Starting phenix.real_space_refine
on Thu Feb 13 20:11:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qvd_4649/02_2025/6qvd_4649.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qvd_4649/02_2025/6qvd_4649.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qvd_4649/02_2025/6qvd_4649.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qvd_4649/02_2025/6qvd_4649.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qvd_4649/02_2025/6qvd_4649.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qvd_4649/02_2025/6qvd_4649.cif"
  }
  resolution = 4.34
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    6094      2.51       5
     N    1472      2.21       5
     O    1576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 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: 9212
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4606
          Classifications: {'peptide': 596}
          Link IDs: {'CIS': 2, 'PTRANS': 26, 'TRANS': 567}
          Chain breaks: 2
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.34, per 1000 atoms: 0.91
  Number of scatterers: 9212
  At special positions: 0
  Unit cell: (101.65, 95.23, 108.07, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      70     16.00
     O    1576      8.00
     N    1472      7.00
     C    6094      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: 2.35
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2200

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      66.7% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'B' and resid 115 through 154
      removed outlier: 4.768A  pdb=" N   GLN B 154 " --> pdb=" O   TYR B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 181
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 190 through 199
      removed outlier: 4.359A  pdb=" N   MET B 194 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 207
    Processing helix  chain 'B' and resid 208 through 225
      removed outlier: 3.785A  pdb=" N   PHE B 212 " --> pdb=" O   THR B 208 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   VAL B 213 " --> pdb=" O   MET B 209 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA B 214 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   VAL B 217 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
      removed outlier: 3.614A  pdb=" N   PHE B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 280
      removed outlier: 3.582A  pdb=" N   GLY B 280 " --> pdb=" O   GLY B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 291
    Processing helix  chain 'B' and resid 298 through 323
      removed outlier: 4.103A  pdb=" N   ARG B 317 " --> pdb=" O   ALA B 313 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ALA B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 377
      removed outlier: 3.572A  pdb=" N   PHE B 351 " --> pdb=" O   GLU B 347 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA B 352 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA B 353 " --> pdb=" O   PRO B 349 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   CYS B 358 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL B 364 " --> pdb=" O   LEU B 360 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   PHE B 365 " --> pdb=" O   LEU B 361 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL B 366 " --> pdb=" O   GLY B 362 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY B 375 " --> pdb=" O   GLN B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 389
      removed outlier: 3.791A  pdb=" N   SER B 383 " --> pdb=" O   HIS B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 403
      removed outlier: 4.557A  pdb=" N   GLY B 395 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 428
    Processing helix  chain 'B' and resid 444 through 450
      removed outlier: 3.571A  pdb=" N   ALA B 447 " --> pdb=" O   GLY B 444 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE B 450 " --> pdb=" O   ALA B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 477
      removed outlier: 3.503A  pdb=" N   ILE B 459 " --> pdb=" O   ASN B 455 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE B 472 " --> pdb=" O   PHE B 468 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL B 473 " --> pdb=" O   TRP B 469 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   MET B 477 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 506
    Processing helix  chain 'B' and resid 521 through 538
      removed outlier: 4.572A  pdb=" N   THR B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 551
      removed outlier: 3.948A  pdb=" N   VAL B 544 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 574
    Processing helix  chain 'B' and resid 576 through 585
    Processing helix  chain 'B' and resid 621 through 632
    Processing helix  chain 'B' and resid 654 through 666
    Processing helix  chain 'B' and resid 833 through 845
    Processing helix  chain 'B' and resid 862 through 871
    Processing helix  chain 'A' and resid 116 through 154
      removed outlier: 4.768A  pdb=" N   GLN A 154 " --> pdb=" O   TYR A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 181
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 190 through 199
      removed outlier: 4.360A  pdb=" N   MET A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 207
    Processing helix  chain 'A' and resid 208 through 225
      removed outlier: 3.784A  pdb=" N   PHE A 212 " --> pdb=" O   THR A 208 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   VAL A 213 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   ALA A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
      removed outlier: 3.613A  pdb=" N   PHE A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 280
      removed outlier: 3.581A  pdb=" N   GLY A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 298 through 323
      removed outlier: 4.102A  pdb=" N   ARG A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ALA A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 377
      removed outlier: 3.572A  pdb=" N   PHE A 351 " --> pdb=" O   GLU A 347 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA A 352 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA A 353 " --> pdb=" O   PRO A 349 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   CYS A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   PHE A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL A 366 " --> pdb=" O   GLY A 362 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLY A 375 " --> pdb=" O   GLN A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 389
      removed outlier: 3.792A  pdb=" N   SER A 383 " --> pdb=" O   HIS A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 403
      removed outlier: 4.557A  pdb=" N   GLY A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 428
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 3.570A  pdb=" N   ALA A 447 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE A 450 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 477
      removed outlier: 3.504A  pdb=" N   ILE A 459 " --> pdb=" O   ASN A 455 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE A 472 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL A 473 " --> pdb=" O   TRP A 469 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   MET A 477 " --> pdb=" O   VAL A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 506
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 4.572A  pdb=" N   THR A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 551
      removed outlier: 3.949A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 574
    Processing helix  chain 'A' and resid 576 through 585
    Processing helix  chain 'A' and resid 621 through 632
    Processing helix  chain 'A' and resid 654 through 666
    Processing helix  chain 'A' and resid 833 through 845
    Processing helix  chain 'A' and resid 862 through 871
    Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512
    Processing sheet with id=AA2, first strand: chain 'B' and resid 636 through 640
      removed outlier: 5.569A  pdb=" N   LEU B 637 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   SER B 651 " --> pdb=" O   LEU B 637 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LEU B 639 " --> pdb=" O   LEU B 649 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER B 651 " --> pdb=" O   ASP B 822 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   ASP B 822 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853
      removed outlier: 6.553A  pdb=" N   ALA B 849 " --> pdb=" O   VAL B 860 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   VAL B 860 " --> pdb=" O   ALA B 849 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL B 851 " --> pdb=" O   ARG B 858 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512
    Processing sheet with id=AA5, first strand: chain 'A' and resid 636 through 640
      removed outlier: 5.569A  pdb=" N   LEU A 637 " --> pdb=" O   SER A 651 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   SER A 651 " --> pdb=" O   LEU A 637 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   LEU A 639 " --> pdb=" O   LEU A 649 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER A 651 " --> pdb=" O   ASP A 822 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   ASP A 822 " --> pdb=" O   SER A 651 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853
      removed outlier: 6.553A  pdb=" N   ALA A 849 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   VAL A 860 " --> pdb=" O   ALA A 849 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL A 851 " --> pdb=" O   ARG A 858 " (cutoff:3.500A)

    555 hydrogen bonds defined for protein.
