Starting phenix.real_space_refine
on Fri Feb 14 07:47:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xlc_22239/02_2025/6xlc_22239.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xlc_22239/02_2025/6xlc_22239.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xlc_22239/02_2025/6xlc_22239.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xlc_22239/02_2025/6xlc_22239.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xlc_22239/02_2025/6xlc_22239.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xlc_22239/02_2025/6xlc_22239.cif"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      18      5.16       5
     C    6286      2.51       5
     N    1620      2.21       5
     O    1926      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9858
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 4897
          Classifications: {'peptide': 606}
          Link IDs: {'PTRANS': 20, 'TRANS': 585}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 4897
          Classifications: {'peptide': 606}
          Link IDs: {'PTRANS': 20, 'TRANS': 585}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.73, per 1000 atoms: 0.58
  Number of scatterers: 9858
  At special positions: 0
  Unit cell: (98.487, 92.133, 131.316, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      18     16.00
     P       6     15.00
     Mg      2     11.99
     O    1926      8.00
     N    1620      7.00
     C    6286      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=0, symmetry=0
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2324

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 10 sheets defined
      43.8% alpha, 15.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 19
      removed outlier: 4.074A  pdb=" N   SER A  17 " --> pdb=" O   THR A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 52
      removed outlier: 4.311A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   SER A  51 " --> pdb=" O   TYR A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 57
    Processing helix  chain 'A' and resid 87 through 92
    Processing helix  chain 'A' and resid 99 through 107
    Processing helix  chain 'A' and resid 123 through 129
      removed outlier: 3.566A  pdb=" N   LEU A 127 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   PHE A 128 " --> pdb=" O   TYR A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 185
      removed outlier: 3.762A  pdb=" N   TYR A 184 " --> pdb=" O   GLN A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 197
    Processing helix  chain 'A' and resid 276 through 280
    Processing helix  chain 'A' and resid 281 through 293
    Processing helix  chain 'A' and resid 384 through 405
      removed outlier: 3.938A  pdb=" N   ILE A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 415
      removed outlier: 3.547A  pdb=" N   PHE A 410 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 428
      removed outlier: 3.502A  pdb=" N   ILE A 421 " --> pdb=" O   PHE A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 437
      removed outlier: 3.834A  pdb=" N   LYS A 437 " --> pdb=" O   ALA A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 459
      removed outlier: 3.650A  pdb=" N   ARG A 459 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.594A  pdb=" N   VAL A 478 " --> pdb=" O   SER A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 490
      removed outlier: 3.833A  pdb=" N   LYS A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 510
      removed outlier: 3.521A  pdb=" N   ALA A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLN A 508 " --> pdb=" O   TYR A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 541
      removed outlier: 3.892A  pdb=" N   GLU A 535 " --> pdb=" O   GLU A 531 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS A 541 " --> pdb=" O   GLU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 555
    Processing helix  chain 'A' and resid 582 through 592
      removed outlier: 3.634A  pdb=" N   GLU A 586 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ARG A 587 " --> pdb=" O   ALA A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 627
      removed outlier: 3.712A  pdb=" N   LYS A 623 " --> pdb=" O   LYS A 619 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ARG A 624 " --> pdb=" O   GLU A 620 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL A 625 " --> pdb=" O   LEU A 621 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ASP A 626 " --> pdb=" O   LYS A 622 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU A 627 " --> pdb=" O   LYS A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 651
      removed outlier: 3.816A  pdb=" N   LYS A 636 " --> pdb=" O   ASP A 632 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ASP A 637 " --> pdb=" O   LYS A 633 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU A 638 " --> pdb=" O   THR A 634 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLY A 651 " --> pdb=" O   LEU A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 672
      removed outlier: 3.827A  pdb=" N   PHE A 660 " --> pdb=" O   GLU A 656 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 22
      removed outlier: 4.447A  pdb=" N   SER B  17 " --> pdb=" O   THR B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 52
      removed outlier: 4.376A  pdb=" N   ARG B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   SER B  51 " --> pdb=" O   TYR B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 57
    Processing helix  chain 'B' and resid 87 through 92
    Processing helix  chain 'B' and resid 99 through 108
    Processing helix  chain 'B' and resid 122 through 129
      removed outlier: 3.521A  pdb=" N   LEU B 127 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE B 128 " --> pdb=" O   TYR B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 185
