Starting phenix.real_space_refine
on Tue Mar 11 22:13:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5tv4_8469/03_2025/5tv4_8469.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5tv4_8469/03_2025/5tv4_8469.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5tv4_8469/03_2025/5tv4_8469.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5tv4_8469/03_2025/5tv4_8469.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5tv4_8469/03_2025/5tv4_8469.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5tv4_8469/03_2025/5tv4_8469.cif"
  }
  resolution = 4.2
  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
-------------------------------------------------------------------------------
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=   0.011
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      16      5.16       5
     C    4040      2.51       5
     N    1234      2.21       5
     O    1254      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6548
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 3205
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 375}
          Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 555}
          Unresolved chain links: 1
          Unresolved chain link angles: 11
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 1255
          Unresolved non-hydrogen angles: 1592
          Unresolved non-hydrogen dihedrals: 1004
          Unresolved non-hydrogen chiralities: 134
          Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 26, 'PHE:plan': 13, 'GLU:plan': 28, 'ARG:plan': 29}
          Unresolved non-hydrogen planarities: 654
    Chain: "B"
      Number of atoms: 3180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 3180
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 386}
          Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 555}
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 1279
          Unresolved non-hydrogen angles: 1619
          Unresolved non-hydrogen dihedrals: 1021
          Unresolved non-hydrogen chiralities: 144
          Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 26, 'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 28}
          Unresolved non-hydrogen planarities: 640
    Chain: "C"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 91
          Unusual residues: {'GMH': 3, 'KDO': 2, 'PA1': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 6
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 12
          Unusual residues: {'PO4': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 9
    Chain: "B"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 60
          Unusual residues: {'DAO': 1, 'FTT': 4, 'MYR': 1, 'PO4': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'DAO:plan-1': 1, 'FTT:plan-1': 4, 'MYR:plan-1': 1}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 5.30, per 1000 atoms: 0.81
  Number of scatterers: 6548
  At special positions: 0
  Unit cell: (91.02, 84.87, 134.07, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     P       4     15.00
     O    1254      8.00
     N    1234      7.00
     C    4040      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  - 3.00
        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=7, symmetry=0
  Links applied
    ?1-6
      " PA1 C   1 " - " PA1 C   2 "
    ?2-4
      " KDO C   3 " - " KDO C   7 "
    ?2-6
      " PA1 C   2 " - " KDO C   3 "
    ALPHA1-3
      " GMH C   4 " - " GMH C   5 "
    ALPHA1-5
      " KDO C   3 " - " GMH C   4 "
    ALPHA1-7
      " GMH C   5 " - " GMH C   6 "
  Number of additional bonds: simple=7, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.23
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2130