    1623 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: 2.98

  Time building geometry restraints manager: 2.73 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1631
        1.32 -     1.45: 2434
        1.45 -     1.57: 5257
        1.57 -     1.69: 4
        1.69 -     1.81: 116
  Bond restraints: 9442
  Sorted by residual:
  bond pdb=" CB  LYS B 518 "
       pdb=" CG  LYS B 518 "
    ideal  model  delta    sigma   weight residual
    1.520  1.628 -0.108 3.00e-02 1.11e+03 1.29e+01
  bond pdb=" CB  LYS A 518 "
       pdb=" CG  LYS A 518 "
    ideal  model  delta    sigma   weight residual
    1.520  1.628 -0.108 3.00e-02 1.11e+03 1.29e+01
  bond pdb=" CG1 ILE B 516 "
       pdb=" CD1 ILE B 516 "
    ideal  model  delta    sigma   weight residual
    1.513  1.409  0.104 3.90e-02 6.57e+02 7.12e+00
  bond pdb=" CG1 ILE A 516 "
       pdb=" CD1 ILE A 516 "
    ideal  model  delta    sigma   weight residual
    1.513  1.410  0.103 3.90e-02 6.57e+02 7.00e+00
  bond pdb=" CA  TYR B 589 "
       pdb=" C   TYR B 589 "
    ideal  model  delta    sigma   weight residual
    1.523  1.556 -0.033 1.34e-02 5.57e+03 5.96e+00
  ... (remaining 9437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.90: 12311
        3.90 -     7.81: 409
        7.81 -    11.71: 87
       11.71 -    15.61: 7
       15.61 -    19.52: 16
  Bond angle restraints: 12830
  Sorted by residual:
  angle pdb=" C   PRO B 588 "
        pdb=" N   TYR B 589 "
        pdb=" CA  TYR B 589 "
      ideal   model   delta    sigma   weight residual
     121.54  140.12  -18.58 1.91e+00 2.74e-01 9.47e+01
  angle pdb=" C   PRO A 588 "
        pdb=" N   TYR A 589 "
        pdb=" CA  TYR A 589 "
      ideal   model   delta    sigma   weight residual
     121.54  140.12  -18.58 1.91e+00 2.74e-01 9.46e+01
  angle pdb=" N   ILE B 510 "
        pdb=" CA  ILE B 510 "
        pdb=" C   ILE B 510 "
      ideal   model   delta    sigma   weight residual
     108.82  120.55  -11.73 1.22e+00 6.72e-01 9.25e+01
  angle pdb=" N   ILE A 510 "
        pdb=" CA  ILE A 510 "
        pdb=" C   ILE A 510 "
      ideal   model   delta    sigma   weight residual
     108.82  120.53  -11.71 1.22e+00 6.72e-01 9.21e+01
  angle pdb=" N   TYR B 589 "
        pdb=" CA  TYR B 589 "
        pdb=" C   TYR B 589 "
      ideal   model   delta    sigma   weight residual
     110.80  125.10  -14.30 2.13e+00 2.20e-01 4.51e+01
  ... (remaining 12825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.62: 4976
       15.62 -    31.24: 396
       31.24 -    46.87: 110
       46.87 -    62.49: 20
       62.49 -    78.11: 6
  Dihedral angle restraints: 5508
    sinusoidal: 2086
      harmonic: 3422
  Sorted by residual:
  dihedral pdb=" CA  GLY A 594 "
           pdb=" C   GLY A 594 "
           pdb=" N   TRP A 595 "
           pdb=" CA  TRP A 595 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  125.75   54.25     0      5.00e+00 4.00e-02 1.18e+02
  dihedral pdb=" CA  GLY B 594 "
           pdb=" C   GLY B 594 "
           pdb=" N   TRP B 595 "
           pdb=" CA  TRP B 595 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  125.77   54.23     0      5.00e+00 4.00e-02 1.18e+02
  dihedral pdb=" CA  LYS B 324 "
           pdb=" C   LYS B 324 "
           pdb=" N   ASP B 325 "
           pdb=" CA  ASP B 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.86  -39.14     0      5.00e+00 4.00e-02 6.13e+01
  ... (remaining 5505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 1194
       0.104 -    0.208: 256
       0.208 -    0.312: 54
       0.312 -    0.416: 10
       0.416 -    0.520: 4
  Chirality restraints: 1518
  Sorted by residual:
  chirality pdb=" CG  LEU B 427 "
            pdb=" CB  LEU B 427 "
            pdb=" CD1 LEU B 427 "
            pdb=" CD2 LEU B 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.07   -0.52 2.00e-01 2.50e+01 6.76e+00
  chirality pdb=" CG  LEU A 427 "
            pdb=" CB  LEU A 427 "
            pdb=" CD1 LEU A 427 "
            pdb=" CD2 LEU A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.07   -0.52 2.00e-01 2.50e+01 6.71e+00
  chirality pdb=" CB  ILE B 329 "
            pdb=" CA  ILE B 329 "
            pdb=" CG1 ILE B 329 "
            pdb=" CG2 ILE B 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    3.07   -0.42 2.00e-01 2.50e+01 4.50e+00
  ... (remaining 1515 not shown)

  Planarity restraints: 1568
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 508 "    0.047 2.00e-02 2.50e+03   9.25e-02 8.56e+01
        pdb=" C   ASP A 508 "   -0.160 2.00e-02 2.50e+03
        pdb=" O   ASP A 508 "    0.059 2.00e-02 2.50e+03
        pdb=" N   GLY A 509 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 508 "   -0.047 2.00e-02 2.50e+03   9.20e-02 8.47e+01
        pdb=" C   ASP B 508 "    0.159 2.00e-02 2.50e+03
        pdb=" O   ASP B 508 "   -0.058 2.00e-02 2.50e+03
        pdb=" N   GLY B 509 "   -0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 588 "    0.028 2.00e-02 2.50e+03   5.83e-02 3.40e+01