      removed outlier: 3.664A  pdb=" N   TYR B 184 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 198
    Processing helix  chain 'B' and resid 281 through 293
    Processing helix  chain 'B' and resid 383 through 405
      removed outlier: 3.625A  pdb=" N   VAL B 387 " --> pdb=" O   LYS B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 417
    Processing helix  chain 'B' and resid 417 through 427
    Processing helix  chain 'B' and resid 431 through 437
      removed outlier: 3.790A  pdb=" N   LYS B 437 " --> pdb=" O   ALA B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 459
      removed outlier: 3.603A  pdb=" N   THR B 458 " --> pdb=" O   THR B 454 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG B 459 " --> pdb=" O   ASP B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 480
      removed outlier: 3.536A  pdb=" N   VAL B 478 " --> pdb=" O   SER B 474 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LYS B 480 " --> pdb=" O   LYS B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 490
      removed outlier: 3.519A  pdb=" N   LYS B 490 " --> pdb=" O   ALA B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 510
      removed outlier: 3.553A  pdb=" N   ALA B 505 " --> pdb=" O   ILE B 501 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLN B 508 " --> pdb=" O   TYR B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 541
    Processing helix  chain 'B' and resid 543 through 555
    Processing helix  chain 'B' and resid 582 through 590
      removed outlier: 3.823A  pdb=" N   ARG B 587 " --> pdb=" O   ALA B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 615 through 627
      removed outlier: 3.573A  pdb=" N   LYS B 623 " --> pdb=" O   LYS B 619 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG B 624 " --> pdb=" O   GLU B 620 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   VAL B 625 " --> pdb=" O   LEU B 621 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP B 626 " --> pdb=" O   LYS B 622 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU B 627 " --> pdb=" O   LYS B 623 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 651
      removed outlier: 3.630A  pdb=" N   LYS B 636 " --> pdb=" O   ASP B 632 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ASP B 637 " --> pdb=" O   LYS B 633 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU B 638 " --> pdb=" O   THR B 634 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLY B 651 " --> pdb=" O   LEU B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 656 through 672
      removed outlier: 3.967A  pdb=" N   PHE B 660 " --> pdb=" O   GLU B 656 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7
      removed outlier: 3.548A  pdb=" N   GLU A   4 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG B 133 " --> pdb=" O   PHE B 176 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG B 174 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ILE B  64 " --> pdb=" O   GLN B 206 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   LEU B 208 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   ILE B  66 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10
      removed outlier: 6.475A  pdb=" N   GLN A   9 " --> pdb=" O   ILE B  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 265
      removed outlier: 6.058A  pdb=" N   ILE A  64 " --> pdb=" O   GLN A 206 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   LEU A 208 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   ILE A  66 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR A  67 " --> pdb=" O   GLU A  76 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLU A  76 " --> pdb=" O   THR A  67 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ARG A 133 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU B   4 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96
    Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 307
      removed outlier: 3.512A  pdb=" N   TYR A 301 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   THR A 347 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL A 341 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   PHE A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 442 through 443
      removed outlier: 4.048A  pdb=" N   ASN A 442 " --> pdb=" O   PHE A 496 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   LEU A 495 " --> pdb=" O   ASN A 466 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   TYR A 468 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   LEU A 497 " --> pdb=" O   TYR A 468 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ILE A 470 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   ILE A 467 " --> pdb=" O   VAL A 518 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 563
      removed outlier: 3.524A  pdb=" N   ILE A 611 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 307
      removed outlier: 3.515A  pdb=" N   VAL B 364 " --> pdb=" O   ILE B 316 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU B 339 " --> pdb=" O   ILE B 346 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443
      removed outlier: 3.885A  pdb=" N   ASN B 442 " --> pdb=" O   PHE B 496 " (cutoff:3.500A)
      removed outlier: 8.834A  pdb=" N   LEU B 495 " --> pdb=" O   ASN B 466 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   TYR B 468 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   LEU B 497 " --> pdb=" O   TYR B 468 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   ILE B 470 " --> pdb=" O   LEU B 497 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   ILE B 467 " --> pdb=" O   VAL B 518 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 561 through 563
      removed outlier: 3.526A  pdb=" N   ILE B 611 " --> pdb=" O   VAL B 562 " (cutoff:3.500A)

    417 hydrogen bonds defined for protein.
    1170 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.21