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 5 sheets defined
      69.4% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 21
      Proline residue:  A  18  - end of helix
    Processing helix  chain 'A' and resid 24 through 48
    Processing helix  chain 'A' and resid 49 through 54
    Processing helix  chain 'A' and resid 62 through 65
    Processing helix  chain 'A' and resid 66 through 110
      removed outlier: 3.754A  pdb=" N   VAL A  70 " --> pdb=" O   TRP A  66 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ILE A  76 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   MET A  98 " --> pdb=" O   GLY A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
    Processing helix  chain 'A' and resid 120 through 148
      removed outlier: 3.736A  pdb=" N   ALA A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   SER A 137 " --> pdb=" O   GLU A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.642A  pdb=" N   ILE A 158 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   MET A 159 " --> pdb=" O   GLY A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 173
    Processing helix  chain 'A' and resid 174 through 193
    Processing helix  chain 'A' and resid 195 through 213
    Processing helix  chain 'A' and resid 213 through 221
    Processing helix  chain 'A' and resid 222 through 251
      removed outlier: 3.894A  pdb=" N   LYS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   SER A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 256
    Processing helix  chain 'A' and resid 257 through 268
      removed outlier: 3.820A  pdb=" N   LEU A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   PHE A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 276
    Processing helix  chain 'A' and resid 280 through 323
      removed outlier: 3.619A  pdb=" N   ILE A 284 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER A 289 " --> pdb=" O   THR A 285 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 4.091A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 390
      removed outlier: 3.993A  pdb=" N   LEU A 388 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 419
    Processing helix  chain 'A' and resid 432 through 437
      removed outlier: 3.817A  pdb=" N   ILE A 437 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 5.689A  pdb=" N   ARG A 441 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLU A 443 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 456
    Processing helix  chain 'A' and resid 459 through 465
    Processing helix  chain 'A' and resid 468 through 472
    Processing helix  chain 'A' and resid 482 through 497
    Processing helix  chain 'A' and resid 512 through 528
    Processing helix  chain 'A' and resid 538 through 545
    Processing helix  chain 'A' and resid 561 through 567
      removed outlier: 3.521A  pdb=" N   LEU A 565 " --> pdb=" O   THR A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 579
    Processing helix  chain 'B' and resid 12 through 21
      removed outlier: 4.059A  pdb=" N   TRP B  17 " --> pdb=" O   PHE B  13 " (cutoff:3.500A)
      Proline residue:  B  18  - end of helix
    Processing helix  chain 'B' and resid 24 through 49
      removed outlier: 3.799A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 55
    Processing helix  chain 'B' and resid 60 through 109
      removed outlier: 3.728A  pdb=" N   LEU B  64 " --> pdb=" O   ASP B  60 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 113 through 118
    Processing helix  chain 'B' and resid 120 through 162
    Processing helix  chain 'B' and resid 164 through 173
    Processing helix  chain 'B' and resid 174 through 213
      removed outlier: 3.979A  pdb=" N   VAL B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 222 through 251
      removed outlier: 3.706A  pdb=" N   PHE B 230 " --> pdb=" O   GLU B 226 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS B 232 " --> pdb=" O   LYS B 228 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   VAL B 233 " --> pdb=" O   ARG B 229 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER B 246 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA B 247 " --> pdb=" O   LYS B 243 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   SER B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 276
      removed outlier: 4.102A  pdb=" N   LEU B 257 " --> pdb=" O   PRO B 253 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   ILE B 258 " --> pdb=" O   ILE B 254 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ALA B 259 " --> pdb=" O   ILE B 255 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   LEU B 267 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   TYR B 268 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      Proline residue:  B 273  - end of helix
      removed outlier: 3.549A  pdb=" N   MET B 276 " --> pdb=" O   PHE B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 287
      removed outlier: 3.952A  pdb=" N   ILE B 284 " --> pdb=" O   THR B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 308
      Proline residue:  B 297  - end of helix
      removed outlier: 3.764A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 323
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 3.693A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 417
    Processing helix  chain 'B' and resid 446 through 456
      removed outlier: 4.510A  pdb=" N   ILE B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 463
    Processing helix  chain 'B' and resid 482 through 497
    Processing helix  chain 'B' and resid 512 through 527
    Processing helix  chain 'B' and resid 540 through 545
      removed outlier: 3.921A  pdb=" N   LYS B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA B 545 " --> pdb=" O   THR B 541 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 540 through 545'
    Processing helix  chain 'B' and resid 561 through 567
      removed outlier: 3.904A  pdb=" N   GLU B 567 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 570 through 579
      removed outlier: 4.202A  pdb=" N   GLN B 574 " --> pdb=" O   GLY B 570 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 367
      removed outlier: 5.316A  pdb=" N   VAL A 347 " --> pdb=" O   ASN A 361 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   ASN A 363 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ARG A 345 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   LYS A 365 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   GLU A 343 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ASP A 341 " --> pdb=" O   PRO A 367 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   VAL A 347 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   GLU A 397 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 374
      removed outlier: 6.407A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 550 through 552
      removed outlier: 6.773A  pdb=" N   VAL A 550 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 344 through 347
      removed outlier: 4.942A  pdb=" N   ARG B 345 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU B 364 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 421
      removed outlier: 6.905A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    536 hydrogen bonds defined for protein.
    1572 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: 2.29

