Starting phenix.real_space_refine
on Thu Mar 14 17:44:24 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/03_2024/8ur3_42480.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/03_2024/8ur3_42480.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/03_2024/8ur3_42480.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/03_2024/8ur3_42480.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/03_2024/8ur3_42480.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/03_2024/8ur3_42480.pdb"
  }
  resolution = 2.61
  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=   0.021
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      44      5.16       5
     C    5982      2.51       5
     N    1544      2.21       5
     O    1806      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  223": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 9376
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 4688
          Classifications: {'peptide': 579}
          Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 4688
          Classifications: {'peptide': 579}
          Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 8
    residue:
      pdb=" N   ARG A  78 " occ=0.86
      ... (9 atoms not shown)
      pdb=" NH2 ARG A  78 " occ=0.86
    residue:
      pdb=" N   GLY A  79 " occ=0.82
      ... (2 atoms not shown)
      pdb=" O   GLY A  79 " occ=0.82
    residue:
      pdb=" N   GLY A  80 " occ=0.83
      ... (2 atoms not shown)
      pdb=" O   GLY A  80 " occ=0.83
    residue:
      pdb=" N   ARG A  81 " occ=0.62
      ... (9 atoms not shown)
      pdb=" NH2 ARG A  81 " occ=0.62
    residue:
      pdb=" N   ARG B  78 " occ=0.86
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  78 " occ=0.86
    residue:
      pdb=" N   GLY B  79 " occ=0.82
      ... (2 atoms not shown)
      pdb=" O   GLY B  79 " occ=0.82
    residue:
      pdb=" N   GLY B  80 " occ=0.83
      ... (2 atoms not shown)
      pdb=" O   GLY B  80 " occ=0.83
    residue:
      pdb=" N   ARG B  81 " occ=0.62
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  81 " occ=0.62
  Time building chain proxies: 5.20, per 1000 atoms: 0.55
  Number of scatterers: 9376
  At special positions: 0
  Unit cell: (101.268, 115.884, 82.476, 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      44     16.00
     O    1806      8.00
     N    1544      7.00
     C    5982      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.39
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2204

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 8 sheets defined
      42.7% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 12
      removed outlier: 3.536A  pdb=" N   ALA A  10 " --> pdb=" O   GLY A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 23
      removed outlier: 3.519A  pdb=" N   ASN A  22 " --> pdb=" O   ASN A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 44
    Processing helix  chain 'A' and resid 48 through 50
      No H-bonds generated for 'chain 'A' and resid 48 through 50'
    Processing helix  chain 'A' and resid 87 through 94
    Processing helix  chain 'A' and resid 106 through 118
    Processing helix  chain 'A' and resid 143 through 155
    Processing helix  chain 'A' and resid 158 through 162
      removed outlier: 3.991A  pdb=" N   ASP A 162 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 176
      removed outlier: 3.596A  pdb=" N   PHE A 175 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.571A  pdb=" N   ILE A 181 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 205
    Processing helix  chain 'A' and resid 206 through 209
      removed outlier: 3.771A  pdb=" N   ILE A 209 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 206 through 209'
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 229 through 240
      removed outlier: 3.533A  pdb=" N   HIS A 240 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 324
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 3.670A  pdb=" N   GLY A 330 " --> pdb=" O   PRO A 327 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ASN A 331 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 354 through 366
    Processing helix  chain 'A' and resid 426 through 430
    Processing helix  chain 'A' and resid 431 through 443
    Processing helix  chain 'A' and resid 449 through 456
      removed outlier: 3.643A  pdb=" N   LEU A 453 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 454 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 523
      removed outlier: 3.584A  pdb=" N   SER A 511 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 537
    Processing helix  chain 'A' and resid 538 through 550
      removed outlier: 3.682A  pdb=" N   ASN A 550 " --> pdb=" O   ILE A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 562 through 576
    Processing helix  chain 'A' and resid 579 through 588
    Processing helix  chain 'B' and resid 6 through 12
      removed outlier: 3.536A  pdb=" N   ALA B  10 " --> pdb=" O   GLY B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 23
      removed outlier: 3.521A  pdb=" N   ASN B  22 " --> pdb=" O   ASN B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 44
    Processing helix  chain 'B' and resid 48 through 50
      No H-bonds generated for 'chain 'B' and resid 48 through 50'
    Processing helix  chain 'B' and resid 87 through 94
    Processing helix  chain 'B' and resid 106 through 118