        pdb=" C   PRO B 588 "   -0.101 2.00e-02 2.50e+03
        pdb=" O   PRO B 588 "    0.038 2.00e-02 2.50e+03
        pdb=" N   TYR B 589 "    0.035 2.00e-02 2.50e+03
  ... (remaining 1565 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 895
        2.73 -     3.28: 9696
        3.28 -     3.82: 16348
        3.82 -     4.36: 17975
        4.36 -     4.90: 28730
  Nonbonded interactions: 73644
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 472 "
            pdb=" OG1 THR B 476 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   ILE A 472 "
            pdb=" OG1 THR A 476 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   CYS A 179 "
            pdb=" OG  SER A 183 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   CYS B 179 "
            pdb=" OG  SER B 183 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   SER B 289 "
            pdb=" OG1 THR B 293 "
     model   vdw
     2.235 3.040
  ... (remaining 73639 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: 0.05
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:             1.960
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     26.590
  Find NCS groups from input model:        0.180
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
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      :  0.010   0.108   9442  Z= 0.615
  Angle     :  1.807  19.518  12830  Z= 0.948
  Chirality :  0.096   0.520   1518
  Planarity :  0.012   0.093   1568
  Dihedral  : 12.959  78.110   3308
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  9.58 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 10.62 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.73 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    Twisted Proline : 3.85 %
    Twisted General : 0.88 %

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: -4.01 (0.20), residues: 1180
  helix: -2.27 (0.15), residues: 764
  sheet: -0.92 (0.99), residues: 20
  loop : -3.28 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.086   0.007   TRP A 469 
 HIS   0.008   0.003   HIS A 389 
 PHE   0.070   0.007   PHE B 464 
 TYR   0.046   0.005   TYR B 146 
 ARG   0.008   0.002   ARG A 390 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 209
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 MET cc_start: 0.9271 (ptp) cc_final: 0.8957 (ptt)
REVERT: B  307 PHE cc_start: 0.9356 (t80) cc_final: 0.8903 (t80)
REVERT: B  315 VAL cc_start: 0.9594 (t) cc_final: 0.9358 (m)
REVERT: B  339 MET cc_start: 0.8880 (ptp) cc_final: 0.8608 (pmm)
REVERT: B  341 PHE cc_start: 0.8529 (t80) cc_final: 0.7624 (t80)
REVERT: B  404 PHE cc_start: 0.9225 (m-10) cc_final: 0.8834 (m-80)
REVERT: B  464 PHE cc_start: 0.8934 (p90) cc_final: 0.8558 (p90)
REVERT: B  468 PHE cc_start: 0.9021 (m-10) cc_final: 0.8714 (m-10)
REVERT: B  470 MET cc_start: 0.9282 (ttm) cc_final: 0.8977 (ttm)
REVERT: B  494 PHE cc_start: 0.9483 (t80) cc_final: 0.9240 (t80)
REVERT: B  559 MET cc_start: 0.9772 (ppp) cc_final: 0.9202 (ppp)
REVERT: B  643 LYS cc_start: 0.9606 (pttp) cc_final: 0.9013 (mmmt)
REVERT: A  135 MET cc_start: 0.9200 (ptp) cc_final: 0.8909 (ptt)
REVERT: A  307 PHE cc_start: 0.9322 (t80) cc_final: 0.8773 (t80)
REVERT: A  315 VAL cc_start: 0.9607 (t) cc_final: 0.9378 (m)
REVERT: A  339 MET cc_start: 0.9040 (ptp) cc_final: 0.8418 (pmm)
REVERT: A  341 PHE cc_start: 0.8824 (t80) cc_final: 0.8351 (t80)
REVERT: A  404 PHE cc_start: 0.9420 (m-10) cc_final: 0.9077 (m-80)
REVERT: A  427 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8946 (tp)
REVERT: A  435 LYS cc_start: 0.9716 (mmtt) cc_final: 0.9429 (tptp)
REVERT: A  464 PHE cc_start: 0.8895 (p90) cc_final: 0.8557 (p90)
REVERT: A  468 PHE cc_start: 0.8983 (m-10) cc_final: 0.8774 (m-80)
REVERT: A  470 MET cc_start: 0.9224 (ttm) cc_final: 0.8800 (ttm)
REVERT: A  494 PHE cc_start: 0.9325 (t80) cc_final: 0.8951 (t80)
REVERT: A  557 LEU cc_start: 0.9664 (mm) cc_final: 0.9399 (tt)
REVERT: A  559 MET cc_start: 0.9823 (ppp) cc_final: 0.9371 (ppp)
  outliers start: 36
  outliers final: 10
  residues processed: 233
  average time/residue: 0.2126
  time to fit residues: 69.4176
Evaluate side-chains
  155 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 49 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 47 optimal weight:   10.0000
   chunk 92 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
B 369 HIS
** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 369 HIS
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.059831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.047337 restraints weight = 67111.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.048371 restraints weight = 50481.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.049351 restraints weight = 40724.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   9442  Z= 0.295
  Angle     :  0.944  11.820  12830  Z= 0.493
  Chirality :  0.051   0.256   1518