  Time building geometry restraints manager: 3.18 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: 2305
        1.34 -     1.46: 775
        1.46 -     1.57: 3475
        1.57 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 6586
  Sorted by residual:
  bond pdb=" C5  PA1 C   2 "
       pdb=" O5  PA1 C   2 "
    ideal  model  delta    sigma   weight residual
    1.417  1.533 -0.116 2.00e-02 2.50e+03 3.38e+01
  bond pdb=" O3  PO4 A 608 "
       pdb=" P   PO4 A 608 "
    ideal  model  delta    sigma   weight residual
    1.569  1.464  0.105 2.00e-02 2.50e+03 2.75e+01
  bond pdb=" O3  PO4 A 610 "
       pdb=" P   PO4 A 610 "
    ideal  model  delta    sigma   weight residual
    1.569  1.466  0.103 2.00e-02 2.50e+03 2.65e+01
  bond pdb=" O1  PO4 A 610 "
       pdb=" P   PO4 A 610 "
    ideal  model  delta    sigma   weight residual
    1.565  1.464  0.101 2.00e-02 2.50e+03 2.58e+01
  bond pdb=" O3  PO4 A 609 "
       pdb=" P   PO4 A 609 "
    ideal  model  delta    sigma   weight residual
    1.569  1.468  0.101 2.00e-02 2.50e+03 2.54e+01
  ... (remaining 6581 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.24: 8813
        3.24 -     6.49: 238
        6.49 -     9.73: 18
        9.73 -    12.98: 2
       12.98 -    16.22: 3
  Bond angle restraints: 9074
  Sorted by residual:
  angle pdb=" N   GLN B 309 "
        pdb=" CA  GLN B 309 "
        pdb=" C   GLN B 309 "
      ideal   model   delta    sigma   weight residual
     113.88  106.52    7.36 1.23e+00 6.61e-01 3.58e+01
  angle pdb=" C6  PA1 C   2 "
        pdb=" C5  PA1 C   2 "
        pdb=" O5  PA1 C   2 "
      ideal   model   delta    sigma   weight residual
     107.26   91.04   16.22 3.00e+00 1.11e-01 2.92e+01
  angle pdb=" CA  SER A 300 "
        pdb=" C   SER A 300 "
        pdb=" N   LEU A 301 "
      ideal   model   delta    sigma   weight residual
     118.17  125.27   -7.10 1.33e+00 5.65e-01 2.85e+01
  angle pdb=" N   GLY B 311 "
        pdb=" CA  GLY B 311 "
        pdb=" C   GLY B 311 "
      ideal   model   delta    sigma   weight residual
     113.24  106.46    6.78 1.31e+00 5.83e-01 2.68e+01
  angle pdb=" C   ARG A 333 "
        pdb=" N   VAL A 334 "
        pdb=" CA  VAL A 334 "
      ideal   model   delta    sigma   weight residual
     121.70  131.00   -9.30 1.80e+00 3.09e-01 2.67e+01
  ... (remaining 9069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.23: 3780
       25.23 -    50.45: 108
       50.45 -    75.68: 27
       75.68 -   100.90: 15
      100.90 -   126.13: 20
  Dihedral angle restraints: 3950
    sinusoidal: 676
      harmonic: 3274
  Sorted by residual:
  dihedral pdb=" CA  TYR B 351 "
           pdb=" C   TYR B 351 "
           pdb=" N   PRO B 352 "
           pdb=" CA  PRO B 352 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.03   40.97     0      5.00e+00 4.00e-02 6.72e+01
  dihedral pdb=" CA  ASP B 498 "
           pdb=" C   ASP B 498 "
           pdb=" N   SER B 499 "
           pdb=" CA  SER B 499 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.68  -38.32     0      5.00e+00 4.00e-02 5.87e+01
  dihedral pdb=" CA  SER B 278 "
           pdb=" C   SER B 278 "
           pdb=" N   LEU B 279 "
           pdb=" CA  LEU B 279 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.85  -37.15     0      5.00e+00 4.00e-02 5.52e+01
  ... (remaining 3947 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.141: 1164
       0.141 -    0.283: 38
       0.283 -    0.424: 0
       0.424 -    0.566: 0
       0.566 -    0.707: 1
  Chirality restraints: 1203
  Sorted by residual:
  chirality pdb=" C1  GMH C   6 "
            pdb=" O7  GMH C   5 "
            pdb=" C2  GMH C   6 "
            pdb=" O5  GMH C   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.32    0.08 2.00e-02 2.50e+03 1.64e+01
  chirality pdb=" C1  GMH C   5 "
            pdb=" O3  GMH C   4 "
            pdb=" C2  GMH C   5 "
            pdb=" O5  GMH C   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.48   -0.08 2.00e-02 2.50e+03 1.55e+01
  chirality pdb=" C5  PA1 C   2 "
            pdb=" C4  PA1 C   2 "
            pdb=" C6  PA1 C   2 "
            pdb=" O5  PA1 C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -3.20    0.71 2.00e-01 2.50e+01 1.25e+01
  ... (remaining 1200 not shown)