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3212
        1.34 -     1.46: 1542
        1.46 -     1.57: 5220
        1.57 -     1.69: 10
        1.69 -     1.80: 38
  Bond restraints: 10022
  Sorted by residual:
  bond pdb=" O3A ANP A 801 "
       pdb=" PB  ANP A 801 "
    ideal  model  delta    sigma   weight residual
    1.700  1.556  0.144 2.00e-02 2.50e+03 5.17e+01
  bond pdb=" O3A ANP B 801 "
       pdb=" PB  ANP B 801 "
    ideal  model  delta    sigma   weight residual
    1.700  1.557  0.143 2.00e-02 2.50e+03 5.12e+01
  bond pdb=" N3B ANP A 801 "
       pdb=" PG  ANP A 801 "
    ideal  model  delta    sigma   weight residual
    1.795  1.692  0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" N3B ANP B 801 "
       pdb=" PG  ANP B 801 "
    ideal  model  delta    sigma   weight residual
    1.795  1.692  0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" O5' ANP B 801 "
       pdb=" PA  ANP B 801 "
    ideal  model  delta    sigma   weight residual
    1.655  1.582  0.073 2.00e-02 2.50e+03 1.35e+01
  ... (remaining 10017 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.46: 13486
        3.46 -     6.93: 30
        6.93 -    10.39: 7
       10.39 -    13.86: 1
       13.86 -    17.32: 2
  Bond angle restraints: 13526
  Sorted by residual:
  angle pdb=" PB  ANP B 801 "
        pdb=" N3B ANP B 801 "
        pdb=" PG  ANP B 801 "
      ideal   model   delta    sigma   weight residual
     126.95  109.63   17.32 3.00e+00 1.11e-01 3.33e+01
  angle pdb=" PB  ANP A 801 "
        pdb=" N3B ANP A 801 "
        pdb=" PG  ANP A 801 "
      ideal   model   delta    sigma   weight residual
     126.95  109.73   17.22 3.00e+00 1.11e-01 3.30e+01
  angle pdb=" O1B ANP B 801 "
        pdb=" PB  ANP B 801 "
        pdb=" O2B ANP B 801 "
      ideal   model   delta    sigma   weight residual
     120.08  109.60   10.48 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" O1B ANP A 801 "
        pdb=" PB  ANP A 801 "
        pdb=" O2B ANP A 801 "
      ideal   model   delta    sigma   weight residual
     120.08  109.69   10.39 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" N   ILE A  20 "
        pdb=" CA  ILE A  20 "
        pdb=" C   ILE A  20 "
      ideal   model   delta    sigma   weight residual
     113.71  110.65    3.06 9.50e-01 1.11e+00 1.04e+01
  ... (remaining 13521 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 5759
       17.80 -    35.60: 330
       35.60 -    53.39: 67
       53.39 -    71.19: 21
       71.19 -    88.99: 15
  Dihedral angle restraints: 6192
    sinusoidal: 2628
      harmonic: 3564
  Sorted by residual:
  dihedral pdb=" CB  GLU B  76 "
           pdb=" CG  GLU B  76 "
           pdb=" CD  GLU B  76 "
           pdb=" OE1 GLU B  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.99   88.99     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU B 513 "
           pdb=" CG  GLU B 513 "
           pdb=" CD  GLU B 513 "
           pdb=" OE1 GLU B 513 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.90  -88.90     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" O1B ANP A 801 "
           pdb=" N3B ANP A 801 "
           pdb=" PB  ANP A 801 "
           pdb=" PG  ANP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15  -53.13   88.28     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 6189 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1325
       0.055 -    0.109: 188
       0.109 -    0.164: 19
       0.164 -    0.218: 0
       0.218 -    0.273: 2
  Chirality restraints: 1534
  Sorted by residual:
  chirality pdb=" C3' ANP B 801 "
            pdb=" C2' ANP B 801 "
            pdb=" C4' ANP B 801 "
            pdb=" O3' ANP B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" C3' ANP A 801 "
            pdb=" C2' ANP A 801 "
            pdb=" C4' ANP A 801 "
            pdb=" O3' ANP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  ILE B  77 "
            pdb=" N   ILE B  77 "
            pdb=" C   ILE B  77 "
            pdb=" CB  ILE B  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 1531 not shown)

