Starting phenix.real_space_refine
on Wed Apr 30 22:49:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8opq_17085/04_2025/8opq_17085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8opq_17085/04_2025/8opq_17085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8opq_17085/04_2025/8opq_17085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8opq_17085/04_2025/8opq_17085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8opq_17085/04_2025/8opq_17085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8opq_17085/04_2025/8opq_17085.cif"
  }
  resolution = 3.28
  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=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     Cl      2      4.86       5
     C    6532      2.51       5
     N    1668      2.21       5
     O    1766      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10006
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 648, 5002
          Classifications: {'peptide': 648}
          Link IDs: {'PTRANS': 28, 'TRANS': 619}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 648, 5002
          Classifications: {'peptide': 648}
          Link IDs: {'PTRANS': 28, 'TRANS': 619}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.58, per 1000 atoms: 0.76
  Number of scatterers: 10006
  At special positions: 0
  Unit cell: (100.905, 121.737, 106.764, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      38     16.00
     O    1766      8.00
     N    1668      7.00
     C    6532      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: 2.90
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2412

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 4 sheets defined
      72.7% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 46
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 76 through 81
    Processing helix  chain 'A' and resid 85 through 116
      removed outlier: 5.327A  pdb=" N   LEU A  91 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   GLY A  92 " --> pdb=" O   ASP A  88 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
      removed outlier: 3.715A  pdb=" N   LEU A 109 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 126
      removed outlier: 4.212A  pdb=" N   GLY A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU A 123 " --> pdb=" O   PRO A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 137
      removed outlier: 4.103A  pdb=" N   PHE A 131 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU A 135 " --> pdb=" O   PHE A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 162
    Processing helix  chain 'A' and resid 170 through 201
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 211 through 236
      removed outlier: 4.024A  pdb=" N   LYS A 232 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   TYR A 233 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 258
    Processing helix  chain 'A' and resid 259 through 262
    Processing helix  chain 'A' and resid 263 through 287
    Processing helix  chain 'A' and resid 296 through 313
    Processing helix  chain 'A' and resid 337 through 339
      No H-bonds generated for 'chain 'A' and resid 337 through 339'
    Processing helix  chain 'A' and resid 340 through 371
      removed outlier: 4.798A  pdb=" N   GLY A 346 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   SER A 347 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   THR A 350 " --> pdb=" O   GLY A 346 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE A 351 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 393
    Processing helix  chain 'A' and resid 401 through 412
      removed outlier: 3.598A  pdb=" N   GLY A 412 " --> pdb=" O   GLN A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 432
      removed outlier: 4.436A  pdb=" N   GLY A 419 " --> pdb=" O   SER A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 438
      removed outlier: 3.691A  pdb=" N   PHE A 437 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 452
      removed outlier: 4.058A  pdb=" N   LEU A 445 " --> pdb=" O   PRO A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 470
      removed outlier: 4.428A  pdb=" N   LEU A 460 " --> pdb=" O   MET A 456 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   SER A 461 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ASP A 462 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   TRP A 467 " --> pdb=" O   MET A 463 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   LYS A 468 " --> pdb=" O   ARG A 464 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 487
    Processing helix  chain 'A' and resid 487 through 509
      removed outlier: 3.946A  pdb=" N   LEU A 491 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL A 494 " --> pdb=" O   ASP A 490 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR A 508 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 565
    Processing helix  chain 'A' and resid 568 through 594
    Processing helix  chain 'A' and resid 656 through 661
    Processing helix  chain 'A' and resid 681 through 698
    Processing helix  chain 'A' and resid 708 through 718
      removed outlier: 3.619A  pdb=" N   VAL A 712 " --> pdb=" O   HIS A 708 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER A 713 " --> pdb=" O   SER A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 728
      No H-bonds generated for 'chain 'A' and resid 726 through 728'
    Processing helix  chain 'A' and resid 733 through 744
    Processing helix  chain 'B' and resid 37 through 46
    Processing helix  chain 'B' and resid 63 through 75
    Processing helix  chain 'B' and resid 76 through 81