    Processing helix  chain 'B' and resid 143 through 155
    Processing helix  chain 'B' and resid 158 through 162
      removed outlier: 3.988A  pdb=" N   ASP B 162 " --> pdb=" O   GLU B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.593A  pdb=" N   PHE B 175 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 187
      removed outlier: 3.571A  pdb=" N   ILE B 181 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR B 185 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 205
    Processing helix  chain 'B' and resid 206 through 209
      removed outlier: 3.771A  pdb=" N   ILE B 209 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 206 through 209'
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'B' and resid 229 through 240
      removed outlier: 3.525A  pdb=" N   HIS B 240 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 324
    Processing helix  chain 'B' and resid 326 through 331
      removed outlier: 3.663A  pdb=" N   GLY B 330 " --> pdb=" O   PRO B 327 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   ASN B 331 " --> pdb=" O   GLU B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 337
    Processing helix  chain 'B' and resid 354 through 366
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 431 through 443
    Processing helix  chain 'B' and resid 449 through 456
      removed outlier: 3.640A  pdb=" N   LEU B 453 " --> pdb=" O   LYS B 449 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA B 454 " --> pdb=" O   ILE B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 523
      removed outlier: 3.584A  pdb=" N   SER B 511 " --> pdb=" O   THR B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 537
    Processing helix  chain 'B' and resid 538 through 550
      removed outlier: 3.681A  pdb=" N   ASN B 550 " --> pdb=" O   ILE B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 559
    Processing helix  chain 'B' and resid 562 through 576
    Processing helix  chain 'B' and resid 579 through 588
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4
    Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245
      removed outlier: 6.273A  pdb=" N   ILE A  52 " --> pdb=" O   GLN A 243 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   GLU A 245 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   ILE A  54 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ALA A  25 " --> pdb=" O   HIS A  53 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   LEU A  55 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LEU A  27 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   THR A 289 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL A 286 " --> pdb=" O   ALA A 492 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   ILE A 494 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL A 288 " --> pdb=" O   ILE A 494 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133
      removed outlier: 4.384A  pdb=" N   MET A 389 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ALA A 413 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   VAL A 346 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 257
      removed outlier: 6.032A  pdb=" N   VAL A 250 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ASP A 270 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASP A 252 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU A 266 " --> pdb=" O   LYS A 254 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ASP A 256 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ALA A 264 " --> pdb=" O   ASP A 256 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4
    Processing sheet with id=AA6, first strand: chain 'B' and resid 243 through 245
      removed outlier: 6.268A  pdb=" N   ILE B  52 " --> pdb=" O   GLN B 243 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   GLU B 245 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   ILE B  54 " --> pdb=" O   GLU B 245 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ALA B  25 " --> pdb=" O   HIS B  53 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   LEU B  55 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU B  27 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   THR B 289 " --> pdb=" O   ILE B  28 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   ALA B 492 " --> pdb=" O   ASP B 284 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL B 286 " --> pdb=" O   ALA B 492 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   ILE B 494 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL B 288 " --> pdb=" O   ILE B 494 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 133
      removed outlier: 4.385A  pdb=" N   MET B 389 " --> pdb=" O   ILE B 382 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA B 413 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   VAL B 346 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 257
      removed outlier: 6.037A  pdb=" N   VAL B 250 " --> pdb=" O   ASP B 270 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ASP B 270 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASP B 252 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU B 266 " --> pdb=" O   LYS B 254 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ASP B 256 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ALA B 264 " --> pdb=" O   ASP B 256 " (cutoff:3.500A)

    337 hydrogen bonds defined for protein.
