb=" O   SER C 400 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 411
    Processing helix  chain 'C' and resid 426 through 437
      removed outlier: 4.129A  pdb=" N   ILE C 430 " --> pdb=" O   SER C 426 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 463
      removed outlier: 3.671A  pdb=" N   LEU C 456 " --> pdb=" O   THR C 452 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   GLN C 458 " --> pdb=" O   GLU C 454 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   CYS C 463 " --> pdb=" O   LEU C 459 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 478 through 488
      removed outlier: 3.653A  pdb=" N   GLY C 488 " --> pdb=" O   VAL C 484 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 504 through 512
      removed outlier: 3.759A  pdb=" N   VAL C 508 " --> pdb=" O   THR C 504 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA C 510 " --> pdb=" O   GLN C 506 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA C 512 " --> pdb=" O   VAL C 508 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 529 through 534
    Processing helix  chain 'C' and resid 555 through 563
      removed outlier: 3.716A  pdb=" N   MET C 559 " --> pdb=" O   ASN C 555 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 580 through 591
      removed outlier: 3.902A  pdb=" N   VAL C 584 " --> pdb=" O   ASN C 580 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 607 through 616
      removed outlier: 3.672A  pdb=" N   SER C 616 " --> pdb=" O   ILE C 612 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 634 through 642
      removed outlier: 3.521A  pdb=" N   ALA C 639 " --> pdb=" O   ALA C 635 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLN C 640 " --> pdb=" O   THR C 636 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 659 through 668
      removed outlier: 3.844A  pdb=" N   GLN C 663 " --> pdb=" O   VAL C 659 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   VAL C 665 " --> pdb=" O   VAL C 661 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLN C 666 " --> pdb=" O   GLU C 662 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 681 through 688
      removed outlier: 5.446A  pdb=" N   ARG C 686 " --> pdb=" O   THR C 683 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 30
      removed outlier: 3.716A  pdb=" N   LEU D  24 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 56
    Processing helix  chain 'D' and resid 56 through 65
      removed outlier: 3.623A  pdb=" N   ARG D  62 " --> pdb=" O   TYR D  58 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLY D  65 " --> pdb=" O   SER D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 88 through 93
    Processing helix  chain 'D' and resid 103 through 114
    Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 16
      removed outlier: 7.020A  pdb=" N   LYS B   5 " --> pdb=" O   VAL B  45 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 417 through 418
      removed outlier: 7.247A  pdb=" N   TYR C 417 " --> pdb=" O   HIS C 444 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR C 496 " --> pdb=" O   ILE C 469 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE C 523 " --> pdb=" O   ASP C 546 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU C 597 " --> pdb=" O   THR C 621 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 43 through 47
      removed outlier: 6.293A  pdb=" N   THR D  37 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)

    359 hydrogen bonds defined for protein.
    1032 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: 2.09

  Time building geometry restraints manager: 2.50 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: 2836
        1.35 -     1.46: 1846
        1.46 -     1.58: 4016
        1.58 -     1.70: 0
        1.70 -     1.82: 79
  Bond restraints: 8777
  Sorted by residual:
  bond pdb=" CD2 TRP C 626 "
       pdb=" CE2 TRP C 626 "
    ideal  model  delta    sigma   weight residual
    1.409  1.446 -0.037 1.70e-02 3.46e+03 4.73e+00
  bond pdb=" CD2 TRP C 577 "
       pdb=" CE2 TRP C 577 "
    ideal  model  delta    sigma   weight residual
    1.409  1.446 -0.037 1.70e-02 3.46e+03 4.67e+00
  bond pdb=" CD2 TRP C 577 "
       pdb=" CE3 TRP C 577 "
    ideal  model  delta    sigma   weight residual
    1.398  1.427 -0.029 1.60e-02 3.91e+03 3.31e+00
  bond pdb=" CD2 TRP C 626 "
       pdb=" CE3 TRP C 626 "
    ideal  model  delta    sigma   weight residual
    1.398  1.427 -0.029 1.60e-02 3.91e+03 3.23e+00
  bond pdb=" C   ARG A 173 "
       pdb=" N   PRO A 174 "
    ideal  model  delta    sigma   weight residual
    1.334  1.366 -0.033 2.34e-02 1.83e+03 1.93e+00
  ... (remaining 8772 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 11620
        2.31 -     4.63: 169
        4.63 -     6.94: 20
        6.94 -     9.26: 8
        9.26 -    11.57: 2
  Bond angle restraints: 11819
  Sorted by residual:
  angle pdb=" C   ASP C 449 "
        pdb=" N   LYS C 450 "
        pdb=" CA  LYS C 450 "
      ideal   model   delta    sigma   weight residual
     121.54  132.63  -11.09 1.91e+00 2.74e-01 3.37e+01
  angle pdb=" N   GLU C 662 "
        pdb=" CA  GLU C 662 "
        pdb=" C   GLU C 662 "
      ideal   model   delta    sigma   weight residual
     113.18  105.49    7.69 1.33e+00 5.65e-01 3.34e+01
  angle pdb=" N   GLN A 178 "
        pdb=" CA  GLN A 178 "