    Processing helix  chain 'B' and resid 85 through 116
      removed outlier: 5.328A  pdb=" N   LEU B  91 " --> pdb=" O   ARG B  87 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   GLY B  92 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
      Proline residue:  B 106  - end of helix
      removed outlier: 3.716A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 126
      removed outlier: 4.212A  pdb=" N   GLY B 122 " --> pdb=" O   PRO B 118 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU B 123 " --> pdb=" O   PRO B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 137
      removed outlier: 4.103A  pdb=" N   PHE B 131 " --> pdb=" O   PHE B 127 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU B 135 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 162
    Processing helix  chain 'B' and resid 170 through 201
    Processing helix  chain 'B' and resid 205 through 210
    Processing helix  chain 'B' and resid 211 through 236
      removed outlier: 4.023A  pdb=" N   LYS B 232 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   TYR B 233 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 258
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 263 through 287
    Processing helix  chain 'B' and resid 296 through 313
    Processing helix  chain 'B' and resid 337 through 339
      No H-bonds generated for 'chain 'B' and resid 337 through 339'
    Processing helix  chain 'B' and resid 340 through 371
      removed outlier: 4.797A  pdb=" N   GLY B 346 " --> pdb=" O   SER B 342 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   SER B 347 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   THR B 350 " --> pdb=" O   GLY B 346 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 393
    Processing helix  chain 'B' and resid 401 through 412
      removed outlier: 3.599A  pdb=" N   GLY B 412 " --> pdb=" O   GLN B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 432
      removed outlier: 4.436A  pdb=" N   GLY B 419 " --> pdb=" O   SER B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 438
      removed outlier: 3.691A  pdb=" N   PHE B 437 " --> pdb=" O   GLY B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 452
      removed outlier: 4.057A  pdb=" N   LEU B 445 " --> pdb=" O   PRO B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 470
      removed outlier: 4.427A  pdb=" N   LEU B 460 " --> pdb=" O   MET B 456 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   SER B 461 " --> pdb=" O   LEU B 457 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ASP B 462 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   TRP B 467 " --> pdb=" O   MET B 463 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   LYS B 468 " --> pdb=" O   ARG B 464 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA B 469 " --> pdb=" O   SER B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 487
    Processing helix  chain 'B' and resid 487 through 509
      removed outlier: 3.946A  pdb=" N   LEU B 491 " --> pdb=" O   LEU B 487 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL B 494 " --> pdb=" O   ASP B 490 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR B 508 " --> pdb=" O   VAL B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 553 through 565
    Processing helix  chain 'B' and resid 568 through 594
    Processing helix  chain 'B' and resid 656 through 661
    Processing helix  chain 'B' and resid 681 through 698
    Processing helix  chain 'B' and resid 708 through 718
      removed outlier: 3.619A  pdb=" N   VAL B 712 " --> pdb=" O   HIS B 708 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER B 713 " --> pdb=" O   SER B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 726 through 728
      No H-bonds generated for 'chain 'B' and resid 726 through 728'
    Processing helix  chain 'B' and resid 733 through 744
    Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145
    Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 527
      removed outlier: 4.430A  pdb=" N   VAL A 542 " --> pdb=" O   LEU A 516 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   GLN A 518 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
      removed outlier: 12.076A  pdb=" N   VAL A 540 " --> pdb=" O   GLN A 518 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LYS A 541 " --> pdb=" O   ILE A 671 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   ASP A 673 " --> pdb=" O   LYS A 541 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   PHE A 543 " --> pdb=" O   ASP A 673 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   PHE A 731 " --> pdb=" O   VAL A 702 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   MET A 704 " --> pdb=" O   PHE A 731 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 144 through 145
    Processing sheet with id=AA4, first strand: chain 'B' and resid 525 through 527
      removed outlier: 4.431A  pdb=" N   VAL B 542 " --> pdb=" O   LEU B 516 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   GLN B 518 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
      removed outlier: 12.076A  pdb=" N   VAL B 540 " --> pdb=" O   GLN B 518 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LYS B 541 " --> pdb=" O   ILE B 671 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   ASP B 673 " --> pdb=" O   LYS B 541 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   PHE B 543 " --> pdb=" O   ASP B 673 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   PHE B 731 " --> pdb=" O   VAL B 702 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   MET B 704 " --> pdb=" O   PHE B 731 " (cutoff:3.500A)

    664 hydrogen bonds defined for protein.