    951 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: 2.55

  Time building geometry restraints manager: 3.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3033
        1.34 -     1.46: 1785
        1.46 -     1.57: 4702
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 9592
  Sorted by residual:
  bond pdb=" C   ILE A 581 "
       pdb=" O   ILE A 581 "
    ideal  model  delta    sigma   weight residual
    1.237  1.225  0.013 1.17e-02 7.31e+03 1.15e+00
  bond pdb=" N   ILE A 461 "
       pdb=" CA  ILE A 461 "
    ideal  model  delta    sigma   weight residual
    1.458  1.450  0.008 7.70e-03 1.69e+04 1.02e+00
  bond pdb=" CB  GLU A 110 "
       pdb=" CG  GLU A 110 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 9.82e-01
  bond pdb=" CA  ILE A 461 "
       pdb=" C   ILE A 461 "
    ideal  model  delta    sigma   weight residual
    1.528  1.536 -0.008 8.50e-03 1.38e+04 9.33e-01
  bond pdb=" CB  GLU B 110 "
       pdb=" CG  GLU B 110 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.23e-01
  ... (remaining 9587 not shown)

  Histogram of bond angle deviations from ideal:
       99.60 -   106.51: 242
      106.51 -   113.42: 5214
      113.42 -   120.33: 3494
      120.33 -   127.24: 3934
      127.24 -   134.15: 114
  Bond angle restraints: 12998
  Sorted by residual:
  angle pdb=" C   HIS A 588 "
        pdb=" N   LYS A 589 "
        pdb=" CA  LYS A 589 "
      ideal   model   delta    sigma   weight residual
     121.54  127.31   -5.77 1.91e+00 2.74e-01 9.14e+00
  angle pdb=" C   HIS B 588 "
        pdb=" N   LYS B 589 "
        pdb=" CA  LYS B 589 "
      ideal   model   delta    sigma   weight residual
     121.54  127.29   -5.75 1.91e+00 2.74e-01 9.07e+00
  angle pdb=" C   GLN A 396 "
        pdb=" N   GLN A 397 "
        pdb=" CA  GLN A 397 "
      ideal   model   delta    sigma   weight residual
     121.70  126.19   -4.49 1.80e+00 3.09e-01 6.21e+00
  angle pdb=" C   GLN B 396 "
        pdb=" N   GLN B 397 "
        pdb=" CA  GLN B 397 "
      ideal   model   delta    sigma   weight residual
     121.70  126.16   -4.46 1.80e+00 3.09e-01 6.14e+00
  angle pdb=" N   VAL B 169 "
        pdb=" CA  VAL B 169 "
        pdb=" C   VAL B 169 "
      ideal   model   delta    sigma   weight residual
     113.47  111.16    2.31 1.01e+00 9.80e-01 5.25e+00
  ... (remaining 12993 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.66: 5074
       14.66 -    29.33: 498
       29.33 -    43.99: 134
       43.99 -    58.66: 24
       58.66 -    73.32: 16
  Dihedral angle restraints: 5746
    sinusoidal: 2336
      harmonic: 3410
  Sorted by residual:
  dihedral pdb=" CA  VAL B 483 "
           pdb=" C   VAL B 483 "
           pdb=" N   VAL B 484 "
           pdb=" CA  VAL B 484 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.48   17.52     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  VAL A 483 "
           pdb=" C   VAL A 483 "
           pdb=" N   VAL A 484 "
           pdb=" CA  VAL A 484 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.62   17.38     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CG  ARG B 540 "
           pdb=" CD  ARG B 540 "
           pdb=" NE  ARG B 540 "
           pdb=" CZ  ARG B 540 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -130.89   40.89     2      1.50e+01 4.44e-03 9.14e+00
  ... (remaining 5743 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 771
       0.030 -    0.059: 406
       0.059 -    0.089: 157
       0.089 -    0.119: 60
       0.119 -    0.148: 32
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" CB  ILE B 278 "
            pdb=" CA  ILE B 278 "
            pdb=" CG1 ILE B 278 "
            pdb=" CG2 ILE B 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CB  ILE A 278 "
            pdb=" CA  ILE A 278 "
            pdb=" CG1 ILE A 278 "
            pdb=" CG2 ILE A 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.18e-01
  chirality pdb=" CA  ILE A 529 "
            pdb=" N   ILE A 529 "
            pdb=" C   ILE A 529 "
            pdb=" CB  ILE A 529 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1423 not shown)