        pdb=" C   GLN A 178 "
      ideal   model   delta    sigma   weight residual
     114.75  108.40    6.35 1.26e+00 6.30e-01 2.54e+01
  angle pdb=" C   TRP A 144 "
        pdb=" N   VAL A 145 "
        pdb=" CA  VAL A 145 "
      ideal   model   delta    sigma   weight residual
     121.97  130.55   -8.58 1.80e+00 3.09e-01 2.27e+01
  angle pdb=" CD2 TRP C 577 "
        pdb=" CE3 TRP C 577 "
        pdb=" CZ3 TRP C 577 "
      ideal   model   delta    sigma   weight residual
     118.60  123.99   -5.39 1.30e+00 5.92e-01 1.72e+01
  ... (remaining 11814 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4491
       17.94 -    35.89: 643
       35.89 -    53.83: 195
       53.83 -    71.77: 29
       71.77 -    89.71: 20
  Dihedral angle restraints: 5378
    sinusoidal: 2205
      harmonic: 3173
  Sorted by residual:
  dihedral pdb=" CB  CYS C 396 "
           pdb=" SG  CYS C 396 "
           pdb=" SG  CYS C 422 "
           pdb=" CB  CYS C 422 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.05  -69.05     1      1.00e+01 1.00e-02 6.17e+01
  dihedral pdb=" CA  GLY A 135 "
           pdb=" C   GLY A 135 "
           pdb=" N   ILE A 136 "
           pdb=" CA  ILE A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.37   27.63     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CA  ILE A 296 "
           pdb=" C   ILE A 296 "
           pdb=" N   GLU A 297 "
           pdb=" CA  GLU A 297 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.51   27.49     0      5.00e+00 4.00e-02 3.02e+01
  ... (remaining 5375 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 928
       0.037 -    0.075: 335
       0.075 -    0.112: 80
       0.112 -    0.149: 13
       0.149 -    0.186: 3
  Chirality restraints: 1359
  Sorted by residual:
  chirality pdb=" CG  LEU A 279 "
            pdb=" CB  LEU A 279 "
            pdb=" CD1 LEU A 279 "
            pdb=" CD2 LEU A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.69e-01
  chirality pdb=" CB  ILE B  85 "
            pdb=" CA  ILE B  85 "
            pdb=" CG1 ILE B  85 "
            pdb=" CG2 ILE B  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.02e-01
  chirality pdb=" CA  LYS C 363 "
            pdb=" N   LYS C 363 "
            pdb=" C   LYS C 363 "
            pdb=" CB  LYS C 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.06e-01
  ... (remaining 1356 not shown)

  Planarity restraints: 1498
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 173 "   -0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO A 174 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 174 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 174 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  24 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.07e+00
        pdb=" C   LEU A  24 "    0.030 2.00e-02 2.50e+03
        pdb=" O   LEU A  24 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG A  25 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 449 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.76e+00
        pdb=" C   ASP C 449 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ASP C 449 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LYS C 450 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1495 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 167
        2.67 -     3.23: 8261
        3.23 -     3.79: 12638
        3.79 -     4.34: 17373
        4.34 -     4.90: 28502
  Nonbonded interactions: 66941
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 337 "
            pdb=" OD1 ASP C 339 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" O   ILE C 381 "
            pdb=" OG  SER C 385 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   PRO A 174 "
            pdb=" N   ASN A 176 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   SER A  36 "
            pdb=" OG  SER A  36 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   LYS A 229 "
            pdb=" OG  SER A 234 "
     model   vdw
     2.253 3.040
  ... (remaining 66936 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.760
  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:             0.000
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.210
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
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   0.037   8778  Z= 0.132
  Angle     :  0.706  11.572  11821  Z= 0.407
  Chirality :  0.040   0.186   1359
  Planarity :  0.003   0.044   1498
  Dihedral  : 18.971  89.715   3301
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 11.65 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 28.32 %
    Favored  : 69.73 %
  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: -2.09 (0.26), residues: 1064
  helix: -0.58 (0.21), residues: 617
  sheet: -1.66 (0.84), residues: 52
  loop : -2.57 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  88 
 HIS   0.007   0.001   HIS A 345 
 PHE   0.019   0.001   PHE A 251 
 TYR   0.011   0.001   TYR A 260 
 ARG   0.004   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18834 (  359)
  hydrogen bonds       : angle       5.99429 ( 1032)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.31163 (    2)
  covalent geometry    : bond        0.00244 ( 8777)
  covalent geometry    : angle       0.70557 (11819)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A  269 LEU cc_start: 0.8233 (mt) cc_final: 0.7981 (mp)