    1950 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.43

  Time building geometry restraints manager: 3.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3163
        1.34 -     1.46: 2037
        1.46 -     1.58: 4958
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 10220
  Sorted by residual:
  bond pdb=" N   VAL A  79 "
       pdb=" CA  VAL A  79 "
    ideal  model  delta    sigma   weight residual
    1.452  1.493 -0.041 1.18e-02 7.18e+03 1.20e+01
  bond pdb=" N   VAL B  79 "
       pdb=" CA  VAL B  79 "
    ideal  model  delta    sigma   weight residual
    1.452  1.492 -0.040 1.18e-02 7.18e+03 1.13e+01
  bond pdb=" N   LEU B  90 "
       pdb=" CA  LEU B  90 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.17e-02 7.31e+03 6.56e+00
  bond pdb=" N   CYS B 565 "
       pdb=" CA  CYS B 565 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.31e-02 5.83e+03 6.52e+00
  bond pdb=" N   ILE B 102 "
       pdb=" CA  ILE B 102 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 1.19e-02 7.06e+03 6.52e+00
  ... (remaining 10215 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 13459
        1.30 -     2.61: 318
        2.61 -     3.91: 99
        3.91 -     5.21: 16
        5.21 -     6.51: 4
  Bond angle restraints: 13896
  Sorted by residual:
  angle pdb=" N   VAL B 451 "
        pdb=" CA  VAL B 451 "
        pdb=" C   VAL B 451 "
      ideal   model   delta    sigma   weight residual
     112.80  108.60    4.20 1.15e+00 7.56e-01 1.33e+01
  angle pdb=" N   VAL A 451 "
        pdb=" CA  VAL A 451 "
        pdb=" C   VAL A 451 "
      ideal   model   delta    sigma   weight residual
     112.80  108.65    4.15 1.15e+00 7.56e-01 1.30e+01
  angle pdb=" N   ASP B 462 "
        pdb=" CA  ASP B 462 "
        pdb=" C   ASP B 462 "
      ideal   model   delta    sigma   weight residual
     111.36  107.46    3.90 1.09e+00 8.42e-01 1.28e+01
  angle pdb=" N   GLN A 575 "
        pdb=" CA  GLN A 575 "
        pdb=" C   GLN A 575 "
      ideal   model   delta    sigma   weight residual
     111.07  107.53    3.54 1.07e+00 8.73e-01 1.10e+01
  angle pdb=" N   VAL A  79 "
        pdb=" CA  VAL A  79 "
        pdb=" C   VAL A  79 "
      ideal   model   delta    sigma   weight residual
     112.96  109.83    3.13 1.00e+00 1.00e+00 9.80e+00
  ... (remaining 13891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.56: 5482
       11.56 -    23.11: 398
       23.11 -    34.67: 128
       34.67 -    46.23: 47
       46.23 -    57.79: 9
  Dihedral angle restraints: 6064
    sinusoidal: 2324
      harmonic: 3740
  Sorted by residual:
  dihedral pdb=" CA  ASP A 736 "
           pdb=" CB  ASP A 736 "
           pdb=" CG  ASP A 736 "
           pdb=" OD1 ASP A 736 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.79   57.79     1      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CA  ASP B 736 "
           pdb=" CB  ASP B 736 "
           pdb=" CG  ASP B 736 "
           pdb=" OD1 ASP B 736 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.49   57.49     1      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  ARG A 140 "
           pdb=" C   ARG A 140 "
           pdb=" N   HIS A 141 "
           pdb=" CA  HIS A 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.26  -15.74     0      5.00e+00 4.00e-02 9.90e+00
  ... (remaining 6061 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1243
       0.042 -    0.084: 314
       0.084 -    0.126: 93
       0.126 -    0.168: 15
       0.168 -    0.210: 3
  Chirality restraints: 1668
  Sorted by residual:
  chirality pdb=" CA  ILE A 102 "
            pdb=" N   ILE A 102 "
            pdb=" C   ILE A 102 "
            pdb=" CB  ILE A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ILE B 102 "
            pdb=" N   ILE B 102 "
            pdb=" C   ILE B 102 "
            pdb=" CB  ILE B 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  LEU A 491 "
            pdb=" N   LEU A 491 "
            pdb=" C   LEU A 491 "
            pdb=" CB  LEU A 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.16e-01
  ... (remaining 1665 not shown)

  Planarity restraints: 1730
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  64 "    0.017 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   ARG B  64 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   ARG B  64 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ALA B  65 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 537 "   -0.013 2.00e-02 2.50e+03   2.67e-02 7.13e+00
        pdb=" C   VAL A 537 "    0.046 2.00e-02 2.50e+03
        pdb=" O   VAL A 537 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG A 538 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 537 "    0.013 2.00e-02 2.50e+03   2.55e-02 6.48e+00