  Planarity restraints: 1225
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 414 "    0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   SER B 414 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   SER B 414 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LEU B 415 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  97 "   -0.012 2.00e-02 2.50e+03   2.32e-02 5.40e+00
        pdb=" C   VAL A  97 "    0.040 2.00e-02 2.50e+03
        pdb=" O   VAL A  97 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   MET A  98 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 519 "    0.011 2.00e-02 2.50e+03   2.29e-02 5.23e+00
        pdb=" C   ILE A 519 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE A 519 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLN A 520 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1222 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 31
        2.19 -     2.87: 3065
        2.87 -     3.54: 10210
        3.54 -     4.22: 13785
        4.22 -     4.90: 21636
  Nonbonded interactions: 48727
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  77 "
            pdb=" CG2 THR A  81 "
     model   vdw
     1.511 3.460
  nonbonded pdb=" O4  PA1 C   2 "
            pdb=" P   PO4 B 601 "
     model   vdw
     1.577 3.400
  nonbonded pdb=" O4  GMH C   5 "
            pdb=" P   PO4 A 610 "
     model   vdw
     1.580 3.400
  nonbonded pdb=" O1  PA1 C   1 "
            pdb=" P   PO4 A 608 "
     model   vdw
     1.591 3.400
  nonbonded pdb=" O4  GMH C   4 "
            pdb=" P   PO4 A 609 "
     model   vdw
     1.600 3.400
  ... (remaining 48722 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 11 through 27 or (resid 28 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 29 through 31 or (resid 32 through 35 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 36 through 40 or (res \ 
id 41 and (name N or name CA or name C or name O or name CB )) or resid 42 or (r \ 
esid 43 through 44 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 45 through 48 or (resid 49 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 50 or (resid 51 through 54 and (name N or name CA or name C or \ 
 name O or name CB )) or (resid 55 through 65 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 66 through 79 or (resid 80 and (name N or name C \ 
A or name C or name O or name CB )) or resid 81 through 83 or (resid 84 through  \ 
86 and (name N or name CA or name C or name O or name CB )) or resid 87 or (resi \ 
d 88 through 90 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 91 through 94 or (resid 95 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 96 through 100 or (resid 101 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 102 through 103 or (resid 104 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 105 through 112 or (resid 113 thro \ 
ugh 121 and (name N or name CA or name C or name O or name CB )) or resid 122 or \ 
 (resid 123 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 
4 through 144 or (resid 145 through 147 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 148 through 152 or (resid 153 through 154 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 155 or (resid 156 through  \ 
160 and (name N or name CA or name C or name O or name CB )) or resid 161 throug \ 
h 171 or (resid 172 through 175 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 176 through 179 or (resid 180 through 187 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 188 through 191 or (resid 192 thro \ 
ugh 200 and (name N or name CA or name C or name O or name CB )) or resid 201 th \ 
rough 219 or (resid 220 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 221 through 232 or (resid 233 through 236 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 237 through 239 or (resid 240 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 241 or (resid 242 through  \ 
249 and (name N or name CA or name C or name O or name CB )) or resid 250 throug \ 
h 252 or (resid 253 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 256 or (resid 257 through 262 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 263 through 264 or (resid 265 through 271 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 272 through 274 or (resid  \ 
275 through 281 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 282 through 302 or (resid 303 through 306 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 307 through 311 or (resid 312 through 318 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 319 through 321 or (re \ 
sid 322 through 330 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 331 through 580 or resid 608))
  selection = (chain 'B' and (resid 11 through 17 or (resid 18 through 19 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 20 through 21 or (resid 22 through \ 
 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 
 36 or (resid 37 through 41 and (name N or name CA or name C or name O or name C \ 
B )) or resid 42 through 81 or (resid 82 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 83 through 84 or (resid 85 through 86 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 87 through 96 or (resid 97 th \ 
rough 99 and (name N or name CA or name C or name O or name CB )) or resid 100 t \ 
hrough 102 or (resid 103 through 104 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 105 through 108 or (resid 109 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 110 through 129 or (resid 130 through 133 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 134 or (resid \ 
 135 through 140 and (name N or name CA or name C or name O or name CB )) or res \ 
id 141 through 143 or (resid 144 through 147 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 148 or (resid 149 and (name CA or name C or name  \ 
O or name CB )) or (resid 150 through 154 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 155 through 161 or (resid 162 through 165 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 166 through 181 or (resi \ 
d 182 through 187 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 188 through 196 or (resid 197 through 200 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 201 through 208 or (resid 209 through 212 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 213 through 216 or ( \ 
resid 217 through 220 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 221 through 224 or (resid 225 through 236 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 237 through 238 or (resid 239 through 240 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 241 through 251  \ 
or (resid 252 through 253 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 254 through 266 or (resid 267 through 271 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 272 through 282 or (resid 283 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 284 through 287 or (resi \ 
d 288 through 291 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 292 through 294 or (resid 295 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 296 through 304 or (resid 305 through 306 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 307 through 309 or (resid 310 an \ 
d (name N or name CA or name C or name O or name CB )) or (resid 311 through 318 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 319 through 3 \ 
20 or (resid 321 through 330 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 331 through 580 or resid 601))
}