REVERT: A  293 GLN cc_start: 0.7833 (pp30) cc_final: 0.7561 (pt0)
REVERT: B   94 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7091 (mmtt)
REVERT: B  144 ASP cc_start: 0.7325 (p0) cc_final: 0.7122 (p0)
REVERT: C  497 MET cc_start: 0.6095 (tpt) cc_final: 0.3589 (mmt)
  outliers start: 19
  outliers final: 14
  residues processed: 152
  average time/residue: 0.2279
  time to fit residues: 47.0288
Evaluate side-chains
  106 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LYS
Chi-restraints excluded: chain C residue  370 ARG
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain C residue  416 ARG
Chi-restraints excluded: chain C residue  494 ARG
Chi-restraints excluded: chain C residue  540 ARG
Chi-restraints excluded: chain C residue  548 ARG
Chi-restraints excluded: chain C residue  614 ARG
Chi-restraints excluded: chain C residue  626 TRP
Chi-restraints excluded: chain C residue  652 ARG
Chi-restraints excluded: chain D residue   28 ARG
Chi-restraints excluded: chain D residue   44 ARG
Chi-restraints excluded: chain D residue   49 ARG
Chi-restraints excluded: chain D residue   62 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:   20.0000
   chunk 80 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 83 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   chunk 96 optimal weight:    9.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 284 GLN
C 447 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4909 r_free = 0.4909 target = 0.273576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.226483 restraints weight = 9678.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.4480 rms_B_bonded: 1.86
r_work: 0.4040 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8778  Z= 0.173
  Angle     :  0.692   9.184  11821  Z= 0.375
  Chirality :  0.043   0.189   1359
  Planarity :  0.004   0.053   1498
  Dihedral  :  7.502  56.944   1184
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.31 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 25.26 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.87 (0.26), residues: 1064
  helix: -0.37 (0.22), residues: 611
  sheet: -1.91 (0.79), residues: 52
  loop : -2.47 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 362 
 HIS   0.007   0.001   HIS A 345 
 PHE   0.022   0.002   PHE A 402 
 TYR   0.027   0.002   TYR A 260 
 ARG   0.005   0.001   ARG A 401 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04580 (  359)
  hydrogen bonds       : angle       4.36784 ( 1032)
  SS BOND              : bond        0.00290 (    1)
  SS BOND              : angle       1.17466 (    2)
  covalent geometry    : bond        0.00392 ( 8777)
  covalent geometry    : angle       0.69143 (11819)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 95
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8324 (tt0) cc_final: 0.7882 (tp-100)
REVERT: A   43 MET cc_start: 0.8210 (mmp) cc_final: 0.7983 (mmt)
REVERT: A  172 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7202 (t80)
REVERT: A  190 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5927 (mt-10)
REVERT: A  241 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6940 (mt-10)
REVERT: A  246 ARG cc_start: 0.7879 (tmm-80) cc_final: 0.7563 (ttp-110)
REVERT: A  278 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.5177 (m-80)
REVERT: A  289 ARG cc_start: 0.8151 (mmp80) cc_final: 0.7815 (ttp80)
REVERT: A  293 GLN cc_start: 0.8185 (pp30) cc_final: 0.7827 (pt0)
REVERT: A  353 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6668 (mp0)
REVERT: B   94 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7438 (mmtm)
REVERT: C  559 MET cc_start: 0.3686 (mmt) cc_final: 0.2824 (mpp)
REVERT: C  595 LYS cc_start: 0.6675 (mtpt) cc_final: 0.6432 (ttpt)
  outliers start: 45
  outliers final: 25
  residues processed: 130
  average time/residue: 0.2020
  time to fit residues: 36.7817
Evaluate side-chains
  111 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 81
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  431 LYS
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain C residue  404 VAL
Chi-restraints excluded: chain C residue  447 ASN
Chi-restraints excluded: chain C residue  548 ARG
Chi-restraints excluded: chain C residue  636 THR
Chi-restraints excluded: chain D residue   44 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 55 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 80 optimal weight:    0.4980
   chunk 103 optimal weight:   50.0000
   chunk 67 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    0.2980
   chunk 37 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 284 GLN
** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.276280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.226874 restraints weight = 9891.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.4543 rms_B_bonded: 1.83
r_work: 0.4252 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.4068 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8778  Z= 0.119
  Angle     :  0.600   9.093  11821  Z= 0.331
  Chirality :  0.040   0.186   1359
  Planarity :  0.003   0.033   1498
  Dihedral  :  6.321  55.234   1142
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.41 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 25.15 %