        pdb=" C   VAL B 537 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   VAL B 537 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ARG B 538 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1727 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1941
        2.78 -     3.31: 10162
        3.31 -     3.84: 16914
        3.84 -     4.37: 18453
        4.37 -     4.90: 33014
  Nonbonded interactions: 80484
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 185 "
            pdb=" O   GLY A 391 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG  SER B 185 "
            pdb=" O   GLY B 391 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG1 THR A 508 "
            pdb=" OH  TYR A 550 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG1 THR B 508 "
            pdb=" OH  TYR B 550 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   ALA B 420 "
            pdb=" OG  SER B 423 "
     model   vdw
     2.258 3.040
  ... (remaining 80479 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.540
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.610
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10220  Z= 0.208
  Angle     :  0.524   6.514  13896  Z= 0.338
  Chirality :  0.041   0.210   1668
  Planarity :  0.005   0.070   1730
  Dihedral  :  9.908  57.785   3652
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.25), residues: 1284
  helix:  1.55 (0.19), residues: 902
  sheet:  0.87 (0.74), residues: 54
  loop : -0.01 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  80 
 HIS   0.004   0.000   HIS A  40 
 PHE   0.011   0.001   PHE A 356 
 TYR   0.012   0.001   TYR A 550 
 ARG   0.002   0.000   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13595 (  664)
  hydrogen bonds       : angle       6.04010 ( 1950)
  covalent geometry    : bond        0.00300 (10220)
  covalent geometry    : angle       0.52372 (13896)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.7383 (t80) cc_final: 0.7107 (t80)
REVERT: A  159 GLU cc_start: 0.7666 (mm-30) cc_final: 0.6855 (mm-30)
REVERT: A  240 SER cc_start: 0.8479 (m) cc_final: 0.8171 (t)
REVERT: A  334 VAL cc_start: 0.8213 (t) cc_final: 0.7954 (p)
REVERT: A  410 SER cc_start: 0.8677 (t) cc_final: 0.8398 (m)
REVERT: A  535 LYS cc_start: 0.8020 (mttp) cc_final: 0.7708 (mtpp)
REVERT: A  568 ASP cc_start: 0.6702 (t0) cc_final: 0.6461 (t0)
REVERT: A  728 LYS cc_start: 0.7454 (mttp) cc_final: 0.7177 (mttm)
REVERT: B  263 LYS cc_start: 0.7661 (mttt) cc_final: 0.7327 (mttt)
REVERT: B  308 ILE cc_start: 0.7923 (mt) cc_final: 0.7700 (mm)
REVERT: B  309 SER cc_start: 0.8020 (t) cc_final: 0.7711 (p)
REVERT: B  334 VAL cc_start: 0.8334 (t) cc_final: 0.8123 (m)
REVERT: B  369 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7737 (mtm-85)
REVERT: B  409 GLU cc_start: 0.6836 (tt0) cc_final: 0.6441 (tt0)
REVERT: B  410 SER cc_start: 0.8646 (t) cc_final: 0.8440 (p)
REVERT: B  521 ASP cc_start: 0.7408 (t0) cc_final: 0.7096 (t0)
REVERT: B  673 ASP cc_start: 0.7617 (t0) cc_final: 0.7393 (t0)
REVERT: B  728 LYS cc_start: 0.7287 (mttp) cc_final: 0.7023 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.2585
  time to fit residues: 93.1266
Evaluate side-chains
  214 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 74 optimal weight:    0.5980
   chunk 116 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN
A 230 GLN
A 394 GLN
A 488 ASN
A 563 GLN
A 664 GLN
B 104 GLN
B 182 GLN
B 230 GLN
B 563 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.134871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.117753 restraints weight = 13763.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.11
r_work: 0.3353 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  10220  Z= 0.246
  Angle     :  0.616  11.278  13896  Z= 0.311
  Chirality :  0.044   0.146   1668
  Planarity :  0.005   0.039   1730
  Dihedral  :  3.930  15.704   1376
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.45 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.24), residues: 1284
  helix:  1.82 (0.18), residues: 902
  sheet:  0.49 (0.72), residues: 54
  loop : -0.05 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  80 
 HIS   0.004   0.001   HIS B 735 
 PHE   0.019   0.002   PHE A 356 
 TYR   0.017   0.002   TYR A 128 
 ARG   0.005   0.001   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04761 (  664)
  hydrogen bonds       : angle       4.24706 ( 1950)
  covalent geometry    : bond        0.00581 (10220)
  covalent geometry    : angle       0.61592 (13896)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 247
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6312 (tmm) cc_final: 0.5794 (tmm)
REVERT: A  102 ILE cc_start: 0.8369 (mm) cc_final: 0.8160 (tp)
REVERT: A  240 SER cc_start: 0.8672 (m) cc_final: 0.8346 (t)
REVERT: A  293 MET cc_start: 0.7140 (ptp) cc_final: 0.6844 (ptp)
REVERT: A  301 THR cc_start: 0.8248 (t) cc_final: 0.7978 (p)
REVERT: A  309 SER cc_start: 0.8153 (t) cc_final: 0.7873 (m)
