Starting phenix.real_space_refine
on Thu Nov 14 21:16:18 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8l_36073/11_2024/8j8l_36073_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8l_36073/11_2024/8j8l_36073.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8l_36073/11_2024/8j8l_36073.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8l_36073/11_2024/8j8l_36073.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8l_36073/11_2024/8j8l_36073_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8l_36073/11_2024/8j8l_36073_neut.cif"
  }
  resolution = 3.56
  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=  -0.003 sd=   0.039
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      27      5.16       5
     C    4809      2.51       5
     N    1187      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 7361
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3656
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3579
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 24, 'TRANS': 438}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Classifications: {'peptide': 1}
  Time building chain proxies: 4.66, per 1000 atoms: 0.63
  Number of scatterers: 7361
  At special positions: 0
  Unit cell: (99.645, 83.22, 129.21, 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      27     16.00
     O    1338      8.00
     N    1187      7.00
     C    4809      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 164 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 977.9 milliseconds
  

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1718

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      58.7% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
    Processing helix  chain 'A' and resid 179 through 207
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.756A  pdb=" N   HIS A 221 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 222'
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 4.445A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
    Processing helix  chain 'A' and resid 248 through 256
    Processing helix  chain 'A' and resid 287 through 302
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 3.575A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 354
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.728A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.624A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 3.615A  pdb=" N   THR A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 445
    Processing helix  chain 'A' and resid 450 through 460
      removed outlier: 3.628A  pdb=" N   PHE A 459 " --> pdb=" O   GLN A 455 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   THR A 460 " --> pdb=" O   LEU A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 519 through 532
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'A' and resid 585 through 589
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
      removed outlier: 3.660A  pdb=" N   VAL B  70 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 79
      removed outlier: 3.946A  pdb=" N   LEU B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.536A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLU B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   THR B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 124
      removed outlier: 4.000A  pdb=" N   GLU B 122 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 158
      removed outlier: 4.789A  pdb=" N   ARG B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      Proline residue:  B 142  - end of helix
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.756A  pdb=" N   ALA B 171 " --> pdb=" O   PRO B 167 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LYS B 172 " --> pdb=" O   GLU B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 221
      removed outlier: 3.678A  pdb=" N   ALA B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE B 219 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 245
      No H-bonds generated for 'chain 'B' and resid 243 through 245'
    Processing helix  chain 'B' and resid 246 through 251
    Processing helix  chain 'B' and resid 269 through 298
      removed outlier: 3.627A  pdb=" N   ASN B 273 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 310 through 321
      removed outlier: 3.645A  pdb=" N   HIS B 319 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY B 321 " --> pdb=" O   ASN B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 357
      removed outlier: 4.647A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ARG B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLU B 356 " --> pdb=" O   VAL B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 389
      removed outlier: 4.003A  pdb=" N   PHE B 389 " --> pdb=" O   LEU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 422
      removed outlier: 3.929A  pdb=" N   SER B 401 " --> pdb=" O   ILE B 397 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE B 416 " --> pdb=" O   ILE B 412 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TRP B 417 " --> pdb=" O   ILE B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 451