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:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     22.970
  Find NCS groups from input model:        0.430
  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:3.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5888
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      :  0.008   0.116   6586  Z= 0.583
  Angle     :  1.264  16.223   9074  Z= 0.748
  Chirality :  0.064   0.707   1203
  Planarity :  0.005   0.045   1225
  Dihedral  : 20.358 126.129   1820
  Min Nonbonded Distance : 1.511

Molprobity Statistics.
  All-atom Clashscore : 46.46
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 13.14 %
    Favored  : 86.16 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 11.06 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 7.69 %
    Twisted General : 0.72 %

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: -5.82 (0.16), residues: 1134
  helix: -3.92 (0.11), residues: 718
  sheet: -3.39 (0.83), residues: 23
  loop : -3.35 (0.23), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B  17 
 HIS   0.021   0.006   HIS B 214 
 PHE   0.036   0.003   PHE A 220 
 TYR   0.028   0.002   TYR B 268 
 ARG   0.007   0.001   ARG A 238 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 LEU cc_start: 0.7112 (tt) cc_final: 0.6893 (tt)
REVERT: A  302 THR cc_start: 0.7128 (p) cc_final: 0.6890 (p)
REVERT: B   75 MET cc_start: 0.5168 (mmp) cc_final: 0.4866 (mmp)
REVERT: B   98 MET cc_start: 0.7031 (mmt) cc_final: 0.6799 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1814
  time to fit residues: 32.4393
Evaluate side-chains
  91 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:   20.0000
   chunk 89 optimal weight:    0.0050
   chunk 34 optimal weight:    0.0050
   chunk 54 optimal weight:    9.9990
   chunk 66 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   overall best weight:    1.4012