  Planarity restraints: 1724
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 354 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.32e+00
        pdb=" N   PRO A 355 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 355 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 355 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  20 "   -0.005 2.00e-02 2.50e+03   9.43e-03 8.90e-01
        pdb=" C   ILE A  20 "    0.016 2.00e-02 2.50e+03
        pdb=" O   ILE A  20 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ASN A  21 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 543 "    0.005 2.00e-02 2.50e+03   6.32e-03 8.00e-01
        pdb=" CG  TYR B 543 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 543 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 543 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 543 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 543 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 543 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 543 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1721 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 128
        2.64 -     3.21: 8674
        3.21 -     3.77: 15184
        3.77 -     4.34: 21623
        4.34 -     4.90: 34910
  Nonbonded interactions: 80519
  Sorted by model distance:
  nonbonded pdb=" O1B ANP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.079 2.170
  nonbonded pdb=" O1B ANP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.089 2.170
  nonbonded pdb=" O1A ANP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.249 2.170
  nonbonded pdb=" OD1 ASN B  37 "
            pdb="MG    MG B 802 "
     model   vdw
     2.250 2.170
  nonbonded pdb=" OH  TYR B 456 "
            pdb=" O   GLU B 493 "
     model   vdw
     2.255 3.040
  ... (remaining 80514 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.940
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.740
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6316
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.144  10022  Z= 0.214
  Angle     :  0.523  17.324  13526  Z= 0.249
  Chirality :  0.039   0.273   1534
  Planarity :  0.002   0.029   1724
  Dihedral  : 12.917  88.987   3868
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  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: -2.69 (0.20), residues: 1196
  helix: -1.88 (0.19), residues: 492
  sheet: -0.99 (0.34), residues: 218
  loop : -1.87 (0.23), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 273 
 HIS   0.001   0.000   HIS A 197 
 PHE   0.006   0.001   PHE A 652 
 TYR   0.016   0.001   TYR B 543 
 ARG   0.001   0.000   ARG B 440 

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6542 (mm-30)
REVERT: A  610 GLU cc_start: 0.7411 (mp0) cc_final: 0.7104 (mp0)
REVERT: A  614 LYS cc_start: 0.6948 (pttm) cc_final: 0.6537 (ptmm)
REVERT: B  379 LEU cc_start: 0.5857 (pt) cc_final: 0.5552 (pp)
REVERT: B  386 LYS cc_start: 0.6026 (mmtm) cc_final: 0.5820 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.2823
  time to fit residues: 98.3700
Evaluate side-chains
  146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 90 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 108 optimal weight:    7.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 431 ASN
A 466 ASN
A 673 ASN
B 304 HIS
B 380 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.131379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.115860 restraints weight = 20755.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.119029 restraints weight = 12347.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.121168 restraints weight = 8479.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.5302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.096  10022  Z= 0.367
  Angle     :  0.726   9.040  13526  Z= 0.375
  Chirality :  0.048   0.187   1534
  Planarity :  0.005   0.049   1724
  Dihedral  :  6.760  81.223   1358
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.64 %
    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: -1.66 (0.22), residues: 1196
  helix: -0.71 (0.22), residues: 490
  sheet: -0.79 (0.35), residues: 208
  loop : -1.51 (0.24), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 357 
 HIS   0.005   0.001   HIS A 426 
 PHE   0.021   0.003   PHE B 652 
 TYR   0.025   0.002   TYR B 125 
 ARG   0.010   0.001   ARG A 174 