  Planarity restraints: 1668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 190 "   -0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO B 191 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B 191 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 191 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 190 "    0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO A 191 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 191 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 191 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 231 "    0.020 5.00e-02 4.00e+02   2.99e-02 1.44e+00
        pdb=" N   PRO A 232 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 232 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 232 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1665 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2281
        2.78 -     3.31: 8750
        3.31 -     3.84: 16605
        3.84 -     4.37: 20500
        4.37 -     4.90: 33708
  Nonbonded interactions: 81844
  Sorted by model distance:
  nonbonded pdb=" O   THR A 185 "
            pdb=" OH  TYR A 412 "
     model   vdw
     2.253 2.440
  nonbonded pdb=" O   THR B 185 "
            pdb=" OH  TYR B 412 "
     model   vdw
     2.256 2.440
  nonbonded pdb=" OG  SER A 431 "
            pdb=" OD1 ASN A 433 "
     model   vdw
     2.265 2.440
  nonbonded pdb=" OG  SER B 431 "
            pdb=" OD1 ASN B 433 "
     model   vdw
     2.265 2.440
  nonbonded pdb=" OD1 ASP A 301 "
            pdb=" OG1 THR A 304 "
     model   vdw
     2.273 2.440
  ... (remaining 81839 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.62 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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          4.160
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     27.000
  Find NCS groups from input model:        0.390
  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:             0.010
  Load rotamer database and sin/cos tables:11.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9592  Z= 0.215
  Angle     :  0.513   6.122  12998  Z= 0.274
  Chirality :  0.045   0.148   1426
  Planarity :  0.003   0.030   1668
  Dihedral  : 13.471  73.321   3542
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.23), residues: 1150
  helix: -0.69 (0.23), residues: 388
  sheet:  0.20 (0.47), residues: 142
  loop : -0.26 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 208 
 PHE   0.009   0.001   PHE A  11 
 TYR   0.008   0.001   TYR A 464 
 ARG   0.001   0.000   ARG B  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8543 (pm20) cc_final: 0.8293 (pm20)
REVERT: A   19 ASN cc_start: 0.8463 (t0) cc_final: 0.8248 (t0)
REVERT: A  132 GLN cc_start: 0.8494 (mp10) cc_final: 0.7930 (mp10)
REVERT: A  233 MET cc_start: 0.9133 (mtm) cc_final: 0.8891 (mtm)
REVERT: A  261 GLN cc_start: 0.8713 (pt0) cc_final: 0.8181 (pm20)
REVERT: A  401 ASP cc_start: 0.8650 (m-30) cc_final: 0.8080 (t0)
REVERT: A  564 MET cc_start: 0.7545 (mmp) cc_final: 0.6731 (tpt)
REVERT: B   18 GLU cc_start: 0.8538 (pm20) cc_final: 0.8296 (pm20)
REVERT: B   19 ASN cc_start: 0.8466 (t0) cc_final: 0.8250 (t0)
REVERT: B  132 GLN cc_start: 0.8488 (mp10) cc_final: 0.7931 (mp10)
REVERT: B  233 MET cc_start: 0.9148 (mtm) cc_final: 0.8909 (mtm)
REVERT: B  261 GLN cc_start: 0.8710 (pt0) cc_final: 0.8186 (pm20)
REVERT: B  564 MET cc_start: 0.7572 (mmp) cc_final: 0.6684 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 1.4682
  time to fit residues: 177.5226
Evaluate side-chains
  67 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0050
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
A 442 HIS
A 553 GLN
B 240 HIS
B 442 HIS
B 553 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   9592  Z= 0.147
  Angle     :  0.450   4.943  12998  Z= 0.241
  Chirality :  0.042   0.153   1426
  Planarity :  0.003   0.027   1668
  Dihedral  :  3.927  14.702   1252
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  6.83 %
    Favored  : 92.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1150
  helix:  0.64 (0.26), residues: 394
  sheet: -0.15 (0.46), residues: 140
  loop : -0.05 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 183 
 HIS   0.001   0.000   HIS A 208 
 PHE   0.009   0.001   PHE A 506 
 TYR   0.015   0.001   TYR A 112 