      removed outlier: 4.270A  pdb=" N   PHE B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE B 439 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ILE B 447 " --> pdb=" O   CYS B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 476
      removed outlier: 3.865A  pdb=" N   ILE B 464 " --> pdb=" O   ILE B 460 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE B 465 " --> pdb=" O   GLY B 461 " (cutoff:3.500A)
      Proline residue:  B 470  - end of helix
      removed outlier: 3.895A  pdb=" N   GLY B 475 " --> pdb=" O   VAL B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 500
    Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227
      removed outlier: 3.590A  pdb=" N   PHE A 467 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262
      removed outlier: 6.853A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 8.722A  pdb=" N   ARG A 349 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 267
    Processing sheet with id=AA4, first strand: chain 'A' and resid 541 through 545
      removed outlier: 3.568A  pdb=" N   PHE A 545 " --> pdb=" O   SER A 553 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU A 621 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   GLY A 622 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   SER A 599 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   LEU A 624 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG A 626 " --> pdb=" O   ASP A 595 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 575 through 576
      removed outlier: 3.569A  pdb=" N   LEU A 575 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1095 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 2.28 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: 2166
        1.34 -     1.46: 1276
        1.46 -     1.58: 4060
        1.58 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 7542
  Sorted by residual:
  bond pdb=" C   DAH B 601 "
       pdb=" OXT DAH B 601 "
    ideal  model  delta    sigma   weight residual
    1.360  1.257  0.103 2.00e-02 2.50e+03 2.64e+01
  bond pdb=" C4  NAG F   1 "
       pdb=" O4  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.409  1.477 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.64e+00
  bond pdb=" C3  NAG F   1 "
       pdb=" O3  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.435 -0.032 2.00e-02 2.50e+03 2.49e+00
  bond pdb=" CB  DAH B 601 "
       pdb=" CG  DAH B 601 "
    ideal  model  delta    sigma   weight residual
    1.487  1.517 -0.030 2.00e-02 2.50e+03 2.24e+00
  ... (remaining 7537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 10027
        2.03 -     4.06: 197
        4.06 -     6.09: 37
        6.09 -     8.12: 7
        8.12 -    10.15: 3
  Bond angle restraints: 10271
  Sorted by residual:
  angle pdb=" C   LEU B 138 "
        pdb=" N   ILE B 139 "
        pdb=" CA  ILE B 139 "
      ideal   model   delta    sigma   weight residual
     123.16  119.05    4.11 1.06e+00 8.90e-01 1.50e+01
  angle pdb=" N   ILE B 429 "
        pdb=" CA  ILE B 429 "
        pdb=" C   ILE B 429 "
      ideal   model   delta    sigma   weight residual
     113.22  117.46   -4.24 1.23e+00 6.61e-01 1.19e+01
  angle pdb=" CA  DAH B 601 "
        pdb=" C   DAH B 601 "
        pdb=" O   DAH B 601 "
      ideal   model   delta    sigma   weight residual
     128.96  118.81   10.15 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" N   PRO B 428 "
        pdb=" CA  PRO B 428 "
        pdb=" C   PRO B 428 "
      ideal   model   delta    sigma   weight residual
     112.47  119.32   -6.85 2.06e+00 2.36e-01 1.11e+01
  angle pdb=" N   GLU B  78 "
        pdb=" CA  GLU B  78 "
        pdb=" C   GLU B  78 "
      ideal   model   delta    sigma   weight residual
     114.31  110.14    4.17 1.29e+00 6.01e-01 1.05e+01
  ... (remaining 10266 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.38: 4227
       25.38 -    50.76: 234
       50.76 -    76.14: 31
       76.14 -   101.53: 15
      101.53 -   126.91: 11
  Dihedral angle restraints: 4518
    sinusoidal: 1845
      harmonic: 2673
  Sorted by residual:
  dihedral pdb=" C2  NAG D   2 "
           pdb=" C1  NAG D   2 "
           pdb=" O5  NAG D   2 "
           pdb=" C5  NAG D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   63.95 -126.91     1      3.00e+01 1.11e-03 1.71e+01
  dihedral pdb=" C2  NAG D   1 "
           pdb=" C3  NAG D   1 "
           pdb=" C4  NAG D   1 "
           pdb=" O4  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   56.03  119.08     1      3.00e+01 1.11e-03 1.59e+01
  dihedral pdb=" O3  NAG D   1 "
           pdb=" C3  NAG D   1 "
           pdb=" C4  NAG D   1 "
           pdb=" O4  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.45  176.99  118.46     1      3.00e+01 1.11e-03 1.57e+01
  ... (remaining 4515 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.279: 1209
       0.279 -    0.558: 1
       0.558 -    0.837: 1
       0.837 -    1.117: 0
       1.117 -    1.396: 1
  Chirality restraints: 1212
  Sorted by residual:
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.70    0.30 2.00e-02 2.50e+03 2.22e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-02 2.50e+03 1.35e+02
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-02 2.50e+03 9.43e+01