    Favored  : 70.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.58 (0.27), residues: 1064
  helix: -0.06 (0.22), residues: 607
  sheet: -1.85 (0.78), residues: 52
  loop : -2.46 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 362 
 HIS   0.006   0.001   HIS B  64 
 PHE   0.015   0.001   PHE A 402 
 TYR   0.015   0.001   TYR A 260 
 ARG   0.002   0.000   ARG A 401 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  359)
  hydrogen bonds       : angle       4.11426 ( 1032)
  SS BOND              : bond        0.00157 (    1)
  SS BOND              : angle       1.18749 (    2)
  covalent geometry    : bond        0.00243 ( 8777)
  covalent geometry    : angle       0.59983 (11819)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 87
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8380 (tt0) cc_final: 0.7924 (tp-100)
REVERT: A  172 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.7174 (t80)
REVERT: A  241 GLU cc_start: 0.7155 (mp0) cc_final: 0.6782 (mt-10)
REVERT: A  246 ARG cc_start: 0.7952 (tmm-80) cc_final: 0.7601 (ttp-110)
REVERT: A  278 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.4385 (m-80)
REVERT: A  289 ARG cc_start: 0.8137 (mmp80) cc_final: 0.7766 (ttp80)
REVERT: A  293 GLN cc_start: 0.8150 (pp30) cc_final: 0.7839 (pt0)
REVERT: A  353 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6478 (mp0)
REVERT: B   94 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7440 (mmtm)
REVERT: C  497 MET cc_start: 0.5262 (tpt) cc_final: 0.4099 (mmm)
REVERT: D   98 LEU cc_start: 0.1472 (OUTLIER) cc_final: 0.1229 (mm)
REVERT: D  113 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6930 (mp)
  outliers start: 40
  outliers final: 18
  residues processed: 119
  average time/residue: 0.1930
  time to fit residues: 32.5321
Evaluate side-chains
  105 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  548 ARG
Chi-restraints excluded: chain C residue  636 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  113 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 86 optimal weight:   40.0000
   chunk 30 optimal weight:    2.9990
   chunk 87 optimal weight:   30.0000
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   chunk 88 optimal weight:    6.9990
   chunk 75 optimal weight:   10.0000
   chunk 95 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 284 GLN
** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.272196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.230126 restraints weight = 9752.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.4584 rms_B_bonded: 1.72
r_work: 0.4253 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.4012 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   8778  Z= 0.212
  Angle     :  0.689   8.953  11821  Z= 0.377
  Chirality :  0.044   0.189   1359
  Planarity :  0.004   0.043   1498
  Dihedral  :  6.467  57.215   1138
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.44 %
    Favored  : 86.09 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 23.72 %
    Favored  : 70.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.85 (0.26), residues: 1064
  helix: -0.39 (0.21), residues: 617
  sheet: -1.07 (0.95), residues: 39
  loop : -2.53 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 362 
 HIS   0.006   0.001   HIS D  60 
 PHE   0.023   0.002   PHE A 402 
 TYR   0.027   0.002   TYR A 208 
 ARG   0.004   0.000   ARG A 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04806 (  359)
  hydrogen bonds       : angle       4.27342 ( 1032)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       1.02918 (    2)
  covalent geometry    : bond        0.00500 ( 8777)
  covalent geometry    : angle       0.68925 (11819)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 91
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8517 (tt0) cc_final: 0.8091 (tp-100)
REVERT: A  172 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7164 (t80)
REVERT: A  214 ASN cc_start: 0.5229 (OUTLIER) cc_final: 0.4875 (p0)
REVERT: A  241 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6821 (mt-10)
REVERT: A  246 ARG cc_start: 0.8121 (tmm-80) cc_final: 0.7789 (ttp-110)
REVERT: A  278 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.5204 (m-80)
REVERT: A  293 GLN cc_start: 0.8400 (pp30) cc_final: 0.7996 (pt0)
REVERT: A  353 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6426 (mp0)
REVERT: B   94 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7475 (mmtm)
REVERT: C  399 MET cc_start: 0.6591 (ptt) cc_final: 0.6223 (ptt)
REVERT: C  492 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7173 (tt)
REVERT: C  497 MET cc_start: 0.5193 (tpt) cc_final: 0.3890 (mmm)
REVERT: D   98 LEU cc_start: 0.1746 (OUTLIER) cc_final: 0.1502 (mm)
REVERT: D  113 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6974 (mp)
  outliers start: 53
  outliers final: 34
  residues processed: 131
  average time/residue: 0.1805
  time to fit residues: 34.1280
Evaluate side-chains
  123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 81
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain C residue  404 VAL
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  489 CYS
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  548 ARG
Chi-restraints excluded: chain C residue  626 TRP
Chi-restraints excluded: chain C residue  636 THR