 ARG   0.004   0.000   ARG A 324 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8613 (pm20) cc_final: 0.8378 (pm20)
REVERT: A  159 GLU cc_start: 0.8851 (mp0) cc_final: 0.8550 (pm20)
REVERT: A  261 GLN cc_start: 0.8691 (pt0) cc_final: 0.8210 (pm20)
REVERT: A  401 ASP cc_start: 0.8650 (m-30) cc_final: 0.8045 (t0)
REVERT: A  564 MET cc_start: 0.7276 (mmp) cc_final: 0.6358 (tmm)
REVERT: B   18 GLU cc_start: 0.8613 (pm20) cc_final: 0.8378 (pm20)
REVERT: B  159 GLU cc_start: 0.8864 (mp0) cc_final: 0.8551 (pm20)
REVERT: B  261 GLN cc_start: 0.8680 (pt0) cc_final: 0.8199 (pm20)
REVERT: B  401 ASP cc_start: 0.8637 (m-30) cc_final: 0.8031 (t0)
REVERT: B  564 MET cc_start: 0.7223 (mmp) cc_final: 0.6496 (tpt)
REVERT: B  574 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8507 (pptt)
REVERT: B  586 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8451 (mttp)
  outliers start: 8
  outliers final: 2
  residues processed: 80
  average time/residue: 1.3889
  time to fit residues: 118.9452
Evaluate side-chains
  68 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  574 LYS
Chi-restraints excluded: chain B residue  586 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 70 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 112 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
B 240 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9592  Z= 0.283
  Angle     :  0.486   4.972  12998  Z= 0.260
  Chirality :  0.044   0.150   1426
  Planarity :  0.003   0.025   1668
  Dihedral  :  4.055  15.152   1252
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  9.71 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1150
  helix:  1.25 (0.27), residues: 394
  sheet: -0.16 (0.44), residues: 138
  loop :  0.11 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 442 
 PHE   0.019   0.001   PHE A 506 
 TYR   0.011   0.001   TYR B 112 
 ARG   0.003   0.000   ARG A  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8946 (m-30) cc_final: 0.8421 (p0)
REVERT: A  401 ASP cc_start: 0.8709 (m-30) cc_final: 0.8119 (t0)
REVERT: A  506 PHE cc_start: 0.8977 (t80) cc_final: 0.8727 (t80)
REVERT: A  564 MET cc_start: 0.7388 (mmp) cc_final: 0.6504 (tmm)
REVERT: B  173 ASP cc_start: 0.8951 (m-30) cc_final: 0.8421 (p0)
REVERT: B  401 ASP cc_start: 0.8674 (m-30) cc_final: 0.8093 (t0)
REVERT: B  506 PHE cc_start: 0.8977 (t80) cc_final: 0.8729 (t80)
REVERT: B  564 MET cc_start: 0.7357 (mmp) cc_final: 0.6708 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 66
  average time/residue: 1.2686
  time to fit residues: 90.4644
Evaluate side-chains
  65 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 104 optimal weight:    0.0370
   chunk 110 optimal weight:    3.9990
   chunk 54 optimal weight:    0.5980
   chunk 98 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.6862

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
B 240 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9592  Z= 0.158
  Angle     :  0.431   4.823  12998  Z= 0.230
  Chirality :  0.042   0.149   1426
  Planarity :  0.003   0.025   1668
  Dihedral  :  3.808  15.131   1252
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 10.29 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.25), residues: 1150
  helix:  1.49 (0.27), residues: 394
  sheet: -0.37 (0.43), residues: 138
  loop :  0.19 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 316 
 HIS   0.001   0.000   HIS A 208 
 PHE   0.010   0.001   PHE A 506 
 TYR   0.012   0.001   TYR B 112 
 ARG   0.002   0.000   ARG B  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8456 (mp10) cc_final: 0.7631 (mp10)
REVERT: A  173 ASP cc_start: 0.8933 (m-30) cc_final: 0.8490 (p0)
REVERT: A  471 TYR cc_start: 0.8752 (p90) cc_final: 0.8347 (p90)
REVERT: A  506 PHE cc_start: 0.8955 (t80) cc_final: 0.8635 (t80)
REVERT: A  564 MET cc_start: 0.7274 (mmp) cc_final: 0.6400 (tmm)
REVERT: B  132 GLN cc_start: 0.8463 (mp10) cc_final: 0.7644 (mp10)
REVERT: B  173 ASP cc_start: 0.8935 (m-30) cc_final: 0.8490 (p0)
REVERT: B  471 TYR cc_start: 0.8756 (p90) cc_final: 0.8347 (p90)
REVERT: B  506 PHE cc_start: 0.8953 (t80) cc_final: 0.8639 (t80)
REVERT: B  564 MET cc_start: 0.7297 (mmp) cc_final: 0.6416 (tmm)
  outliers start: 7
  outliers final: 4
  residues processed: 64
  average time/residue: 1.2787