REVERT: A  334 VAL cc_start: 0.8100 (t) cc_final: 0.7859 (p)
REVERT: A  358 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7449 (mt)
REVERT: A  409 GLU cc_start: 0.7394 (tt0) cc_final: 0.7071 (tt0)
REVERT: A  458 ARG cc_start: 0.7338 (tpt170) cc_final: 0.7099 (ttt180)
REVERT: A  568 ASP cc_start: 0.7178 (t0) cc_final: 0.6752 (t0)
REVERT: A  698 ILE cc_start: 0.8339 (tt) cc_final: 0.8087 (tt)
REVERT: A  699 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7282 (mm-30)
REVERT: A  728 LYS cc_start: 0.7688 (mttp) cc_final: 0.7298 (mttm)
REVERT: B  293 MET cc_start: 0.6872 (ptp) cc_final: 0.6573 (ptp)
REVERT: B  309 SER cc_start: 0.8346 (t) cc_final: 0.7966 (p)
REVERT: B  334 VAL cc_start: 0.8311 (t) cc_final: 0.7970 (m)
REVERT: B  369 ARG cc_start: 0.8331 (ttm170) cc_final: 0.8128 (ttm170)
REVERT: B  498 ILE cc_start: 0.7929 (mm) cc_final: 0.7517 (mt)
REVERT: B  521 ASP cc_start: 0.7649 (t0) cc_final: 0.7358 (t0)
REVERT: B  699 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7444 (mm-30)
REVERT: B  728 LYS cc_start: 0.7647 (mttp) cc_final: 0.7405 (mttp)
  outliers start: 24
  outliers final: 16
  residues processed: 263
  average time/residue: 0.2514
  time to fit residues: 90.3981
Evaluate side-chains
  251 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 234
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 127 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 67 optimal weight:    0.3980
   chunk 8 optimal weight:    0.1980
   chunk 111 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 86 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 488 ASN
A 708 HIS
B 416 GLN
B 664 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.135864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.118541 restraints weight = 13880.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.13
r_work: 0.3359 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10220  Z= 0.159
  Angle     :  0.554  11.837  13896  Z= 0.275
  Chirality :  0.041   0.148   1668
  Planarity :  0.005   0.082   1730
  Dihedral  :  3.928  15.796   1376
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.64 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.24), residues: 1284
  helix:  1.95 (0.18), residues: 900
  sheet:  0.16 (0.69), residues: 54
  loop : -0.06 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  80 
 HIS   0.014   0.001   HIS A 708 
 PHE   0.028   0.002   PHE A 731 
 TYR   0.011   0.001   TYR B 550 
 ARG   0.003   0.000   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04189 (  664)
  hydrogen bonds       : angle       3.98660 ( 1950)
  covalent geometry    : bond        0.00365 (10220)
  covalent geometry    : angle       0.55419 (13896)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 247
  time to evaluate  : 1.396 
Fit side-chains
REVERT: A   31 MET cc_start: 0.6350 (tmm) cc_final: 0.6077 (tmm)
REVERT: A   93 ASP cc_start: 0.7441 (m-30) cc_final: 0.7184 (t0)
REVERT: A  102 ILE cc_start: 0.8317 (mm) cc_final: 0.8085 (tp)
REVERT: A  240 SER cc_start: 0.8672 (m) cc_final: 0.8357 (t)
REVERT: A  293 MET cc_start: 0.7108 (ptp) cc_final: 0.6810 (ptp)
REVERT: A  309 SER cc_start: 0.8204 (t) cc_final: 0.7941 (m)
REVERT: A  334 VAL cc_start: 0.8077 (t) cc_final: 0.7842 (p)
REVERT: A  358 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7436 (mt)
REVERT: A  458 ARG cc_start: 0.7316 (tpt170) cc_final: 0.7077 (ttt180)
REVERT: A  568 ASP cc_start: 0.7141 (t0) cc_final: 0.6718 (t0)
REVERT: A  686 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7443 (mttm)
REVERT: A  698 ILE cc_start: 0.8320 (tt) cc_final: 0.8063 (tt)
REVERT: A  699 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7257 (mm-30)
REVERT: A  728 LYS cc_start: 0.7859 (mttp) cc_final: 0.7612 (mttm)
REVERT: B  133 TYR cc_start: 0.7998 (t80) cc_final: 0.7648 (t80)
REVERT: B  309 SER cc_start: 0.8342 (t) cc_final: 0.7978 (p)
REVERT: B  334 VAL cc_start: 0.8281 (t) cc_final: 0.7947 (m)
REVERT: B  358 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7474 (mt)
REVERT: B  369 ARG cc_start: 0.8413 (ttm170) cc_final: 0.8160 (ttm170)
REVERT: B  564 ARG cc_start: 0.8308 (mtt90) cc_final: 0.8086 (mtt90)
REVERT: B  699 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7482 (mm-30)
REVERT: B  728 LYS cc_start: 0.7741 (mttp) cc_final: 0.7372 (ttmm)
  outliers start: 33
  outliers final: 26
  residues processed: 267
  average time/residue: 0.3589
  time to fit residues: 132.5610
Evaluate side-chains
  257 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 229
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 112 optimal weight:    0.0980
   chunk 109 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0870
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