  Planarity :  0.006   0.065   1568
  Dihedral  :  7.312  34.344   1256
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 20.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

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: -2.17 (0.23), residues: 1180
  helix: -0.76 (0.17), residues: 766
  sheet: -0.07 (0.86), residues: 20
  loop : -2.76 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP B 469 
 HIS   0.005   0.001   HIS A 835 
 PHE   0.038   0.003   PHE A 464 
 TYR   0.018   0.002   TYR A 578 
 ARG   0.008   0.001   ARG A 496 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 MET cc_start: 0.9230 (ptp) cc_final: 0.8860 (ptt)
REVERT: B  341 PHE cc_start: 0.8255 (t80) cc_final: 0.7729 (t80)
REVERT: B  404 PHE cc_start: 0.9270 (m-10) cc_final: 0.8918 (m-80)
REVERT: B  410 MET cc_start: 0.9084 (tpt) cc_final: 0.8476 (tpt)
REVERT: B  464 PHE cc_start: 0.9155 (p90) cc_final: 0.8596 (p90)
REVERT: B  468 PHE cc_start: 0.9180 (m-10) cc_final: 0.8757 (m-80)
REVERT: B  470 MET cc_start: 0.9553 (ttm) cc_final: 0.8971 (mtt)
REVERT: B  494 PHE cc_start: 0.9584 (t80) cc_final: 0.9224 (t80)
REVERT: B  547 PHE cc_start: 0.9472 (p90) cc_final: 0.9229 (m-80)
REVERT: B  568 MET cc_start: 0.9461 (ppp) cc_final: 0.9243 (ppp)
REVERT: B  643 LYS cc_start: 0.9597 (pttp) cc_final: 0.9012 (mmmt)
REVERT: A  122 VAL cc_start: 0.9238 (m) cc_final: 0.9006 (m)
REVERT: A  135 MET cc_start: 0.9168 (ptp) cc_final: 0.8795 (ptt)
REVERT: A  227 ILE cc_start: 0.9246 (tp) cc_final: 0.9024 (tp)
REVERT: A  307 PHE cc_start: 0.9309 (t80) cc_final: 0.9030 (t80)
REVERT: A  341 PHE cc_start: 0.8657 (t80) cc_final: 0.8238 (t80)
REVERT: A  410 MET cc_start: 0.9127 (tpt) cc_final: 0.8784 (tpp)
REVERT: A  436 HIS cc_start: 0.9137 (m-70) cc_final: 0.8845 (m-70)
REVERT: A  470 MET cc_start: 0.9531 (ttm) cc_final: 0.8976 (tmm)
REVERT: A  494 PHE cc_start: 0.9448 (t80) cc_final: 0.8949 (t80)
REVERT: A  559 MET cc_start: 0.9827 (ppp) cc_final: 0.9585 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2020
  time to fit residues: 51.8525
Evaluate side-chains
  142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   chunk 86 optimal weight:    0.6980
   chunk 22 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 97 optimal weight:   10.0000
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B 379 HIS
** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 HIS
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 847 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.061508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.048145 restraints weight = 64021.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.049381 restraints weight = 47796.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.050337 restraints weight = 38181.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9442  Z= 0.226
  Angle     :  0.846  10.137  12830  Z= 0.436
  Chirality :  0.049   0.246   1518
  Planarity :  0.006   0.053   1568
  Dihedral  :  6.682  32.719   1256
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

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: -1.49 (0.24), residues: 1180
  helix: -0.18 (0.18), residues: 770
  sheet:  0.17 (0.93), residues: 20
  loop : -2.64 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 595 
 HIS   0.007   0.001   HIS A 835 
 PHE   0.030   0.003   PHE B 365 
 TYR   0.015   0.001   TYR B 137 
 ARG   0.003   0.000   ARG B 496 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  122 VAL cc_start: 0.9139 (m) cc_final: 0.8916 (m)
REVERT: B  135 MET cc_start: 0.9167 (ptp) cc_final: 0.8872 (ptt)
REVERT: B  303 TRP cc_start: 0.8739 (t60) cc_final: 0.8475 (t60)
REVERT: B  339 MET cc_start: 0.9040 (ptp) cc_final: 0.8520 (ptp)
REVERT: B  341 PHE cc_start: 0.8139 (t80) cc_final: 0.7654 (t80)
REVERT: B  404 PHE cc_start: 0.9182 (m-10) cc_final: 0.8769 (m-80)
REVERT: B  410 MET cc_start: 0.8943 (tpt) cc_final: 0.8314 (tpt)
REVERT: B  464 PHE cc_start: 0.9121 (p90) cc_final: 0.8645 (p90)
REVERT: B  468 PHE cc_start: 0.9107 (m-10) cc_final: 0.8868 (m-10)
REVERT: B  494 PHE cc_start: 0.9544 (t80) cc_final: 0.9164 (t80)
REVERT: B  568 MET cc_start: 0.9474 (ppp) cc_final: 0.9252 (ppp)
REVERT: B  643 LYS cc_start: 0.9557 (pttp) cc_final: 0.8953 (mmmt)
REVERT: A  122 VAL cc_start: 0.9178 (m) cc_final: 0.8963 (m)
REVERT: A  135 MET cc_start: 0.9139 (ptp) cc_final: 0.8867 (ptt)
REVERT: A  307 PHE cc_start: 0.9181 (t80) cc_final: 0.8977 (t80)
REVERT: A  339 MET cc_start: 0.8889 (ptp) cc_final: 0.8659 (pmm)
REVERT: A  341 PHE cc_start: 0.8449 (t80) cc_final: 0.8014 (t80)
REVERT: A  401 ILE cc_start: 0.9704 (pt) cc_final: 0.9500 (pt)
REVERT: A  410 MET cc_start: 0.9033 (tpt) cc_final: 0.8692 (tpp)
REVERT: A  494 PHE cc_start: 0.9359 (t80) cc_final: 0.8893 (t80)
REVERT: A  559 MET cc_start: 0.9714 (ppp) cc_final: 0.9372 (ppp)
REVERT: A  643 LYS cc_start: 0.9590 (pttp) cc_final: 0.8918 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1946