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 138
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7216 (mm-30)
REVERT: A  205 ILE cc_start: 0.7588 (mm) cc_final: 0.7279 (mt)
REVERT: A  314 ARG cc_start: 0.7711 (mpt-90) cc_final: 0.7412 (mmt-90)
REVERT: A  589 MET cc_start: 0.7633 (mmt) cc_final: 0.7428 (mmt)
REVERT: B  205 ILE cc_start: 0.7489 (mm) cc_final: 0.7116 (mt)
REVERT: B  386 LYS cc_start: 0.7303 (mmtm) cc_final: 0.6886 (tptp)
REVERT: B  589 MET cc_start: 0.7356 (mmt) cc_final: 0.7065 (mmt)
  outliers start: 31
  outliers final: 17
  residues processed: 158
  average time/residue: 0.2512
  time to fit residues: 54.8828
Evaluate side-chains
  114 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  441 TYR
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  471 THR
Chi-restraints excluded: chain B residue  611 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 105 optimal weight:    0.3980
   chunk 98 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
B 426 HIS
B 431 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.132405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.117369 restraints weight = 20745.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.120503 restraints weight = 12190.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.122636 restraints weight = 8289.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.5663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10022  Z= 0.170
  Angle     :  0.519   7.957  13526  Z= 0.266
  Chirality :  0.042   0.171   1534
  Planarity :  0.003   0.039   1724
  Dihedral  :  6.184  78.424   1358
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.70 %
    Favored  : 82.20 %
  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: -0.90 (0.24), residues: 1196
  helix:  0.17 (0.24), residues: 490
  sheet: -0.86 (0.34), residues: 216
  loop : -1.15 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 148 
 HIS   0.003   0.000   HIS B 426 
 PHE   0.021   0.001   PHE A 579 
 TYR   0.008   0.001   TYR A 125 
 ARG   0.005   0.000   ARG A 174 

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7155 (mm-30)
REVERT: A  205 ILE cc_start: 0.7640 (mm) cc_final: 0.7235 (mt)
REVERT: B  105 MET cc_start: 0.8111 (mmm) cc_final: 0.7864 (mmm)
REVERT: B  116 MET cc_start: 0.7292 (mpp) cc_final: 0.6852 (mtt)
REVERT: B  205 ILE cc_start: 0.7482 (mm) cc_final: 0.6988 (mt)
REVERT: B  386 LYS cc_start: 0.7392 (mmtm) cc_final: 0.6858 (tptp)
REVERT: B  396 LEU cc_start: 0.9054 (tp) cc_final: 0.8839 (tp)
REVERT: B  589 MET cc_start: 0.7220 (mmt) cc_final: 0.6956 (mmt)
REVERT: B  614 LYS cc_start: 0.7888 (mmtm) cc_final: 0.7058 (tmtt)
  outliers start: 12
  outliers final: 9
  residues processed: 123
  average time/residue: 0.2200
  time to fit residues: 39.0319
Evaluate side-chains
  98 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  474 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   chunk 85 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0670
   chunk 96 optimal weight:    3.9990
   chunk 109 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0570
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
B  14 GLN
B  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.132756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.117657 restraints weight = 20407.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.120777 restraints weight = 12012.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.122844 restraints weight = 8157.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.5949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10022  Z= 0.141
  Angle     :  0.491   7.510  13526  Z= 0.249
  Chirality :  0.041   0.171   1534
  Planarity :  0.003   0.037   1724
  Dihedral  :  6.104  77.914   1358
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 17.16 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.25), residues: 1196
  helix:  0.55 (0.25), residues: 490
  sheet: -0.76 (0.35), residues: 216
  loop : -0.90 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 148 
 HIS   0.000   0.000   HIS A 304 
 PHE   0.018   0.001   PHE A 579 
 TYR   0.011   0.001   TYR B 289 
 ARG   0.004   0.000   ARG A 174 

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  205 ILE cc_start: 0.7595 (mm) cc_final: 0.7286 (mt)
REVERT: A  589 MET cc_start: 0.7796 (mmt) cc_final: 0.7560 (mmt)
REVERT: B  105 MET cc_start: 0.8111 (mmm) cc_final: 0.7887 (mmm)
REVERT: B  116 MET cc_start: 0.7076 (mpp) cc_final: 0.6769 (mtt)
REVERT: B  205 ILE cc_start: 0.7505 (mm) cc_final: 0.7207 (mt)
REVERT: B  386 LYS cc_start: 0.7355 (mmtm) cc_final: 0.6845 (tptp)
REVERT: B  396 LEU cc_start: 0.9059 (tp) cc_final: 0.8858 (tp)
REVERT: B  547 THR cc_start: 0.7061 (p) cc_final: 0.6742 (p)
REVERT: B  581 TRP cc_start: 0.7938 (m-10) cc_final: 0.7657 (m-10)
REVERT: B  614 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7094 (tmtt)
  outliers start: 13
  outliers final: 8
  residues processed: 114
  average time/residue: 0.2055
  time to fit residues: 34.8838
Evaluate side-chains
  93 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain A residue  656 GLU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  147 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    0.2980
   chunk 19 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0010
   chunk 43 optimal weight:    2.9990
   chunk 105 optimal weight:    0.5980
   chunk 56 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9980
   chunk 8 optimal weight:    0.2980
   chunk 68 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   overall best weight:    0.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 304 HIS
A 381 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.132812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.117786 restraints weight = 20427.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.120924 restraints weight = 12084.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.123024 restraints weight = 8207.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.6167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10022  Z= 0.137
  Angle     :  0.478   6.652  13526  Z= 0.244
  Chirality :  0.040   0.162   1534
  Planarity :  0.003   0.039   1724
  Dihedral  :  6.010  76.115   1358
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 18.36 %
    Favored  : 80.54 %
  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: -0.23 (0.25), residues: 1196
  helix:  0.78 (0.25), residues: 488
  sheet: -0.52 (0.36), residues: 216
  loop : -0.82 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 148 
 HIS   0.001   0.000   HIS A 304 
 PHE   0.018   0.001   PHE A   6 
 TYR   0.004   0.001   TYR A 203 
 ARG   0.006   0.000   ARG B 343 