  ... (remaining 1209 not shown)

  Planarity restraints: 1275
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.328 2.00e-02 2.50e+03   2.82e-01 9.96e+02
        pdb=" C7  NAG D   2 "   -0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.026 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.490 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.211 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.300 2.00e-02 2.50e+03   2.52e-01 7.94e+02
        pdb=" C7  NAG D   1 "    0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.188 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.431 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "   -0.294 2.00e-02 2.50e+03   2.50e-01 7.79e+02
        pdb=" C7  NAG F   1 "    0.076 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "   -0.182 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "    0.430 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 1272 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 873
        2.75 -     3.28: 7800
        3.28 -     3.82: 12211
        3.82 -     4.36: 13372
        4.36 -     4.90: 22899
  Nonbonded interactions: 57155
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 356 "
            pdb=" OG  SER A 359 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" NH2 ARG B 419 "
            pdb=" O   LYS B 422 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OD1 ASN A 366 "
            pdb=" C8  NAG D   2 "
     model   vdw
     2.219 3.460
  nonbonded pdb=" O   TYR A 251 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   ILE B 268 "
            pdb=" ND2 ASN B 273 "
     model   vdw
     2.256 3.120
  ... (remaining 57150 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.750
  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:          0.240
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     19.840
  Find NCS groups from input model:        0.110
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
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      :  0.004   0.103   7542  Z= 0.240
  Angle     :  0.694  10.145  10271  Z= 0.354
  Chirality :  0.062   1.396   1212
  Planarity :  0.016   0.282   1271
  Dihedral  : 17.563 126.907   2797
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  0.89 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.29), residues: 928
  helix:  1.32 (0.25), residues: 481
  sheet:  0.09 (0.67), residues: 59
  loop : -1.48 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 184 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.014   0.001   PHE B 402 
 TYR   0.015   0.001   TYR B 289 
 ARG   0.008   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.8006 (m-30) cc_final: 0.7689 (m-30)
REVERT: B   84 LEU cc_start: 0.9120 (tp) cc_final: 0.8914 (tt)
REVERT: B  141 ARG cc_start: 0.8992 (mmp80) cc_final: 0.8547 (mmp80)
REVERT: B  259 TYR cc_start: 0.8902 (m-80) cc_final: 0.8506 (m-80)
REVERT: B  383 MET cc_start: 0.8573 (tpp) cc_final: 0.7994 (mpp)
  outliers start: 7
  outliers final: 2
  residues processed: 107
  average time/residue: 0.1745
  time to fit residues: 26.4006
Evaluate side-chains
  66 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 429 ASN
A 561 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7542  Z= 0.195
  Angle     :  0.720  11.384  10271  Z= 0.335
  Chirality :  0.045   0.332   1212
  Planarity :  0.005   0.048   1271
  Dihedral  : 14.328 103.780   1159
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.55 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.28), residues: 928
  helix:  1.76 (0.24), residues: 492
  sheet: -0.30 (0.63), residues: 66
  loop : -1.20 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 325 
 HIS   0.006   0.001   HIS B 367 
 PHE   0.021   0.001   PHE A 190 
 TYR   0.015   0.002   TYR B 103 
 ARG   0.005   0.001   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.7745 (m-30) cc_final: 0.7506 (m-30)
REVERT: A  508 MET cc_start: 0.9044 (ptp) cc_final: 0.8652 (ptp)
REVERT: B  120 MET cc_start: 0.8943 (ppp) cc_final: 0.8495 (ppp)
REVERT: B  141 ARG cc_start: 0.8969 (mmp80) cc_final: 0.8630 (mmp80)
REVERT: B  259 TYR cc_start: 0.8989 (m-80) cc_final: 0.8646 (m-80)
REVERT: B  267 MET cc_start: 0.9021 (mpp) cc_final: 0.8707 (pmm)
REVERT: B  383 MET cc_start: 0.8628 (tpp) cc_final: 0.8122 (mpp)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.1662
  time to fit residues: 19.5957
Evaluate side-chains
  65 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 221 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7542  Z= 0.188
  Angle     :  0.649  12.451  10271  Z= 0.302
  Chirality :  0.041   0.223   1212
  Planarity :  0.004   0.057   1271
  Dihedral  : 13.300 111.066   1157
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 12.33 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.29), residues: 928
  helix:  1.99 (0.24), residues: 486
  sheet: -0.28 (0.65), residues: 66
  loop : -1.11 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 477 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.020   0.001   PHE B 402 
 TYR   0.013   0.001   TYR B 103 
 ARG   0.005   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.7726 (m-30) cc_final: 0.7496 (m-30)