** A 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 708 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.136683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.119526 restraints weight = 13670.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.10
r_work: 0.3365 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10220  Z= 0.132
  Angle     :  0.528  12.351  13896  Z= 0.262
  Chirality :  0.040   0.144   1668
  Planarity :  0.005   0.093   1730
  Dihedral  :  3.892  15.865   1376
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 15.45 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.24), residues: 1284
  helix:  2.01 (0.18), residues: 908
  sheet: -0.06 (0.68), residues: 54
  loop :  0.02 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  80 
 HIS   0.007   0.000   HIS B 708 
 PHE   0.016   0.001   PHE A 731 
 TYR   0.010   0.001   TYR A 550 
 ARG   0.007   0.000   ARG A 544 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03827 (  664)
  hydrogen bonds       : angle       3.85371 ( 1950)
  covalent geometry    : bond        0.00298 (10220)
  covalent geometry    : angle       0.52753 (13896)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 230
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A   31 MET cc_start: 0.6276 (tmm) cc_final: 0.6048 (tmm)
REVERT: A   93 ASP cc_start: 0.7471 (m-30) cc_final: 0.7213 (t0)
REVERT: A  240 SER cc_start: 0.8683 (m) cc_final: 0.8310 (t)
REVERT: A  293 MET cc_start: 0.7096 (ptp) cc_final: 0.6799 (ptp)
REVERT: A  309 SER cc_start: 0.8196 (t) cc_final: 0.7935 (m)
REVERT: A  334 VAL cc_start: 0.8083 (t) cc_final: 0.7844 (p)
REVERT: A  358 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7454 (mt)
REVERT: A  458 ARG cc_start: 0.7341 (tpt170) cc_final: 0.7083 (ttt180)
REVERT: A  535 LYS cc_start: 0.8295 (mttp) cc_final: 0.7963 (mtpp)
REVERT: A  568 ASP cc_start: 0.7104 (t0) cc_final: 0.6669 (t0)
REVERT: A  686 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7451 (mttm)
REVERT: A  698 ILE cc_start: 0.8318 (tt) cc_final: 0.8077 (tt)
REVERT: A  699 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7247 (mm-30)
REVERT: A  728 LYS cc_start: 0.7848 (mttp) cc_final: 0.7604 (mttm)
REVERT: B  133 TYR cc_start: 0.7934 (t80) cc_final: 0.7659 (t80)
REVERT: B  309 SER cc_start: 0.8318 (t) cc_final: 0.7962 (p)
REVERT: B  334 VAL cc_start: 0.8269 (t) cc_final: 0.7925 (m)
REVERT: B  358 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7503 (mt)
REVERT: B  498 ILE cc_start: 0.7915 (mm) cc_final: 0.7507 (mt)
REVERT: B  699 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7469 (mm-30)
REVERT: B  728 LYS cc_start: 0.7852 (mttp) cc_final: 0.7496 (ttmm)
  outliers start: 41
  outliers final: 28
  residues processed: 255
  average time/residue: 0.2319
  time to fit residues: 82.3444
Evaluate side-chains
  253 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 222
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  686 LYS
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 118 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0050
   chunk 14 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
B 370 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.135012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.117992 restraints weight = 13758.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.07
r_work: 0.3344 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10220  Z= 0.164
  Angle     :  0.550  12.686  13896  Z= 0.272
  Chirality :  0.041   0.143   1668
  Planarity :  0.004   0.047   1730
  Dihedral  :  3.953  16.437   1376
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 16.45 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.24), residues: 1284
  helix:  1.94 (0.18), residues: 908
  sheet: -0.13 (0.67), residues: 54
  loop :  0.00 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  80 
 HIS   0.005   0.001   HIS B 708 
 PHE   0.015   0.002   PHE B 121 
 TYR   0.013   0.001   TYR A 133 
 ARG   0.004   0.000   ARG A 544 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  664)
  hydrogen bonds       : angle       3.86558 ( 1950)
  covalent geometry    : bond        0.00386 (10220)
  covalent geometry    : angle       0.54959 (13896)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 237
  time to evaluate  : 1.041 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.7500 (m-30) cc_final: 0.7261 (t0)
REVERT: A  240 SER cc_start: 0.8705 (m) cc_final: 0.8405 (t)
REVERT: A  293 MET cc_start: 0.7114 (ptp) cc_final: 0.6816 (ptp)
REVERT: A  309 SER cc_start: 0.8257 (t) cc_final: 0.8000 (m)
REVERT: A  334 VAL cc_start: 0.8051 (t) cc_final: 0.7813 (p)
REVERT: A  358 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7489 (mt)
REVERT: A  458 ARG cc_start: 0.7336 (tpt170) cc_final: 0.7067 (ttt180)
REVERT: A  498 ILE cc_start: 0.8107 (mm) cc_final: 0.7802 (mt)
REVERT: A  568 ASP cc_start: 0.7102 (t0) cc_final: 0.6689 (t0)
REVERT: A  662 LEU cc_start: 0.8756 (mt) cc_final: 0.8512 (mp)