  time to fit residues: 51.3224
Evaluate side-chains
  144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0070
   chunk 57 optimal weight:   20.0000
   chunk 54 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.6802

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

Flipped N/Q/H residues before XYZ refinement:
B 379 HIS
B 451 HIS
A 451 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.064482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.050918 restraints weight = 62125.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.052181 restraints weight = 46515.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.053281 restraints weight = 37075.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.4221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9442  Z= 0.198
  Angle     :  0.817   9.950  12830  Z= 0.416
  Chirality :  0.048   0.246   1518
  Planarity :  0.005   0.052   1568
  Dihedral  :  6.257  30.924   1256
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 16.51
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.71 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.14 (0.24), residues: 1180
  helix:  0.21 (0.18), residues: 770
  sheet:  0.29 (1.06), residues: 20
  loop : -2.78 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 595 
 HIS   0.010   0.002   HIS B 664 
 PHE   0.031   0.002   PHE B 488 
 TYR   0.023   0.001   TYR A 146 
 ARG   0.003   0.000   ARG A 317 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 MET cc_start: 0.9106 (ptp) cc_final: 0.8858 (ptt)
REVERT: B  339 MET cc_start: 0.9127 (ptp) cc_final: 0.8684 (ptp)
REVERT: B  341 PHE cc_start: 0.8205 (t80) cc_final: 0.7748 (t80)
REVERT: B  400 VAL cc_start: 0.9268 (p) cc_final: 0.9017 (p)
REVERT: B  404 PHE cc_start: 0.9167 (m-10) cc_final: 0.8663 (m-80)
REVERT: B  410 MET cc_start: 0.8893 (tpt) cc_final: 0.8162 (tpt)
REVERT: B  464 PHE cc_start: 0.9195 (p90) cc_final: 0.8815 (p90)
REVERT: B  477 MET cc_start: 0.8828 (ppp) cc_final: 0.8548 (ppp)
REVERT: B  485 MET cc_start: 0.9476 (pmm) cc_final: 0.9261 (pmm)
REVERT: B  487 VAL cc_start: 0.9167 (t) cc_final: 0.8951 (p)
REVERT: B  488 PHE cc_start: 0.9246 (m-10) cc_final: 0.9023 (m-80)
REVERT: B  494 PHE cc_start: 0.9561 (t80) cc_final: 0.9244 (t80)
REVERT: B  568 MET cc_start: 0.9473 (ppp) cc_final: 0.9245 (ppp)
REVERT: B  643 LYS cc_start: 0.9519 (pttp) cc_final: 0.8944 (mmmt)
REVERT: A  122 VAL cc_start: 0.9084 (m) cc_final: 0.8858 (m)
REVERT: A  135 MET cc_start: 0.9063 (ptp) cc_final: 0.8815 (ptt)
REVERT: A  339 MET cc_start: 0.8814 (ptp) cc_final: 0.8608 (pmm)
REVERT: A  341 PHE cc_start: 0.8479 (t80) cc_final: 0.7901 (t80)
REVERT: A  400 VAL cc_start: 0.9266 (m) cc_final: 0.9051 (p)
REVERT: A  410 MET cc_start: 0.8759 (tpt) cc_final: 0.8462 (tpt)
REVERT: A  494 PHE cc_start: 0.9383 (t80) cc_final: 0.8949 (t80)
REVERT: A  556 ILE cc_start: 0.9705 (tt) cc_final: 0.9502 (pt)
REVERT: A  559 MET cc_start: 0.9672 (ppp) cc_final: 0.9336 (ppp)
REVERT: A  836 LYS cc_start: 0.9454 (mttt) cc_final: 0.9144 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1955
  time to fit residues: 51.8234
Evaluate side-chains
  144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0970
   chunk 33 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 108 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.066044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.051389 restraints weight = 60763.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.053191 restraints weight = 40759.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.054493 restraints weight = 30514.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5912
moved from start:          0.4654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9442  Z= 0.207
  Angle     :  0.793   9.875  12830  Z= 0.406
  Chirality :  0.048   0.235   1518
  Planarity :  0.005   0.041   1568
  Dihedral  :  6.042  29.396   1256
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 16.08
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.64 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.91 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.25), residues: 1180
  helix:  0.35 (0.18), residues: 778
  sheet:  0.74 (1.13), residues: 20
  loop : -2.85 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 469 
 HIS   0.006   0.001   HIS B 389 
 PHE   0.027   0.002   PHE B 365 
 TYR   0.020   0.001   TYR A 146 
 ARG   0.002   0.000   ARG B 317 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 PHE cc_start: 0.7962 (t80) cc_final: 0.7411 (t80)
REVERT: B  410 MET cc_start: 0.9141 (tpt) cc_final: 0.8830 (tpt)
REVERT: B  427 LEU cc_start: 0.9614 (tp) cc_final: 0.9354 (tp)
REVERT: B  494 PHE cc_start: 0.9471 (t80) cc_final: 0.9170 (t80)
REVERT: A  122 VAL cc_start: 0.7865 (m) cc_final: 0.7259 (m)
REVERT: A  339 MET cc_start: 0.8432 (ptp) cc_final: 0.8098 (pmm)
REVERT: A  341 PHE cc_start: 0.8137 (t80) cc_final: 0.7658 (t80)