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
B 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.109105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.093414 restraints weight = 31698.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.093789 restraints weight = 24040.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.094257 restraints weight = 21721.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6744
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6586  Z= 0.230
  Angle     :  0.819   9.047   9074  Z= 0.430
  Chirality :  0.048   0.216   1203
  Planarity :  0.005   0.044   1225
  Dihedral  : 16.083 127.446   1365
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.85 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  3.85 %
    Favored  : 95.67 %
  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: -2.79 (0.22), residues: 1134
  helix: -1.33 (0.17), residues: 729
  sheet: -3.52 (0.68), residues: 32
  loop : -2.50 (0.28), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  17 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.035   0.002   PHE A 161 
 TYR   0.009   0.001   TYR B 130 
 ARG   0.020   0.002   ARG B 238 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A  302 THR cc_start: 0.7239 (p) cc_final: 0.6942 (p)
REVERT: B   45 LEU cc_start: 0.8373 (mm) cc_final: 0.8165 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 117
  average time/residue: 0.1535
  time to fit residues: 25.0015
Evaluate side-chains
  89 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 94 optimal weight:   20.0000
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9990
   chunk 97 optimal weight:   20.0000
   chunk 66 optimal weight:    0.2980
   chunk 95 optimal weight:   10.0000
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN
B 223 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.108708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.095111 restraints weight = 32293.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.094259 restraints weight = 39454.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.094626 restraints weight = 36568.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6622
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6586  Z= 0.192
  Angle     :  0.687  10.238   9074  Z= 0.353
  Chirality :  0.045   0.155   1203
  Planarity :  0.004   0.044   1225
  Dihedral  : 13.233 104.634   1365
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  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: -1.12 (0.24), residues: 1134
  helix:  0.18 (0.18), residues: 737
  sheet: -3.64 (0.50), residues: 54
  loop : -2.14 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  17 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.027   0.002   PHE A 157 
 TYR   0.014   0.001   TYR B 268 
 ARG   0.012   0.001   ARG A 148 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A   35 ILE cc_start: 0.9030 (mt) cc_final: 0.8663 (mt)
REVERT: A  302 THR cc_start: 0.7331 (p) cc_final: 0.7033 (p)
REVERT: B   71 VAL cc_start: 0.8336 (p) cc_final: 0.8113 (t)
REVERT: B  109 MET cc_start: 0.7633 (ptp) cc_final: 0.7258 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1601
  time to fit residues: 23.9813
Evaluate side-chains
  90 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:   30.0000
   chunk 57 optimal weight:    0.0980
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 91 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    4.0188

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.105825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.089764 restraints weight = 32042.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.090610 restraints weight = 23999.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.091307 restraints weight = 19371.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.4710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6586  Z= 0.247
  Angle     :  0.703   8.584   9074  Z= 0.360
  Chirality :  0.044   0.139   1203
  Planarity :  0.004   0.045   1225
  Dihedral  : 12.471 102.704   1365
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  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: -0.60 (0.25), residues: 1134
  helix:  0.55 (0.19), residues: 749
  sheet: -3.12 (0.59), residues: 50
  loop : -2.03 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  17 
 HIS   0.006   0.002   HIS A 214 
 PHE   0.020   0.001   PHE A 272 
 TYR   0.009   0.001   TYR B  83 
 ARG   0.009   0.001   ARG A 238 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 ILE cc_start: 0.9045 (mt) cc_final: 0.8822 (mt)
REVERT: A  302 THR cc_start: 0.7753 (p) cc_final: 0.7535 (p)
REVERT: B  295 MET cc_start: 0.8467 (tmm) cc_final: 0.8044 (tmm)
REVERT: B  302 THR cc_start: 0.7178 (m) cc_final: 0.6892 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1580
  time to fit residues: 22.6253
Evaluate side-chains
  83 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 94 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0020
   chunk 106 optimal weight:   50.0000
   chunk 88 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 42 optimal weight:   50.0000
   chunk 25 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   overall best weight:    3.9996