REVERT: A  698 ILE cc_start: 0.8332 (tt) cc_final: 0.8078 (tt)
REVERT: A  699 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7373 (mm-30)
REVERT: A  728 LYS cc_start: 0.7864 (mttp) cc_final: 0.7585 (mttm)
REVERT: A  730 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7677 (mp)
REVERT: B  133 TYR cc_start: 0.7948 (t80) cc_final: 0.7683 (t80)
REVERT: B  309 SER cc_start: 0.8319 (t) cc_final: 0.7951 (p)
REVERT: B  334 VAL cc_start: 0.8239 (t) cc_final: 0.7895 (m)
REVERT: B  358 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7513 (mt)
REVERT: B  498 ILE cc_start: 0.7935 (mm) cc_final: 0.7544 (mt)
REVERT: B  509 GLN cc_start: 0.8504 (mt0) cc_final: 0.8279 (mt0)
REVERT: B  699 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7631 (mm-30)
REVERT: B  728 LYS cc_start: 0.7857 (mttp) cc_final: 0.7502 (ttmm)
  outliers start: 47
  outliers final: 31
  residues processed: 266
  average time/residue: 0.2167
  time to fit residues: 80.9483
Evaluate side-chains
  270 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 236
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 124 optimal weight:    0.8980
   chunk 105 optimal weight:    0.4980
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 459 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.133189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.116233 restraints weight = 13857.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.06
r_work: 0.3337 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10220  Z= 0.192
  Angle     :  0.576  13.526  13896  Z= 0.284
  Chirality :  0.042   0.156   1668
  Planarity :  0.004   0.052   1730
  Dihedral  :  4.030  17.130   1376
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 17.64 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.24), residues: 1284
  helix:  1.88 (0.18), residues: 908
  sheet: -0.29 (0.66), residues: 54
  loop : -0.10 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  80 
 HIS   0.003   0.001   HIS B 708 
 PHE   0.016   0.002   PHE B 121 
 TYR   0.013   0.002   TYR B  29 
 ARG   0.003   0.000   ARG A 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  664)
  hydrogen bonds       : angle       3.89496 ( 1950)
  covalent geometry    : bond        0.00456 (10220)
  covalent geometry    : angle       0.57650 (13896)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 232
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A  240 SER cc_start: 0.8743 (m) cc_final: 0.8456 (t)
REVERT: A  293 MET cc_start: 0.7146 (ptp) cc_final: 0.6829 (ptp)
REVERT: A  301 THR cc_start: 0.8314 (t) cc_final: 0.8089 (p)
REVERT: A  309 SER cc_start: 0.8308 (t) cc_final: 0.8061 (m)
REVERT: A  334 VAL cc_start: 0.8033 (t) cc_final: 0.7796 (p)
REVERT: A  458 ARG cc_start: 0.7365 (tpt170) cc_final: 0.7118 (ttt180)
REVERT: A  498 ILE cc_start: 0.8145 (mm) cc_final: 0.7845 (mt)
REVERT: A  568 ASP cc_start: 0.7125 (t0) cc_final: 0.6725 (t0)
REVERT: A  662 LEU cc_start: 0.8785 (mt) cc_final: 0.8556 (mp)
REVERT: A  686 LYS cc_start: 0.7897 (mttp) cc_final: 0.7684 (mttm)
REVERT: A  699 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7416 (mm-30)
REVERT: A  728 LYS cc_start: 0.7855 (mttp) cc_final: 0.7582 (mttm)
REVERT: B  133 TYR cc_start: 0.7953 (t80) cc_final: 0.7712 (t80)
REVERT: B  309 SER cc_start: 0.8339 (t) cc_final: 0.7969 (p)
REVERT: B  334 VAL cc_start: 0.8197 (t) cc_final: 0.7877 (m)
REVERT: B  358 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7605 (mt)
REVERT: B  369 ARG cc_start: 0.8468 (ttm170) cc_final: 0.8193 (ttm170)
REVERT: B  498 ILE cc_start: 0.7995 (mm) cc_final: 0.7601 (mt)
REVERT: B  699 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7645 (mm-30)
REVERT: B  728 LYS cc_start: 0.7874 (mttp) cc_final: 0.7539 (ttmm)
  outliers start: 47
  outliers final: 38
  residues processed: 261
  average time/residue: 0.2281
  time to fit residues: 82.5353
Evaluate side-chains
  266 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 227
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  238 HIS
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  582 LYS
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 416 GLN
B 416 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.134007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.117316 restraints weight = 13969.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.01
r_work: 0.3332 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10220  Z= 0.220
  Angle     :  0.594  14.106  13896  Z= 0.295
  Chirality :  0.043   0.149   1668
  Planarity :  0.005   0.053   1730
  Dihedral  :  4.145  18.330   1376
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 17.55 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.24), residues: 1284
  helix:  1.86 (0.18), residues: 900
  sheet: -0.59 (0.65), residues: 54
  loop : -0.19 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  80 