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.8597 (tpt) cc_final: 0.8315 (tpt)
REVERT: A  205 ILE cc_start: 0.7575 (mm) cc_final: 0.7238 (mt)
REVERT: A  644 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6714 (mm-30)
REVERT: B  116 MET cc_start: 0.7014 (mpp) cc_final: 0.6767 (mtt)
REVERT: B  386 LYS cc_start: 0.7347 (mmtm) cc_final: 0.6910 (tptp)
REVERT: B  547 THR cc_start: 0.7049 (p) cc_final: 0.6766 (p)
REVERT: B  581 TRP cc_start: 0.7941 (m-10) cc_final: 0.7666 (m-10)
REVERT: B  614 LYS cc_start: 0.7785 (mmtm) cc_final: 0.7113 (tmtt)
  outliers start: 12
  outliers final: 8
  residues processed: 111
  average time/residue: 0.1974
  time to fit residues: 32.8064
Evaluate side-chains
  90 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain A residue  656 GLU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  313 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 110 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0270
   chunk 14 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 115 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.8046

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

Flipped N/Q/H residues before XYZ refinement:
B 442 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.124188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.108881 restraints weight = 20671.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.111978 restraints weight = 12296.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.114042 restraints weight = 8408.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.7226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10022  Z= 0.267
  Angle     :  0.587   8.711  13526  Z= 0.302
  Chirality :  0.044   0.162   1534
  Planarity :  0.004   0.049   1724
  Dihedral  :  6.342  74.408   1358
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.17 %
    Favored  : 79.61 %
  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: -0.44 (0.25), residues: 1196
  helix:  0.58 (0.24), residues: 490
  sheet: -0.60 (0.36), residues: 216
  loop : -0.94 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 581 
 HIS   0.002   0.000   HIS A 426 
 PHE   0.024   0.002   PHE A   6 
 TYR   0.011   0.001   TYR A 125 
 ARG   0.011   0.001   ARG B 376 

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 1.155 
Fit side-chains
REVERT: A  116 MET cc_start: 0.7268 (mtt) cc_final: 0.7056 (mtt)
REVERT: A  192 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8104 (tt0)
REVERT: A  205 ILE cc_start: 0.7599 (mm) cc_final: 0.7281 (mt)
REVERT: A  314 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7149 (mmt-90)
REVERT: A  589 MET cc_start: 0.7651 (mmt) cc_final: 0.7370 (mmt)
REVERT: A  614 LYS cc_start: 0.8086 (mmpt) cc_final: 0.7724 (ptmt)
REVERT: B  205 ILE cc_start: 0.7645 (mm) cc_final: 0.7155 (mt)
REVERT: B  322 ARG cc_start: 0.5697 (ppt170) cc_final: 0.5060 (ttt180)
REVERT: B  386 LYS cc_start: 0.7839 (mmtm) cc_final: 0.7429 (tptp)
REVERT: B  553 ILE cc_start: 0.7774 (mm) cc_final: 0.7411 (mm)
REVERT: B  614 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7179 (tmtt)
  outliers start: 24
  outliers final: 13
  residues processed: 119
  average time/residue: 0.2379
  time to fit residues: 39.9960
Evaluate side-chains
  91 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  192 GLU
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain A residue  656 GLU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  471 THR
Chi-restraints excluded: chain B residue  611 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 69 optimal weight:    0.0970
   chunk 30 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 112 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    2.2186