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.105646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.088974 restraints weight = 31870.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.089875 restraints weight = 23668.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.090568 restraints weight = 18739.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6916
moved from start:          0.5141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6586  Z= 0.232
  Angle     :  0.681   9.113   9074  Z= 0.350
  Chirality :  0.044   0.154   1203
  Planarity :  0.004   0.037   1225
  Dihedral  : 12.272 107.483   1365
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  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: -0.13 (0.25), residues: 1134
  helix:  0.98 (0.19), residues: 740
  sheet: -3.00 (0.65), residues: 49
  loop : -1.98 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  17 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.022   0.002   PHE A 157 
 TYR   0.008   0.001   TYR B 162 
 ARG   0.007   0.001   ARG B 236 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 ILE cc_start: 0.9058 (mt) cc_final: 0.8849 (mt)
REVERT: A   75 MET cc_start: 0.7601 (tmm) cc_final: 0.7325 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1429
  time to fit residues: 20.3756
Evaluate side-chains
  83 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 37 optimal weight:   50.0000
   chunk 84 optimal weight:    0.0270
   chunk 51 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 99 optimal weight:   30.0000
   chunk 86 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 10 optimal weight:    0.0370
   overall best weight:    3.2122

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.105819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.094249 restraints weight = 32150.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.092928 restraints weight = 43105.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.092701 restraints weight = 36894.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.5530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6586  Z= 0.201
  Angle     :  0.642   8.752   9074  Z= 0.331
  Chirality :  0.043   0.141   1203
  Planarity :  0.003   0.037   1225
  Dihedral  : 12.101 109.658   1365
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  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:  0.12 (0.26), residues: 1134
  helix:  1.13 (0.19), residues: 761
  sheet: -2.37 (0.92), residues: 32
  loop : -2.08 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP A  66 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.027   0.002   PHE A 157 
 TYR   0.009   0.001   TYR B  83 
 ARG   0.007   0.001   ARG A  61 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.6933 (tmm) cc_final: 0.6711 (tmm)
REVERT: A  157 PHE cc_start: 0.7139 (m-80) cc_final: 0.6908 (m-80)
REVERT: B  109 MET cc_start: 0.7128 (mtp) cc_final: 0.6830 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1322
  time to fit residues: 18.8207
Evaluate side-chains
  84 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 101 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 46 optimal weight:   20.0000
   chunk 26 optimal weight:    0.0270
   chunk 62 optimal weight:   10.0000
   chunk 102 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    2.7844

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.105920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.095106 restraints weight = 31654.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.093404 restraints weight = 49062.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.093177 restraints weight = 42603.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6742
moved from start:          0.5843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6586  Z= 0.193
  Angle     :  0.618   8.298   9074  Z= 0.318
  Chirality :  0.043   0.139   1203
  Planarity :  0.003   0.036   1225
  Dihedral  : 11.803 111.850   1365
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  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:  0.33 (0.26), residues: 1134
  helix:  1.33 (0.19), residues: 764
  sheet: -2.25 (0.94), residues: 32
  loop : -2.16 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  66 
 HIS   0.004   0.001   HIS A 214 
 PHE   0.020   0.001   PHE A 272 
 TYR   0.007   0.001   TYR B 162 
 ARG   0.010   0.001   ARG A 238 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 PHE cc_start: 0.7104 (m-80) cc_final: 0.6877 (m-80)
REVERT: A  242 MET cc_start: 0.6884 (mtt) cc_final: 0.6656 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1267
  time to fit residues: 18.6273
Evaluate side-chains
  86 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 96 optimal weight:   40.0000
   chunk 51 optimal weight:    0.0070
   chunk 111 optimal weight:   50.0000
   chunk 78 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0170
   chunk 21 optimal weight:    0.0670
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.4178