  time to fit residues: 88.4125
Evaluate side-chains
  66 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  508 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0970
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
B 240 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9592  Z= 0.187
  Angle     :  0.436   4.827  12998  Z= 0.233
  Chirality :  0.042   0.145   1426
  Planarity :  0.003   0.025   1668
  Dihedral  :  3.759  14.541   1252
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.81 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.25), residues: 1150
  helix:  1.65 (0.27), residues: 396
  sheet: -0.45 (0.43), residues: 138
  loop :  0.26 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 316 
 HIS   0.002   0.001   HIS B 442 
 PHE   0.011   0.001   PHE A 506 
 TYR   0.010   0.001   TYR A 112 
 ARG   0.002   0.000   ARG B  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7256 (mtm)
REVERT: A  132 GLN cc_start: 0.8473 (mp10) cc_final: 0.7632 (mp10)
REVERT: A  173 ASP cc_start: 0.8936 (m-30) cc_final: 0.8502 (p0)
REVERT: A  506 PHE cc_start: 0.8959 (t80) cc_final: 0.8705 (t80)
REVERT: A  539 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8233 (mt)
REVERT: A  564 MET cc_start: 0.7309 (mmp) cc_final: 0.6431 (tmm)
REVERT: B  132 GLN cc_start: 0.8474 (mp10) cc_final: 0.7633 (mp10)
REVERT: B  173 ASP cc_start: 0.8954 (m-30) cc_final: 0.8493 (p0)
REVERT: B  449 LYS cc_start: 0.9045 (ptpt) cc_final: 0.8700 (ptmm)
REVERT: B  471 TYR cc_start: 0.8806 (p90) cc_final: 0.8430 (p90)
REVERT: B  506 PHE cc_start: 0.8953 (t80) cc_final: 0.8655 (t80)
REVERT: B  539 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8202 (mm)
REVERT: B  564 MET cc_start: 0.7324 (mmp) cc_final: 0.6342 (tmm)
  outliers start: 13
  outliers final: 0
  residues processed: 75
  average time/residue: 1.2413
  time to fit residues: 100.4644
Evaluate side-chains
  67 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain B residue  539 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 110 optimal weight:    4.9990
   chunk 91 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9592  Z= 0.260
  Angle     :  0.466   4.889  12998  Z= 0.250
  Chirality :  0.043   0.142   1426
  Planarity :  0.003   0.027   1668
  Dihedral  :  3.912  14.765   1252
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.77 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.25), residues: 1150
  helix:  1.63 (0.27), residues: 398
  sheet: -0.44 (0.43), residues: 138
  loop :  0.24 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 442 
 PHE   0.012   0.001   PHE B 506 
 TYR   0.009   0.001   TYR B 226 
 ARG   0.005   0.000   ARG B  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8436 (mp10) cc_final: 0.7537 (mp10)
REVERT: A  173 ASP cc_start: 0.8970 (m-30) cc_final: 0.8429 (p0)
REVERT: A  506 PHE cc_start: 0.9045 (t80) cc_final: 0.8797 (t80)
REVERT: A  564 MET cc_start: 0.7377 (mmp) cc_final: 0.6484 (tmm)
REVERT: B  132 GLN cc_start: 0.8434 (mp10) cc_final: 0.7536 (mp10)
REVERT: B  173 ASP cc_start: 0.8973 (m-30) cc_final: 0.8427 (p0)
REVERT: B  449 LYS cc_start: 0.9041 (ptpt) cc_final: 0.8684 (ptmm)
REVERT: B  506 PHE cc_start: 0.9045 (t80) cc_final: 0.8801 (t80)
REVERT: B  539 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8219 (mm)
REVERT: B  564 MET cc_start: 0.7383 (mmp) cc_final: 0.6506 (tmm)
  outliers start: 15
  outliers final: 5
  residues processed: 74
  average time/residue: 1.3520
  time to fit residues: 107.7943
Evaluate side-chains
  69 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  539 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    0.0670
   chunk 12 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0980
   chunk 109 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.0324

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
B 240 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9592  Z= 0.208
  Angle     :  0.452   4.850  12998  Z= 0.242
  Chirality :  0.043   0.141   1426
  Planarity :  0.003   0.029   1668
  Dihedral  :  3.878  14.992   1252
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.67 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.25), residues: 1150
  helix:  1.66 (0.27), residues: 398