REVERT: A  379 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.8765 (t-90)
REVERT: A  427 LEU cc_start: 0.9165 (tp) cc_final: 0.8924 (tp)
REVERT: A  449 TRP cc_start: 0.8028 (m100) cc_final: 0.7789 (m100)
REVERT: A  490 LEU cc_start: 0.8919 (mm) cc_final: 0.8665 (mm)
REVERT: A  494 PHE cc_start: 0.9336 (t80) cc_final: 0.9003 (t80)
REVERT: A  559 MET cc_start: 0.9464 (ppp) cc_final: 0.9205 (ppp)
REVERT: A  564 ILE cc_start: 0.9392 (pt) cc_final: 0.9132 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1880
  time to fit residues: 49.5966
Evaluate side-chains
  131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 106 optimal weight:    0.0870
   chunk 35 optimal weight:    8.9990
   chunk 95 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 13 optimal weight:    9.9990
   chunk 110 optimal weight:    0.0370
   chunk 107 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    0.8242

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

Flipped N/Q/H residues before XYZ refinement:
B 538 HIS
A 369 HIS
A 379 HIS
A 538 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.065531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.051888 restraints weight = 61246.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.053265 restraints weight = 46258.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.054400 restraints weight = 36931.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.5074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9442  Z= 0.193
  Angle     :  0.782   9.464  12830  Z= 0.399
  Chirality :  0.047   0.234   1518
  Planarity :  0.005   0.043   1568
  Dihedral  :  5.897  27.984   1256
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.05 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    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: -0.82 (0.25), residues: 1180
  helix:  0.52 (0.19), residues: 776
  sheet:  1.06 (1.14), residues: 20
  loop : -2.91 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 469 
 HIS   0.004   0.001   HIS B 835 
 PHE   0.038   0.002   PHE A 468 
 TYR   0.017   0.001   TYR A 146 
 ARG   0.002   0.000   ARG B 317 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 MET cc_start: 0.8913 (ptt) cc_final: 0.8688 (ptt)
REVERT: B  341 PHE cc_start: 0.8295 (t80) cc_final: 0.7777 (t80)
REVERT: B  410 MET cc_start: 0.8742 (tpt) cc_final: 0.8062 (tpt)
REVERT: B  494 PHE cc_start: 0.9560 (t80) cc_final: 0.9221 (t80)
REVERT: B  854 MET cc_start: 0.9459 (ppp) cc_final: 0.9252 (ppp)
REVERT: A  339 MET cc_start: 0.8745 (ptp) cc_final: 0.8212 (pmm)
REVERT: A  341 PHE cc_start: 0.8428 (t80) cc_final: 0.7938 (t80)
REVERT: A  404 PHE cc_start: 0.9345 (m-80) cc_final: 0.8970 (m-80)
REVERT: A  427 LEU cc_start: 0.9352 (tp) cc_final: 0.9151 (tp)
REVERT: A  485 MET cc_start: 0.9445 (pmm) cc_final: 0.9202 (pmm)
REVERT: A  494 PHE cc_start: 0.9363 (t80) cc_final: 0.8960 (t80)
REVERT: A  559 MET cc_start: 0.9623 (ppp) cc_final: 0.9276 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.1958
  time to fit residues: 51.0682
Evaluate side-chains
  137 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 107 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   chunk 106 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 112 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 436 HIS
** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.067028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.052110 restraints weight = 62145.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.053871 restraints weight = 42263.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.055326 restraints weight = 31640.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5957
moved from start:          0.5329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9442  Z= 0.211
  Angle     :  0.781   8.948  12830  Z= 0.397
  Chirality :  0.047   0.229   1518
  Planarity :  0.005   0.041   1568
  Dihedral  :  5.764  26.854   1256
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.05 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    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: -0.68 (0.25), residues: 1180
  helix:  0.62 (0.19), residues: 780
  sheet:  1.22 (1.11), residues: 20
  loop : -2.88 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 469 
 HIS   0.006   0.001   HIS A 538 
 PHE   0.027   0.002   PHE B 365 
 TYR   0.019   0.002   TYR A 146 
 ARG   0.003   0.000   ARG A 334 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 PHE cc_start: 0.8186 (t80) cc_final: 0.7663 (t80)
REVERT: B  410 MET cc_start: 0.9077 (tpt) cc_final: 0.8746 (tpt)
REVERT: B  427 LEU cc_start: 0.9572 (tp) cc_final: 0.9322 (tp)
REVERT: B  494 PHE cc_start: 0.9465 (t80) cc_final: 0.9130 (t80)
REVERT: B  854 MET cc_start: 0.9427 (ppp) cc_final: 0.9215 (ppp)
REVERT: A  339 MET cc_start: 0.8353 (ptp) cc_final: 0.8020 (pmm)
REVERT: A  341 PHE cc_start: 0.8479 (t80) cc_final: 0.8024 (t80)