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.121583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.106329 restraints weight = 20934.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.109449 restraints weight = 12395.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.111511 restraints weight = 8460.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.7916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10022  Z= 0.288
  Angle     :  0.598   7.505  13526  Z= 0.306
  Chirality :  0.044   0.159   1534
  Planarity :  0.004   0.054   1724
  Dihedral  :  6.359  70.790   1358
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.65 %
    Favored  : 78.23 %
  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: -0.55 (0.25), residues: 1196
  helix:  0.54 (0.25), residues: 490
  sheet: -0.72 (0.36), residues: 216
  loop : -1.02 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 581 
 HIS   0.002   0.001   HIS A 426 
 PHE   0.025   0.002   PHE B 124 
 TYR   0.015   0.001   TYR A 203 
 ARG   0.009   0.001   ARG A 133 

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 1.164 
Fit side-chains
REVERT: A  205 ILE cc_start: 0.7705 (mm) cc_final: 0.7355 (mt)
REVERT: A  260 VAL cc_start: 0.5986 (OUTLIER) cc_final: 0.5673 (m)
REVERT: A  281 THR cc_start: 0.7139 (p) cc_final: 0.6865 (m)
REVERT: A  314 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7179 (mmt-90)
REVERT: A  589 MET cc_start: 0.7687 (mmt) cc_final: 0.7290 (mmt)
REVERT: B  205 ILE cc_start: 0.7666 (mm) cc_final: 0.7107 (mt)
REVERT: B  322 ARG cc_start: 0.5763 (ppt170) cc_final: 0.5213 (ttt180)
REVERT: B  386 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7705 (tptp)
REVERT: B  553 ILE cc_start: 0.7908 (mm) cc_final: 0.7604 (mm)
  outliers start: 23
  outliers final: 14
  residues processed: 100
  average time/residue: 0.2075
  time to fit residues: 31.1075
Evaluate side-chains
  86 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  471 THR
Chi-restraints excluded: chain B residue  474 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   overall best weight:    2.3388

-------------------------------------------------------------------------------
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 = 0.3774 r_free = 0.3774 target = 0.119500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.104960 restraints weight = 20766.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.107942 restraints weight = 12204.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.109974 restraints weight = 8305.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.8329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  10022  Z= 0.313
  Angle     :  0.628   7.411  13526  Z= 0.322
  Chirality :  0.044   0.160   1534
  Planarity :  0.004   0.058   1724
  Dihedral  :  6.454  71.135   1358
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.76 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.25), residues: 1196
  helix:  0.46 (0.24), residues: 490
  sheet: -0.74 (0.36), residues: 216
  loop : -1.04 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 296 
 HIS   0.003   0.001   HIS A 426 
 PHE   0.020   0.002   PHE B 124 
 TYR   0.017   0.001   TYR A 203 
 ARG   0.005   0.001   ARG B 536 

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 1.233 
Fit side-chains
REVERT: A  205 ILE cc_start: 0.7665 (mm) cc_final: 0.7355 (mt)
REVERT: A  311 LEU cc_start: 0.7122 (tp) cc_final: 0.6846 (pt)
REVERT: A  314 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7190 (mmt-90)
REVERT: A  589 MET cc_start: 0.7640 (mmt) cc_final: 0.7311 (mmt)
REVERT: A  644 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6188 (mm-30)
REVERT: B  195 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7756 (tttm)
REVERT: B  205 ILE cc_start: 0.7671 (mm) cc_final: 0.7135 (mt)
REVERT: B  322 ARG cc_start: 0.5855 (ppt170) cc_final: 0.5480 (ttt180)
REVERT: B  385 MET cc_start: 0.6693 (tpp) cc_final: 0.5894 (ptt)
REVERT: B  386 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7845 (tptp)
REVERT: B  553 ILE cc_start: 0.7880 (mm) cc_final: 0.7576 (mm)
  outliers start: 21
  outliers final: 15
  residues processed: 94
  average time/residue: 0.2384
  time to fit residues: 32.7051
Evaluate side-chains
  86 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  471 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 110 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.122665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.108134 restraints weight = 20587.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.111147 restraints weight = 12219.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.113205 restraints weight = 8344.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.8392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10022  Z= 0.196
  Angle     :  0.549   7.860  13526  Z= 0.281
  Chirality :  0.042   0.160   1534
  Planarity :  0.004   0.058   1724
  Dihedral  :  6.220  71.752   1358
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 21.86 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.25), residues: 1196
  helix:  0.63 (0.25), residues: 490
  sheet: -0.67 (0.36), residues: 216
  loop : -0.94 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 148 
 HIS   0.001   0.000   HIS B 304 
 PHE   0.020   0.001   PHE B 124 
 TYR   0.010   0.001   TYR A 203 
 ARG   0.004   0.000   ARG A 575 