  sheet: -0.46 (0.43), residues: 138
  loop :  0.24 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 316 
 HIS   0.002   0.001   HIS B 442 
 PHE   0.010   0.001   PHE A 506 
 TYR   0.010   0.001   TYR A 112 
 ARG   0.004   0.000   ARG A  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7294 (mtm)
REVERT: A  132 GLN cc_start: 0.8435 (mp10) cc_final: 0.7597 (mp10)
REVERT: A  173 ASP cc_start: 0.8945 (m-30) cc_final: 0.8510 (p0)
REVERT: A  401 ASP cc_start: 0.8658 (m-30) cc_final: 0.8023 (t0)
REVERT: A  471 TYR cc_start: 0.8782 (p90) cc_final: 0.8436 (p90)
REVERT: A  506 PHE cc_start: 0.9014 (t80) cc_final: 0.8724 (t80)
REVERT: A  564 MET cc_start: 0.7347 (mmp) cc_final: 0.6343 (tmm)
REVERT: B  132 GLN cc_start: 0.8432 (mp10) cc_final: 0.7595 (mp10)
REVERT: B  173 ASP cc_start: 0.8946 (m-30) cc_final: 0.8508 (p0)
REVERT: B  401 ASP cc_start: 0.8638 (m-30) cc_final: 0.8033 (t0)
REVERT: B  449 LYS cc_start: 0.9036 (ptpt) cc_final: 0.8718 (ptmm)
REVERT: B  471 TYR cc_start: 0.8781 (p90) cc_final: 0.8431 (p90)
REVERT: B  506 PHE cc_start: 0.9013 (t80) cc_final: 0.8729 (t80)
REVERT: B  564 MET cc_start: 0.7299 (mmp) cc_final: 0.6325 (tmm)
  outliers start: 13
  outliers final: 5
  residues processed: 72
  average time/residue: 1.2401
  time to fit residues: 96.4608
Evaluate side-chains
  74 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain B residue  389 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 65 optimal weight:    0.3980
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 69 optimal weight:    0.2980
   chunk 74 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 105 optimal weight:    4.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
B 240 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9592  Z= 0.147
  Angle     :  0.433   5.292  12998  Z= 0.232
  Chirality :  0.042   0.140   1426
  Planarity :  0.003   0.029   1668
  Dihedral  :  3.725  14.669   1252
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 11.54 %
    Favored  : 87.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.25), residues: 1150
  helix:  1.77 (0.27), residues: 396
  sheet: -0.43 (0.43), residues: 138
  loop :  0.30 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 183 
 HIS   0.001   0.000   HIS B 240 
 PHE   0.008   0.001   PHE B  94 
 TYR   0.011   0.001   TYR A 112 
 ARG   0.002   0.000   ARG A  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8437 (mp10) cc_final: 0.7590 (mp10)
REVERT: A  173 ASP cc_start: 0.8939 (m-30) cc_final: 0.8495 (p0)
REVERT: A  401 ASP cc_start: 0.8638 (m-30) cc_final: 0.8023 (t0)
REVERT: A  471 TYR cc_start: 0.8736 (p90) cc_final: 0.8384 (p90)
REVERT: A  506 PHE cc_start: 0.8969 (t80) cc_final: 0.8663 (t80)
REVERT: A  564 MET cc_start: 0.7345 (mmp) cc_final: 0.6361 (tmm)
REVERT: B  132 GLN cc_start: 0.8437 (mp10) cc_final: 0.7616 (mp10)
REVERT: B  173 ASP cc_start: 0.8941 (m-30) cc_final: 0.8493 (p0)
REVERT: B  401 ASP cc_start: 0.8642 (m-30) cc_final: 0.8020 (t0)
REVERT: B  449 LYS cc_start: 0.9012 (ptpt) cc_final: 0.8674 (ptmm)
REVERT: B  471 TYR cc_start: 0.8734 (p90) cc_final: 0.8368 (p90)
REVERT: B  506 PHE cc_start: 0.8973 (t80) cc_final: 0.8668 (t80)
REVERT: B  564 MET cc_start: 0.7334 (mmp) cc_final: 0.6381 (tmm)
  outliers start: 5
  outliers final: 3
  residues processed: 73
  average time/residue: 1.2520
  time to fit residues: 98.6808
Evaluate side-chains
  71 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain B residue  389 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 102 optimal weight:    0.8980
   chunk 105 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0470
   chunk 92 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9592  Z= 0.147
  Angle     :  0.434   5.841  12998  Z= 0.231
  Chirality :  0.042   0.141   1426
  Planarity :  0.003   0.030   1668
  Dihedral  :  3.671  14.150   1252
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 11.35 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.25), residues: 1150
  helix:  1.77 (0.27), residues: 398
  sheet: -0.34 (0.43), residues: 138
  loop :  0.32 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 316 
 HIS   0.001   0.000   HIS A 240 
 PHE   0.008   0.001   PHE B  94 
 TYR   0.010   0.001   TYR B 112 