Chi-restraints excluded: chain C residue  661 VAL
Chi-restraints excluded: chain D residue   72 ASN
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   chunk 81 optimal weight:    9.9990
   chunk 30 optimal weight:    0.5980
   chunk 105 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 90 optimal weight:    7.9990
   chunk 103 optimal weight:   40.0000
   chunk 41 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 284 GLN
B  23 GLN
C 458 GLN
** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 555 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4892 r_free = 0.4892 target = 0.272178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.229292 restraints weight = 9771.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.4570 rms_B_bonded: 1.79
r_work: 0.4225 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3987 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8778  Z= 0.192
  Angle     :  0.687   8.934  11821  Z= 0.374
  Chirality :  0.044   0.228   1359
  Planarity :  0.004   0.041   1498
  Dihedral  :  6.468  56.872   1138
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.50 %
    Favored  : 87.03 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 24.74 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.88 (0.26), residues: 1064
  helix: -0.41 (0.21), residues: 617
  sheet: -1.70 (0.78), residues: 52
  loop : -2.47 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 362 
 HIS   0.005   0.001   HIS D  60 
 PHE   0.020   0.001   PHE A 402 
 TYR   0.022   0.002   TYR A 208 
 ARG   0.003   0.000   ARG A 401 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04499 (  359)
  hydrogen bonds       : angle       4.19244 ( 1032)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       0.98377 (    2)
  covalent geometry    : bond        0.00451 ( 8777)
  covalent geometry    : angle       0.68703 (11819)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 84
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8489 (tt0) cc_final: 0.8069 (tp-100)
REVERT: A  172 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7172 (t80)
REVERT: A  241 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6845 (mt-10)
REVERT: A  246 ARG cc_start: 0.8155 (tmm-80) cc_final: 0.7791 (ttp-110)
REVERT: A  278 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.4508 (m-80)
REVERT: A  293 GLN cc_start: 0.8426 (pp30) cc_final: 0.8017 (pt0)
REVERT: A  353 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6469 (mp0)
REVERT: B   94 LYS cc_start: 0.7666 (mmtt) cc_final: 0.7425 (mmtm)
REVERT: C  399 MET cc_start: 0.6604 (ptt) cc_final: 0.6329 (ptt)
REVERT: C  492 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7063 (tt)
REVERT: C  497 MET cc_start: 0.5175 (tpt) cc_final: 0.4050 (mmm)
REVERT: D   98 LEU cc_start: 0.1665 (OUTLIER) cc_final: 0.1436 (mm)
REVERT: D  113 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6900 (mp)
  outliers start: 53
  outliers final: 34
  residues processed: 123
  average time/residue: 0.1806
  time to fit residues: 31.7643
Evaluate side-chains
  118 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 77
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain C residue  404 VAL
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  548 ARG
Chi-restraints excluded: chain C residue  574 CYS
Chi-restraints excluded: chain C residue  626 TRP
Chi-restraints excluded: chain C residue  636 THR
Chi-restraints excluded: chain C residue  661 VAL
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 98 optimal weight:   20.0000
   chunk 38 optimal weight:    0.5980
   chunk 81 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 91 optimal weight:   10.0000
   chunk 93 optimal weight:   50.0000
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 284 GLN
C 458 GLN
** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 555 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4913 r_free = 0.4913 target = 0.274962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.231227 restraints weight = 9814.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.4591 rms_B_bonded: 1.76
r_work: 0.4271 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.4060 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8778  Z= 0.131
  Angle     :  0.614   8.877  11821  Z= 0.337
  Chirality :  0.041   0.189   1359
  Planarity :  0.003   0.031   1498
  Dihedral  :  6.240  55.907   1138
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 12.12 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 25.66 %
    Favored  : 69.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.56 (0.27), residues: 1064
  helix: -0.06 (0.22), residues: 607
  sheet: -1.11 (0.94), residues: 39
  loop : -2.50 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 362 
 HIS   0.004   0.001   HIS D  60 
 PHE   0.015   0.001   PHE A 402 
 TYR   0.013   0.001   TYR A 260 
 ARG   0.002   0.000   ARG A 401 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03606 (  359)
  hydrogen bonds       : angle       3.96398 ( 1032)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       0.82528 (    2)
  covalent geometry    : bond        0.00282 ( 8777)
  covalent geometry    : angle       0.61372 (11819)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 86
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8486 (tt0) cc_final: 0.8073 (tp-100)