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 1.278 
Fit side-chains
REVERT: A  205 ILE cc_start: 0.7770 (mm) cc_final: 0.7438 (mt)
REVERT: A  314 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7208 (mmt-90)
REVERT: A  644 GLU cc_start: 0.6409 (mm-30) cc_final: 0.6142 (mm-30)
REVERT: B  205 ILE cc_start: 0.7581 (mm) cc_final: 0.7040 (mt)
REVERT: B  378 MET cc_start: 0.6957 (ppp) cc_final: 0.6722 (ppp)
REVERT: B  385 MET cc_start: 0.6495 (tpp) cc_final: 0.5780 (ptt)
REVERT: B  386 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7854 (tptp)
REVERT: B  553 ILE cc_start: 0.7569 (mm) cc_final: 0.7234 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 87
  average time/residue: 0.2303
  time to fit residues: 28.7808
Evaluate side-chains
  79 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  471 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0010
   chunk 68 optimal weight:    9.9990
   chunk 87 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 110 optimal weight:    0.1980
   overall best weight:    0.5586

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.124941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.110458 restraints weight = 20486.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.113478 restraints weight = 12085.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.115538 restraints weight = 8221.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.8427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10022  Z= 0.161
  Angle     :  0.535   7.761  13526  Z= 0.273
  Chirality :  0.042   0.160   1534
  Planarity :  0.004   0.058   1724
  Dihedral  :  6.099  72.730   1358
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 22.32 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.25), residues: 1196
  helix:  0.81 (0.25), residues: 490
  sheet: -0.66 (0.36), residues: 218
  loop : -0.84 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 148 
 HIS   0.001   0.000   HIS B 304 
 PHE   0.017   0.001   PHE B 124 
 TYR   0.007   0.001   TYR A 203 
 ARG   0.012   0.001   ARG B 343 

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 1.210 
Fit side-chains
REVERT: A  205 ILE cc_start: 0.7670 (mm) cc_final: 0.7370 (mt)
REVERT: B  386 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7789 (tptp)
REVERT: B  536 ARG cc_start: 0.6474 (ptm-80) cc_final: 0.5694 (ptp90)
REVERT: B  553 ILE cc_start: 0.7447 (mm) cc_final: 0.7113 (mm)
REVERT: B  560 LYS cc_start: 0.7409 (pttm) cc_final: 0.7175 (ttpt)
  outliers start: 9
  outliers final: 5
  residues processed: 90
  average time/residue: 0.2286
  time to fit residues: 30.0728
Evaluate side-chains
  78 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  260 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   chunk 75 optimal weight:    9.9990
   chunk 70 optimal weight:    0.0870
   chunk 104 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   chunk 6 optimal weight:    0.1980
   chunk 27 optimal weight:    6.9990
   overall best weight:    0.3558

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

Flipped N/Q/H residues before XYZ refinement:
B  14 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.125602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.111071 restraints weight = 20445.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.114186 restraints weight = 11732.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.116315 restraints weight = 7864.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.8463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10022  Z= 0.155
  Angle     :  0.538   7.799  13526  Z= 0.274
  Chirality :  0.041   0.160   1534
  Planarity :  0.004   0.058   1724
  Dihedral  :  6.053  72.375   1358
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 23.06 %
    Favored  : 76.11 %
  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: -0.13 (0.25), residues: 1196
  helix:  0.84 (0.25), residues: 496
  sheet: -0.58 (0.38), residues: 202
  loop : -0.72 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 148 
 HIS   0.001   0.000   HIS B 304 
 PHE   0.019   0.001   PHE B 124 
 TYR   0.007   0.001   TYR A 203 
 ARG   0.013   0.001   ARG B 343 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2789.46 seconds
wall clock time: 51 minutes 19.31 seconds (3079.31 seconds total)