 ARG   0.002   0.000   ARG A  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8406 (mp10) cc_final: 0.7559 (mp10)
REVERT: A  173 ASP cc_start: 0.8929 (m-30) cc_final: 0.8490 (p0)
REVERT: A  401 ASP cc_start: 0.8626 (m-30) cc_final: 0.8030 (t0)
REVERT: A  449 LYS cc_start: 0.8992 (ptpt) cc_final: 0.8602 (ptmm)
REVERT: A  471 TYR cc_start: 0.8762 (p90) cc_final: 0.8398 (p90)
REVERT: A  506 PHE cc_start: 0.8922 (t80) cc_final: 0.8593 (t80)
REVERT: A  564 MET cc_start: 0.7346 (mmp) cc_final: 0.6352 (tmm)
REVERT: B  132 GLN cc_start: 0.8404 (mp10) cc_final: 0.7558 (mp10)
REVERT: B  173 ASP cc_start: 0.8940 (m-30) cc_final: 0.8490 (p0)
REVERT: B  401 ASP cc_start: 0.8621 (m-30) cc_final: 0.8020 (t0)
REVERT: B  449 LYS cc_start: 0.8991 (ptpt) cc_final: 0.8599 (ptmm)
REVERT: B  471 TYR cc_start: 0.8763 (p90) cc_final: 0.8392 (p90)
REVERT: B  506 PHE cc_start: 0.8924 (t80) cc_final: 0.8612 (t80)
REVERT: B  543 MET cc_start: 0.8371 (mtm) cc_final: 0.7807 (ptp)
REVERT: B  550 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8200 (p0)
REVERT: B  564 MET cc_start: 0.7345 (mmp) cc_final: 0.6362 (tmm)
  outliers start: 8
  outliers final: 4
  residues processed: 72
  average time/residue: 1.2741
  time to fit residues: 98.9126
Evaluate side-chains
  72 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  550 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 113 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 71 optimal weight:    0.4980
   chunk 96 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
B 240 HIS
** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   9592  Z= 0.398
  Angle     :  0.537   6.128  12998  Z= 0.287
  Chirality :  0.046   0.143   1426
  Planarity :  0.003   0.034   1668
  Dihedral  :  4.195  14.981   1252
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.83 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.25), residues: 1150
  helix:  1.63 (0.27), residues: 398
  sheet: -0.41 (0.43), residues: 138
  loop :  0.27 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 316 
 HIS   0.005   0.001   HIS B 442 
 PHE   0.015   0.001   PHE B 506 
 TYR   0.011   0.001   TYR A 226 
 ARG   0.004   0.000   ARG A  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8391 (mp10) cc_final: 0.7530 (mp10)
REVERT: A  173 ASP cc_start: 0.8967 (m-30) cc_final: 0.8447 (p0)
REVERT: A  401 ASP cc_start: 0.8651 (m-30) cc_final: 0.8102 (t0)
REVERT: A  449 LYS cc_start: 0.9010 (ptpt) cc_final: 0.8673 (ptmm)
REVERT: A  564 MET cc_start: 0.7422 (mmp) cc_final: 0.6432 (tmm)
REVERT: B  132 GLN cc_start: 0.8389 (mp10) cc_final: 0.7528 (mp10)
REVERT: B  173 ASP cc_start: 0.8981 (m-30) cc_final: 0.8460 (p0)
REVERT: B  401 ASP cc_start: 0.8649 (m-30) cc_final: 0.8102 (t0)
REVERT: B  449 LYS cc_start: 0.9008 (ptpt) cc_final: 0.8654 (ptmm)
REVERT: B  564 MET cc_start: 0.7435 (mmp) cc_final: 0.6462 (tmm)
  outliers start: 6
  outliers final: 2
  residues processed: 67
  average time/residue: 1.3219
  time to fit residues: 95.6017
Evaluate side-chains
  70 residues out of total 1040 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  508 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 93 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0000
   overall best weight:    0.7184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.075801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.062199 restraints weight = 20965.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 2.74
r_work: 0.2826 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9592  Z= 0.166
  Angle     :  0.458   5.924  12998  Z= 0.243
  Chirality :  0.042   0.143   1426
  Planarity :  0.003   0.029   1668
  Dihedral  :  3.891  15.068   1252
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 11.83 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.25), residues: 1150
  helix:  1.71 (0.27), residues: 400
  sheet: -0.32 (0.43), residues: 138
  loop :  0.31 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 316 
 HIS   0.001   0.000   HIS A 208 
 PHE   0.008   0.001   PHE A 506 
 TYR   0.010   0.001   TYR B 112 
 ARG   0.003   0.000   ARG A  81 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2791.22 seconds
wall clock time: 50 minutes 31.24 seconds (3031.24 seconds total)