REVERT: A  112 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7289 (m-30)
REVERT: A  172 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7165 (t80)
REVERT: A  241 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6858 (mt-10)
REVERT: A  246 ARG cc_start: 0.8138 (tmm-80) cc_final: 0.7800 (ttp-170)
REVERT: A  278 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.4620 (m-80)
REVERT: A  293 GLN cc_start: 0.8317 (pp30) cc_final: 0.7953 (pt0)
REVERT: A  353 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6227 (mp0)
REVERT: B   19 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7423 (mm-30)
REVERT: B   94 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7445 (mmtm)
REVERT: C  399 MET cc_start: 0.6447 (ptt) cc_final: 0.6013 (ptt)
REVERT: C  447 ASN cc_start: 0.7590 (m-40) cc_final: 0.7318 (m-40)
REVERT: C  492 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7091 (tt)
REVERT: C  497 MET cc_start: 0.5041 (tpt) cc_final: 0.4107 (mmm)
REVERT: D   98 LEU cc_start: 0.1469 (OUTLIER) cc_final: 0.1257 (mm)
REVERT: D  113 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6949 (mp)
  outliers start: 47
  outliers final: 28
  residues processed: 123
  average time/residue: 0.1951
  time to fit residues: 34.2223
Evaluate side-chains
  117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 81
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain C residue  340 GLU
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain C residue  404 VAL
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  548 ARG
Chi-restraints excluded: chain C residue  636 THR
Chi-restraints excluded: chain C residue  661 VAL
Chi-restraints excluded: chain C residue  690 MET
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    0.1980
   chunk 44 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 284 GLN
C 444 HIS
** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.276551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.229120 restraints weight = 9898.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.4500 rms_B_bonded: 1.95
r_work: 0.4066 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8778  Z= 0.123
  Angle     :  0.591   8.876  11821  Z= 0.326
  Chirality :  0.040   0.180   1359
  Planarity :  0.003   0.031   1498
  Dihedral  :  6.022  57.573   1138
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.28 %
    Favored  : 88.44 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 25.66 %
    Favored  : 69.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.32 (0.27), residues: 1064
  helix:  0.16 (0.22), residues: 604
  sheet: -1.66 (0.77), residues: 52
  loop : -2.35 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 362 
 HIS   0.004   0.001   HIS D  60 
 PHE   0.014   0.001   PHE A 402 
 TYR   0.011   0.001   TYR A 260 
 ARG   0.002   0.000   ARG A 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03314 (  359)
  hydrogen bonds       : angle       3.80974 ( 1032)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       0.85867 (    2)
  covalent geometry    : bond        0.00259 ( 8777)
  covalent geometry    : angle       0.59078 (11819)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 87
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8318 (tt0) cc_final: 0.7913 (tp-100)
REVERT: A  112 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7193 (m-30)
REVERT: A  172 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.7073 (t80)
REVERT: A  241 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6900 (mt-10)
REVERT: A  246 ARG cc_start: 0.8028 (tmm-80) cc_final: 0.7696 (ttp-110)
REVERT: A  278 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.4568 (m-80)
REVERT: A  293 GLN cc_start: 0.8217 (pp30) cc_final: 0.7890 (pt0)
REVERT: B   19 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7396 (mm-30)
REVERT: B   94 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7441 (mmtm)
REVERT: C  492 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7704 (tt)
REVERT: C  497 MET cc_start: 0.5650 (tpt) cc_final: 0.5000 (mmm)
REVERT: D  113 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6923 (mp)
  outliers start: 46
  outliers final: 29
  residues processed: 123
  average time/residue: 0.1928
  time to fit residues: 33.8027
Evaluate side-chains
  114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 79
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain C residue  340 GLU
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain C residue  404 VAL
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  548 ARG
Chi-restraints excluded: chain C residue  574 CYS
Chi-restraints excluded: chain C residue  636 THR
Chi-restraints excluded: chain C residue  661 VAL
Chi-restraints excluded: chain C residue  690 MET
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 82 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 62 optimal weight:    0.6980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 284 GLN
B  23 GLN
B  90 GLN
** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4901 r_free = 0.4901 target = 0.271599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.230036 restraints weight = 9912.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.4515 rms_B_bonded: 1.70
r_work: 0.4106 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.4106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8778  Z= 0.155