REVERT: B  120 MET cc_start: 0.8966 (ppp) cc_final: 0.8458 (ppp)
REVERT: B  141 ARG cc_start: 0.8974 (mmp80) cc_final: 0.8641 (mmp80)
REVERT: B  267 MET cc_start: 0.9057 (mpp) cc_final: 0.8615 (pmm)
REVERT: B  383 MET cc_start: 0.8654 (tpp) cc_final: 0.8174 (mpp)
  outliers start: 7
  outliers final: 5
  residues processed: 75
  average time/residue: 0.1565
  time to fit residues: 17.3736
Evaluate side-chains
  68 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7542  Z= 0.175
  Angle     :  0.634   9.931  10271  Z= 0.298
  Chirality :  0.042   0.257   1212
  Planarity :  0.004   0.048   1271
  Dihedral  : 12.090 110.475   1157
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 14.23 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.29), residues: 928
  helix:  2.02 (0.24), residues: 486
  sheet: -0.33 (0.65), residues: 66
  loop : -1.04 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 319 
 PHE   0.014   0.001   PHE B 402 
 TYR   0.012   0.001   TYR B 472 
 ARG   0.006   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.7702 (m-30) cc_final: 0.7464 (m-30)
REVERT: B  120 MET cc_start: 0.9009 (ppp) cc_final: 0.8374 (ppp)
REVERT: B  267 MET cc_start: 0.9022 (mpp) cc_final: 0.8686 (pmm)
REVERT: B  297 PHE cc_start: 0.8287 (t80) cc_final: 0.8072 (t80)
REVERT: B  365 MET cc_start: 0.7872 (mmm) cc_final: 0.6588 (mmm)
REVERT: B  383 MET cc_start: 0.8640 (tpp) cc_final: 0.8164 (mpp)
  outliers start: 10
  outliers final: 8
  residues processed: 77
  average time/residue: 0.1789
  time to fit residues: 19.8229
Evaluate side-chains
  70 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 36 optimal weight:    0.8980
   chunk 75 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 0 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7542  Z= 0.207
  Angle     :  0.660  12.517  10271  Z= 0.303
  Chirality :  0.041   0.231   1212
  Planarity :  0.004   0.063   1271
  Dihedral  : 11.612 111.156   1157
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.63 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.29), residues: 928
  helix:  2.09 (0.24), residues: 486
  sheet: -0.47 (0.65), residues: 66
  loop : -1.01 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 134 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.021   0.001   PHE B 402 
 TYR   0.008   0.001   TYR B 248 
 ARG   0.008   0.001   ARG B 355 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.7703 (m-30) cc_final: 0.7457 (m-30)
REVERT: B   47 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7667 (mm-40)
REVERT: B  120 MET cc_start: 0.9009 (ppp) cc_final: 0.8458 (ppp)
REVERT: B  267 MET cc_start: 0.8997 (mpp) cc_final: 0.8552 (pmm)
REVERT: B  297 PHE cc_start: 0.8289 (t80) cc_final: 0.8081 (t80)
REVERT: B  383 MET cc_start: 0.8676 (tpp) cc_final: 0.8192 (mpp)
  outliers start: 14
  outliers final: 8
  residues processed: 71
  average time/residue: 0.1655
  time to fit residues: 17.2800
Evaluate side-chains
  69 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0770
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    1.8146

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7542  Z= 0.212
  Angle     :  0.654  11.956  10271  Z= 0.302
  Chirality :  0.041   0.234   1212
  Planarity :  0.004   0.061   1271
  Dihedral  : 11.230 110.906   1156
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.14 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.29), residues: 928
  helix:  2.21 (0.24), residues: 483
  sheet: -0.55 (0.64), residues: 66
  loop : -0.99 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.007   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B 402 
 TYR   0.009   0.001   TYR B 248 
 ARG   0.006   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.7754 (m-30) cc_final: 0.7482 (m-30)
REVERT: B  120 MET cc_start: 0.9021 (ppp) cc_final: 0.8463 (ppp)
REVERT: B  267 MET cc_start: 0.9021 (mpp) cc_final: 0.8621 (pmm)
REVERT: B  383 MET cc_start: 0.8676 (tpp) cc_final: 0.8193 (mpp)
  outliers start: 11
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1705
  time to fit residues: 17.6377
Evaluate side-chains
  69 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:    0.0970
   chunk 50 optimal weight:    8.9990
   chunk 65 optimal weight:    0.0870
   chunk 74 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 55 optimal weight:    0.2980
   chunk 54 optimal weight:    0.9990
   chunk 40 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7542  Z= 0.149
  Angle     :  0.646  10.993  10271  Z= 0.297
  Chirality :  0.041   0.248   1212
  Planarity :  0.004   0.069   1271
  Dihedral  : 10.786 110.286   1156
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 17.15 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.29), residues: 928
  helix:  2.29 (0.24), residues: 483
  sheet: -0.44 (0.64), residues: 66
  loop : -0.92 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 134 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B 402 
 TYR   0.009   0.001   TYR B 248 
 ARG   0.006   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.7755 (m-30) cc_final: 0.7500 (m-30)
REVERT: B  120 MET cc_start: 0.9024 (ppp) cc_final: 0.8471 (ppp)
REVERT: B  267 MET cc_start: 0.8912 (mpp) cc_final: 0.8438 (pmm)