REVERT: A  427 LEU cc_start: 0.9386 (tp) cc_final: 0.8957 (tp)
REVERT: A  494 PHE cc_start: 0.9349 (t80) cc_final: 0.9080 (t80)
REVERT: A  559 MET cc_start: 0.9365 (ppp) cc_final: 0.9120 (ppp)
REVERT: A  564 ILE cc_start: 0.9440 (pt) cc_final: 0.9182 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1937
  time to fit residues: 50.3291
Evaluate side-chains
  134 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0670
   chunk 43 optimal weight:    0.0980
   chunk 75 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 117 optimal weight:    7.9990
   chunk 58 optimal weight:    0.3980
   chunk 65 optimal weight:    0.9990
   chunk 115 optimal weight:    6.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 835 HIS
** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.069763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.053562 restraints weight = 60831.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.055427 restraints weight = 41669.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.056867 restraints weight = 31371.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5927
moved from start:          0.5600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9442  Z= 0.193
  Angle     :  0.823   8.927  12830  Z= 0.417
  Chirality :  0.049   0.227   1518
  Planarity :  0.005   0.047   1568
  Dihedral  :  5.698  25.961   1256
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.31 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    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: -0.58 (0.25), residues: 1180
  helix:  0.72 (0.19), residues: 768
  sheet:  1.37 (1.09), residues: 20
  loop : -2.81 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP A 469 
 HIS   0.006   0.001   HIS A 538 
 PHE   0.045   0.002   PHE A 488 
 TYR   0.018   0.001   TYR B 296 
 ARG   0.002   0.000   ARG B 317 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 MET cc_start: 0.8874 (ptt) cc_final: 0.8587 (ptt)
REVERT: B  341 PHE cc_start: 0.8250 (t80) cc_final: 0.7737 (t80)
REVERT: B  410 MET cc_start: 0.9146 (tpt) cc_final: 0.8912 (tpt)
REVERT: B  414 MET cc_start: 0.8417 (ptt) cc_final: 0.7397 (ptt)
REVERT: B  449 TRP cc_start: 0.8151 (m100) cc_final: 0.7820 (m100)
REVERT: B  470 MET cc_start: 0.9320 (tmm) cc_final: 0.9116 (tmm)
REVERT: B  490 LEU cc_start: 0.9155 (mm) cc_final: 0.8596 (mm)
REVERT: B  494 PHE cc_start: 0.9477 (t80) cc_final: 0.9194 (t80)
REVERT: B  854 MET cc_start: 0.9413 (ppp) cc_final: 0.9193 (ppp)
REVERT: A  122 VAL cc_start: 0.8149 (m) cc_final: 0.7714 (m)
REVERT: A  307 PHE cc_start: 0.9366 (t80) cc_final: 0.9165 (t80)
REVERT: A  339 MET cc_start: 0.8402 (ptp) cc_final: 0.8130 (pmm)
REVERT: A  341 PHE cc_start: 0.8441 (t80) cc_final: 0.8020 (t80)
REVERT: A  410 MET cc_start: 0.9264 (tpt) cc_final: 0.9031 (tpt)
REVERT: A  427 LEU cc_start: 0.9417 (tp) cc_final: 0.8969 (tp)
REVERT: A  494 PHE cc_start: 0.9347 (t80) cc_final: 0.9054 (t80)
REVERT: A  559 MET cc_start: 0.9294 (ppp) cc_final: 0.9057 (ppp)
REVERT: A  564 ILE cc_start: 0.9469 (pt) cc_final: 0.9153 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1983
  time to fit residues: 52.4722
Evaluate side-chains
  136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 107 optimal weight:    8.9990
   chunk 105 optimal weight:    0.2980
   chunk 28 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 111 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 87 optimal weight:    0.0980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 538 HIS
A 436 HIS
A 538 HIS
A 835 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.069457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.053706 restraints weight = 59101.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.055505 restraints weight = 40955.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.056915 restraints weight = 30933.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5825
moved from start:          0.5863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9442  Z= 0.190
  Angle     :  0.807   9.216  12830  Z= 0.403
  Chirality :  0.048   0.224   1518
  Planarity :  0.005   0.041   1568
  Dihedral  :  5.628  26.617   1256
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 15.28
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.14 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    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: -0.54 (0.25), residues: 1180
  helix:  0.75 (0.19), residues: 768
  sheet:  1.28 (1.02), residues: 20
  loop : -2.76 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP A 469 
 HIS   0.004   0.001   HIS A 538 
 PHE   0.039   0.002   PHE B 306 
 TYR   0.016   0.001   TYR A 146 
 ARG   0.002   0.000   ARG B 317 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 PHE cc_start: 0.8164 (t80) cc_final: 0.7668 (t80)
REVERT: B  410 MET cc_start: 0.9095 (tpt) cc_final: 0.8872 (tpt)
REVERT: B  414 MET cc_start: 0.8483 (ptt) cc_final: 0.7428 (ptt)