  Angle     :  0.632   9.068  11821  Z= 0.345
  Chirality :  0.042   0.176   1359
  Planarity :  0.003   0.030   1498
  Dihedral  :  6.121  58.988   1138
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 12.12 %
    Favored  : 87.59 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 25.36 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.27), residues: 1064
  helix:  0.06 (0.22), residues: 607
  sheet: -1.12 (0.92), residues: 39
  loop : -2.33 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 362 
 HIS   0.005   0.001   HIS D  60 
 PHE   0.019   0.001   PHE A 402 
 TYR   0.015   0.002   TYR A 260 
 ARG   0.002   0.000   ARG A 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 (  359)
  hydrogen bonds       : angle       3.92308 ( 1032)
  SS BOND              : bond        0.00405 (    1)
  SS BOND              : angle       0.85991 (    2)
  covalent geometry    : bond        0.00355 ( 8777)
  covalent geometry    : angle       0.63239 (11819)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 77
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8262 (tt0) cc_final: 0.7876 (tp-100)
REVERT: A  112 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7229 (m-30)
REVERT: A  172 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6992 (t80)
REVERT: A  241 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6866 (mt-10)
REVERT: A  246 ARG cc_start: 0.7951 (tmm-80) cc_final: 0.7656 (ttp-110)
REVERT: A  278 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.4504 (m-80)
REVERT: A  293 GLN cc_start: 0.8220 (pp30) cc_final: 0.7893 (pt0)
REVERT: A  353 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6295 (mp0)
REVERT: B   94 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7489 (mmtm)
REVERT: C  447 ASN cc_start: 0.7151 (m-40) cc_final: 0.6918 (m-40)
REVERT: C  492 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7914 (tt)
REVERT: C  497 MET cc_start: 0.5936 (tpt) cc_final: 0.5382 (mmm)
  outliers start: 44
  outliers final: 32
  residues processed: 109
  average time/residue: 0.2104
  time to fit residues: 31.8404
Evaluate side-chains
  114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 76
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain C residue  340 GLU
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain C residue  404 VAL
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  548 ARG
Chi-restraints excluded: chain C residue  574 CYS
Chi-restraints excluded: chain C residue  636 THR
Chi-restraints excluded: chain C residue  661 VAL
Chi-restraints excluded: chain C residue  690 MET
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0980
   chunk 68 optimal weight:    0.0980
   chunk 96 optimal weight:   10.0000
   chunk 40 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 284 GLN
** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4933 r_free = 0.4933 target = 0.274980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.234578 restraints weight = 9851.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.4607 rms_B_bonded: 1.64
r_work: 0.4300 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.4084 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8778  Z= 0.116
  Angle     :  0.590   8.880  11821  Z= 0.324
  Chirality :  0.040   0.177   1359
  Planarity :  0.003   0.030   1498
  Dihedral  :  5.960  57.309   1138
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.37 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 26.48 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.27), residues: 1064
  helix:  0.28 (0.22), residues: 613
  sheet: -1.11 (0.93), residues: 39
  loop : -2.45 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 167 
 HIS   0.004   0.001   HIS A 345 
 PHE   0.013   0.001   PHE A 402 
 TYR   0.010   0.001   TYR A 260 
 ARG   0.001   0.000   ARG A 289 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  359)
  hydrogen bonds       : angle       3.77635 ( 1032)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.83245 (    2)
  covalent geometry    : bond        0.00238 ( 8777)
  covalent geometry    : angle       0.59003 (11819)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 81
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8377 (tt0) cc_final: 0.7982 (tp-100)
REVERT: A  112 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7182 (m-30)
REVERT: A  172 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7109 (t80)
REVERT: A  241 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6891 (mt-10)
REVERT: A  246 ARG cc_start: 0.8075 (tmm-80) cc_final: 0.7714 (ttp-110)
REVERT: A  278 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.4575 (m-80)
REVERT: A  293 GLN cc_start: 0.8178 (pp30) cc_final: 0.7857 (pt0)
REVERT: A  353 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6294 (mp0)
REVERT: B   19 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7239 (mm-30)
REVERT: B   94 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7209 (mmtp)
REVERT: C  482 MET cc_start: 0.5702 (mmt) cc_final: 0.5273 (mmt)
REVERT: C  492 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7169 (tt)
REVERT: C  497 MET cc_start: 0.4828 (tpt) cc_final: 0.4306 (mmm)
  outliers start: 36
  outliers final: 27
  residues processed: 107
  average time/residue: 0.2042
  time to fit residues: 31.3045