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.106691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.093309 restraints weight = 31550.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.092504 restraints weight = 46443.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.092987 restraints weight = 39478.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.6135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6586  Z= 0.157
  Angle     :  0.595   9.581   9074  Z= 0.301
  Chirality :  0.042   0.155   1203
  Planarity :  0.003   0.036   1225
  Dihedral  : 11.404 112.255   1365
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  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:  0.60 (0.26), residues: 1134
  helix:  1.57 (0.20), residues: 759
  sheet: -2.30 (0.80), residues: 39
  loop : -2.07 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  17 
 HIS   0.003   0.001   HIS B 107 
 PHE   0.022   0.001   PHE A 272 
 TYR   0.007   0.001   TYR B 162 
 ARG   0.007   0.001   ARG A  78 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 PHE cc_start: 0.7216 (m-80) cc_final: 0.6737 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1503
  time to fit residues: 21.5433
Evaluate side-chains
  84 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 44 optimal weight:   50.0000
   chunk 16 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 47 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 34 optimal weight:   50.0000
   chunk 91 optimal weight:   20.0000
   chunk 64 optimal weight:    7.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 214 HIS
B 134 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.106197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.093668 restraints weight = 31787.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.093668 restraints weight = 42414.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.092937 restraints weight = 41896.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6741
moved from start:          0.6306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6586  Z= 0.172
  Angle     :  0.592   9.767   9074  Z= 0.301
  Chirality :  0.042   0.152   1203
  Planarity :  0.003   0.035   1225
  Dihedral  : 11.164 112.353   1365
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  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:  0.69 (0.26), residues: 1134
  helix:  1.62 (0.19), residues: 767
  sheet: -2.15 (0.74), residues: 48
  loop : -2.05 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  17 
 HIS   0.004   0.001   HIS A 214 
 PHE   0.022   0.001   PHE A 272 
 TYR   0.006   0.001   TYR B 162 
 ARG   0.007   0.001   ARG A  78 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 PHE cc_start: 0.7357 (m-80) cc_final: 0.6909 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1412
  time to fit residues: 20.6741
Evaluate side-chains
  87 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 49 optimal weight:   30.0000
   chunk 0 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 32 optimal weight:   40.0000
   chunk 97 optimal weight:   30.0000
   chunk 25 optimal weight:    6.9990
   chunk 92 optimal weight:   50.0000
   chunk 111 optimal weight:   40.0000
   chunk 39 optimal weight:   30.0000
   chunk 5 optimal weight:   20.0000
   overall best weight:   11.7996

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.099030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.089697 restraints weight = 33406.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.088104 restraints weight = 48133.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.087573 restraints weight = 44768.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.6668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.125   6586  Z= 0.529
  Angle     :  0.990  11.214   9074  Z= 0.534
  Chirality :  0.052   0.235   1203
  Planarity :  0.006   0.074   1225
  Dihedral  : 12.755 105.430   1365
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.41 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  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: -1.34 (0.24), residues: 1134
  helix: -0.04 (0.18), residues: 759
  sheet: -3.64 (0.90), residues: 17
  loop : -2.51 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.006   TRP A  66 
 HIS   0.006   0.003   HIS A 107 
 PHE   0.023   0.003   PHE A 308 
 TYR   0.021   0.003   TYR A  87 
 ARG   0.017   0.002   ARG B 310 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A   75 MET cc_start: 0.7327 (tmm) cc_final: 0.7012 (tmm)
REVERT: A   78 ARG cc_start: 0.8776 (mmm160) cc_final: 0.8506 (mmm-85)
REVERT: B  109 MET cc_start: 0.8697 (mpp) cc_final: 0.8345 (mpp)
REVERT: B  295 MET cc_start: 0.8378 (tmm) cc_final: 0.7951 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1438
  time to fit residues: 17.5953
Evaluate side-chains
  73 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:   30.0000
   chunk 46 optimal weight:   40.0000
   chunk 32 optimal weight:   30.0000
   chunk 75 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 44 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   overall best weight:    5.1588

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.101212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.090319 restraints weight = 33391.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.089137 restraints weight = 43925.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.089338 restraints weight = 39869.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.6855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6586  Z= 0.259
  Angle     :  0.717   8.837   9074  Z= 0.377
  Chirality :  0.045   0.151   1203
  Planarity :  0.004   0.059   1225
  Dihedral  : 12.117 109.064   1365
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  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: -0.80 (0.25), residues: 1134
  helix:  0.46 (0.19), residues: 766
  sheet: -3.22 (0.79), residues: 31
  loop : -2.53 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A  66 
 HIS   0.004   0.001   HIS A 107 
 PHE   0.018   0.002   PHE A 272 
 TYR   0.011   0.001   TYR A  87 
 ARG   0.013   0.002   ARG B 310 

===============================================================================
Job complete
usr+sys time: 1937.81 seconds
wall clock time: 34 minutes 6.48 seconds (2046.48 seconds total)