REVERT: B  449 TRP cc_start: 0.7880 (m100) cc_final: 0.7587 (m100)
REVERT: B  470 MET cc_start: 0.9323 (tmm) cc_final: 0.9004 (tmm)
REVERT: B  490 LEU cc_start: 0.8961 (mm) cc_final: 0.8637 (mm)
REVERT: B  494 PHE cc_start: 0.9477 (t80) cc_final: 0.9178 (t80)
REVERT: B  498 VAL cc_start: 0.9131 (m) cc_final: 0.8927 (p)
REVERT: B  854 MET cc_start: 0.9406 (ppp) cc_final: 0.9185 (ppp)
REVERT: A  341 PHE cc_start: 0.8337 (t80) cc_final: 0.7880 (t80)
REVERT: A  400 VAL cc_start: 0.9172 (p) cc_final: 0.8970 (m)
REVERT: A  427 LEU cc_start: 0.9408 (tp) cc_final: 0.8987 (tp)
REVERT: A  494 PHE cc_start: 0.9338 (t80) cc_final: 0.9079 (t80)
REVERT: A  564 ILE cc_start: 0.9424 (pt) cc_final: 0.9200 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1857
  time to fit residues: 48.4997
Evaluate side-chains
  136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0170
   chunk 33 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0020
   chunk 41 optimal weight:    8.9990
   chunk 63 optimal weight:    0.4980
   overall best weight:    0.4226

-------------------------------------------------------------------------------
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 = 0.3675 r_free = 0.3675 target = 0.070519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.054478 restraints weight = 59566.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.056312 restraints weight = 41032.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.057750 restraints weight = 31121.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5915
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      :  0.003   0.041   9442  Z= 0.189
  Angle     :  0.822   9.677  12830  Z= 0.407
  Chirality :  0.048   0.220   1518
  Planarity :  0.005   0.044   1568
  Dihedral  :  5.565  30.310   1256
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.22 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.25), residues: 1180
  helix:  0.74 (0.19), residues: 768
  sheet:  1.46 (1.03), residues: 20
  loop : -2.76 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP A 469 
 HIS   0.011   0.001   HIS B 436 
 PHE   0.050   0.002   PHE A 488 
 TYR   0.017   0.001   TYR B 296 
 ARG   0.002   0.000   ARG B 317 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 PHE cc_start: 0.8170 (t80) cc_final: 0.7705 (t80)
REVERT: B  410 MET cc_start: 0.9140 (tpt) cc_final: 0.8890 (tpt)
REVERT: B  414 MET cc_start: 0.8570 (ptt) cc_final: 0.7455 (ptt)
REVERT: B  449 TRP cc_start: 0.8040 (m100) cc_final: 0.7815 (m100)
REVERT: B  470 MET cc_start: 0.9351 (tmm) cc_final: 0.9051 (tmm)
REVERT: B  490 LEU cc_start: 0.8991 (mm) cc_final: 0.8682 (mm)
REVERT: B  494 PHE cc_start: 0.9493 (t80) cc_final: 0.9203 (t80)
REVERT: B  854 MET cc_start: 0.9412 (ppp) cc_final: 0.9187 (ppp)
REVERT: A  122 VAL cc_start: 0.8156 (m) cc_final: 0.7824 (m)
REVERT: A  341 PHE cc_start: 0.8336 (t80) cc_final: 0.7868 (t80)
REVERT: A  400 VAL cc_start: 0.9172 (p) cc_final: 0.8968 (m)
REVERT: A  410 MET cc_start: 0.9298 (tpt) cc_final: 0.9092 (tpt)
REVERT: A  427 LEU cc_start: 0.9210 (tp) cc_final: 0.8936 (tp)
REVERT: A  449 TRP cc_start: 0.8259 (m100) cc_final: 0.7920 (m100)
REVERT: A  494 PHE cc_start: 0.9398 (t80) cc_final: 0.9122 (t80)
REVERT: A  559 MET cc_start: 0.9111 (ppp) cc_final: 0.8817 (ppp)
REVERT: A  564 ILE cc_start: 0.9439 (pt) cc_final: 0.9203 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.2009
  time to fit residues: 52.5135
Evaluate side-chains
  137 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 109 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 108 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 98 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 106 optimal weight:    0.1980
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.105693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.092623 restraints weight = 67414.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.094244 restraints weight = 40228.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.095325 restraints weight = 26886.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.6322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9442  Z= 0.188
  Angle     :  0.816  10.262  12830  Z= 0.407
  Chirality :  0.047   0.200   1518
  Planarity :  0.005   0.039   1568
  Dihedral  :  5.459  29.046   1256
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.80 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.35 %
    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: -0.50 (0.26), residues: 1180
  helix:  0.76 (0.19), residues: 766
  sheet:  1.62 (1.04), residues: 20
  loop : -2.70 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP A 469 
 HIS   0.007   0.001   HIS A 436 
 PHE   0.029   0.002   PHE B 306 
 TYR   0.015   0.001   TYR B 146 
 ARG   0.002   0.000   ARG B 317 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2782.32 seconds
wall clock time: 50 minutes 51.48 seconds (3051.48 seconds total)