Evaluate side-chains
  109 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 76
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  548 ARG
Chi-restraints excluded: chain C residue  574 CYS
Chi-restraints excluded: chain C residue  661 VAL
Chi-restraints excluded: chain C residue  690 MET
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 71 optimal weight:    8.9990
   chunk 97 optimal weight:    8.9990
   chunk 64 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 102 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 101 optimal weight:    8.9990
   chunk 86 optimal weight:   20.0000
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 284 GLN
** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4920 r_free = 0.4920 target = 0.273793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.232289 restraints weight = 9792.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.4589 rms_B_bonded: 1.66
r_work: 0.4272 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.4066 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8778  Z= 0.131
  Angle     :  0.603   9.138  11821  Z= 0.330
  Chirality :  0.041   0.176   1359
  Planarity :  0.003   0.029   1498
  Dihedral  :  5.905  54.473   1138
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.37 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 26.58 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.15 (0.27), residues: 1064
  helix:  0.30 (0.22), residues: 613
  sheet: -1.16 (0.90), residues: 39
  loop : -2.38 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 362 
 HIS   0.004   0.001   HIS D  60 
 PHE   0.016   0.001   PHE A 402 
 TYR   0.013   0.001   TYR A 260 
 ARG   0.002   0.000   ARG A 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (  359)
  hydrogen bonds       : angle       3.76548 ( 1032)
  SS BOND              : bond        0.00241 (    1)
  SS BOND              : angle       0.92218 (    2)
  covalent geometry    : bond        0.00285 ( 8777)
  covalent geometry    : angle       0.60278 (11819)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 77
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8366 (tt0) cc_final: 0.7968 (tp-100)
REVERT: A  112 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7120 (m-30)
REVERT: A  172 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7124 (t80)
REVERT: A  241 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6861 (mt-10)
REVERT: A  246 ARG cc_start: 0.8042 (tmm-80) cc_final: 0.7669 (ttp-110)
REVERT: A  278 TYR cc_start: 0.6602 (OUTLIER) cc_final: 0.4492 (m-80)
REVERT: A  293 GLN cc_start: 0.8167 (pp30) cc_final: 0.7857 (pt0)
REVERT: A  353 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6325 (mp0)
REVERT: B   94 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7159 (mmtp)
REVERT: C  482 MET cc_start: 0.5625 (mmt) cc_final: 0.5195 (mmt)
REVERT: C  492 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7120 (tt)
REVERT: C  497 MET cc_start: 0.5034 (tpt) cc_final: 0.4429 (mmm)
  outliers start: 35
  outliers final: 26
  residues processed: 103
  average time/residue: 0.1982
  time to fit residues: 29.0528
Evaluate side-chains
  108 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 76
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  172 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain C residue  397 ARG
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  548 ARG
Chi-restraints excluded: chain C residue  574 CYS
Chi-restraints excluded: chain C residue  661 VAL
Chi-restraints excluded: chain C residue  690 MET
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 95 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    0.2980
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 66 optimal weight:    0.4980
   chunk 80 optimal weight:    0.0270
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 284 GLN
** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4941 r_free = 0.4941 target = 0.275933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.236287 restraints weight = 9810.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.4623 rms_B_bonded: 1.76
r_work: 0.4287 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.4071 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8778  Z= 0.113
  Angle     :  0.582   9.061  11821  Z= 0.319
  Chirality :  0.040   0.175   1359
  Planarity :  0.003   0.030   1498
  Dihedral  :  5.806  56.325   1138
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.00 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 26.79 %
    Favored  : 69.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.27), residues: 1064
  helix:  0.40 (0.22), residues: 613
  sheet: -1.16 (0.90), residues: 39
  loop : -2.37 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 167 
 HIS   0.004   0.001   HIS A 345 
 PHE   0.013   0.001   PHE A 402 
 TYR   0.010   0.001   TYR A  42 
 ARG   0.001   0.000   ARG A 289 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03062 (  359)
  hydrogen bonds       : angle       3.65812 ( 1032)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.84108 (    2)
  covalent geometry    : bond        0.00230 ( 8777)
  covalent geometry    : angle       0.58188 (11819)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4907.63 seconds
wall clock time: 85 minutes 32.19 seconds (5132.19 seconds total)