REVERT: B  365 MET cc_start: 0.7693 (mmm) cc_final: 0.5998 (mmm)
REVERT: B  383 MET cc_start: 0.8632 (tpp) cc_final: 0.8189 (mpp)
  outliers start: 11
  outliers final: 7
  residues processed: 80
  average time/residue: 0.1700
  time to fit residues: 19.4912
Evaluate side-chains
  72 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  294 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 77 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7542  Z= 0.173
  Angle     :  0.668  13.353  10271  Z= 0.302
  Chirality :  0.042   0.252   1212
  Planarity :  0.004   0.068   1271
  Dihedral  : 10.427 109.807   1156
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.92 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.29), residues: 928
  helix:  2.30 (0.24), residues: 486
  sheet: -0.47 (0.64), residues: 66
  loop : -0.86 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 
 PHE   0.022   0.001   PHE B 402 
 TYR   0.021   0.001   TYR A 251 
 ARG   0.007   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.7758 (m-30) cc_final: 0.7514 (m-30)
REVERT: B  120 MET cc_start: 0.9029 (ppp) cc_final: 0.8472 (ppp)
REVERT: B  383 MET cc_start: 0.8602 (tpp) cc_final: 0.8144 (mpp)
  outliers start: 13
  outliers final: 10
  residues processed: 74
  average time/residue: 0.1683
  time to fit residues: 18.3786
Evaluate side-chains
  75 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  473 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 84 optimal weight:    0.2980
   chunk 49 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 87 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7542  Z= 0.172
  Angle     :  0.681  12.436  10271  Z= 0.308
  Chirality :  0.042   0.258   1212
  Planarity :  0.004   0.056   1271
  Dihedral  : 10.142 109.604   1156
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 18.42 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.29), residues: 928
  helix:  2.23 (0.24), residues: 493
  sheet: -0.43 (0.65), residues: 66
  loop : -0.88 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 134 
 HIS   0.002   0.001   HIS B 319 
 PHE   0.022   0.001   PHE B 402 
 TYR   0.021   0.001   TYR A 251 
 ARG   0.006   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.7764 (m-30) cc_final: 0.7516 (m-30)
REVERT: B  120 MET cc_start: 0.9030 (ppp) cc_final: 0.8470 (ppp)
REVERT: B  145 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8779 (mp10)
REVERT: B  267 MET cc_start: 0.9160 (mpp) cc_final: 0.8803 (pmm)
REVERT: B  383 MET cc_start: 0.8572 (tpp) cc_final: 0.8176 (mpp)
  outliers start: 10
  outliers final: 9
  residues processed: 73
  average time/residue: 0.1629
  time to fit residues: 17.5784
Evaluate side-chains
  73 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  473 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 84 optimal weight:   30.0000
   chunk 72 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7542  Z= 0.226
  Angle     :  0.703  11.869  10271  Z= 0.320
  Chirality :  0.042   0.257   1212
  Planarity :  0.004   0.055   1271
  Dihedral  :  9.821 110.015   1156
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.55 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.29), residues: 928
  helix:  2.26 (0.24), residues: 492
  sheet: -0.54 (0.64), residues: 66
  loop : -0.81 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.003   0.001   HIS A 266 
 PHE   0.022   0.001   PHE B 402 
 TYR   0.019   0.001   TYR A 251 
 ARG   0.007   0.000   ARG A 614 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.7827 (m-30) cc_final: 0.7573 (m-30)
REVERT: B  120 MET cc_start: 0.9031 (ppp) cc_final: 0.8410 (ppp)
REVERT: B  267 MET cc_start: 0.9158 (mpp) cc_final: 0.8798 (pmm)
REVERT: B  383 MET cc_start: 0.8566 (tpp) cc_final: 0.8158 (mpp)
  outliers start: 13
  outliers final: 10
  residues processed: 73
  average time/residue: 0.1859
  time to fit residues: 19.2689
Evaluate side-chains
  73 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  473 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 75 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0030
   chunk 4 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.063049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.046504 restraints weight = 38596.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.047925 restraints weight = 21300.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.048846 restraints weight = 15145.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7542  Z= 0.160
  Angle     :  0.689  12.345  10271  Z= 0.311
  Chirality :  0.042   0.262   1212
  Planarity :  0.004   0.054   1271
  Dihedral  :  9.470 109.862   1156
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 18.81 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.29), residues: 928
  helix:  2.31 (0.24), residues: 490
  sheet: -0.43 (0.65), residues: 66
  loop : -0.86 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 134 
 HIS   0.002   0.000   HIS B 367 
 PHE   0.022   0.001   PHE B 402 
 TYR   0.023   0.001   TYR A 251 
 ARG   0.007   0.000   ARG A 614 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1464.41 seconds
wall clock time: 27 minutes 49.35 seconds (1669.35 seconds total)