 HIS   0.003   0.001   HIS B 735 
 PHE   0.032   0.002   PHE B 720 
 TYR   0.013   0.002   TYR B  29 
 ARG   0.003   0.000   ARG A 538 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04146 (  664)
  hydrogen bonds       : angle       3.97335 ( 1950)
  covalent geometry    : bond        0.00525 (10220)
  covalent geometry    : angle       0.59433 (13896)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 237
  time to evaluate  : 1.710 
Fit side-chains
REVERT: A   31 MET cc_start: 0.6214 (tmm) cc_final: 0.5849 (tmm)
REVERT: A  240 SER cc_start: 0.8733 (m) cc_final: 0.8447 (t)
REVERT: A  293 MET cc_start: 0.7210 (ptp) cc_final: 0.6884 (ptp)
REVERT: A  301 THR cc_start: 0.8329 (t) cc_final: 0.8113 (p)
REVERT: A  309 SER cc_start: 0.8328 (t) cc_final: 0.8072 (m)
REVERT: A  334 VAL cc_start: 0.8040 (t) cc_final: 0.7795 (p)
REVERT: A  458 ARG cc_start: 0.7370 (tpt170) cc_final: 0.7117 (ttt180)
REVERT: A  498 ILE cc_start: 0.8143 (mm) cc_final: 0.7863 (mt)
REVERT: A  568 ASP cc_start: 0.7124 (t0) cc_final: 0.6756 (t0)
REVERT: A  662 LEU cc_start: 0.8786 (mt) cc_final: 0.8483 (mp)
REVERT: A  699 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7484 (mm-30)
REVERT: A  728 LYS cc_start: 0.7810 (mttp) cc_final: 0.7533 (mttm)
REVERT: A  742 LEU cc_start: 0.8374 (mt) cc_final: 0.8118 (mp)
REVERT: B  133 TYR cc_start: 0.7951 (t80) cc_final: 0.7640 (t80)
REVERT: B  293 MET cc_start: 0.6933 (ptp) cc_final: 0.6623 (ptp)
REVERT: B  309 SER cc_start: 0.8367 (t) cc_final: 0.7981 (p)
REVERT: B  334 VAL cc_start: 0.8174 (t) cc_final: 0.7848 (m)
REVERT: B  358 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7565 (mt)
REVERT: B  369 ARG cc_start: 0.8447 (ttm170) cc_final: 0.8165 (ttm170)
REVERT: B  699 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7668 (mm-30)
REVERT: B  728 LYS cc_start: 0.7857 (mttp) cc_final: 0.7520 (ttmm)
  outliers start: 50
  outliers final: 42
  residues processed: 266
  average time/residue: 0.2750
  time to fit residues: 101.6049
Evaluate side-chains
  275 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 232
  time to evaluate  : 1.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  739 THR
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  238 HIS
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 41 optimal weight:    0.0970
   chunk 109 optimal weight:    1.9990
   chunk 113 optimal weight:    0.2980
   chunk 77 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   chunk 116 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 81 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0770
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
A 370 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.135780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.118564 restraints weight = 13879.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.12
r_work: 0.3359 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10220  Z= 0.123
  Angle     :  0.558  14.859  13896  Z= 0.271
  Chirality :  0.040   0.181   1668
  Planarity :  0.004   0.052   1730
  Dihedral  :  3.998  17.692   1376
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 19.09 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.24), residues: 1284
  helix:  2.03 (0.18), residues: 904
  sheet: -0.61 (0.65), residues: 54
  loop : -0.03 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  80 
 HIS   0.002   0.000   HIS B 512 
 PHE   0.025   0.001   PHE B 720 
 TYR   0.010   0.001   TYR A 550 
 ARG   0.003   0.000   ARG B 544 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03576 (  664)
  hydrogen bonds       : angle       3.83806 ( 1950)
  covalent geometry    : bond        0.00278 (10220)
  covalent geometry    : angle       0.55829 (13896)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 238
  time to evaluate  : 2.228 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.7419 (t70) cc_final: 0.7149 (t0)
REVERT: A  240 SER cc_start: 0.8724 (m) cc_final: 0.8424 (t)
REVERT: A  293 MET cc_start: 0.7154 (ptp) cc_final: 0.6823 (ptp)
REVERT: A  309 SER cc_start: 0.8250 (t) cc_final: 0.8011 (m)
REVERT: A  334 VAL cc_start: 0.8039 (t) cc_final: 0.7788 (p)
REVERT: A  498 ILE cc_start: 0.8048 (mm) cc_final: 0.7745 (mt)
REVERT: A  662 LEU cc_start: 0.8775 (mt) cc_final: 0.8461 (mp)
REVERT: A  699 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7379 (mm-30)
REVERT: A  728 LYS cc_start: 0.7815 (mttp) cc_final: 0.7528 (mttm)
REVERT: A  730 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7617 (mp)
REVERT: B  133 TYR cc_start: 0.7915 (t80) cc_final: 0.7679 (t80)
REVERT: B  293 MET cc_start: 0.6869 (ptp) cc_final: 0.6582 (ptp)
REVERT: B  309 SER cc_start: 0.8306 (t) cc_final: 0.7957 (p)
REVERT: B  334 VAL cc_start: 0.8200 (t) cc_final: 0.7863 (m)
REVERT: B  358 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7447 (mt)
REVERT: B  369 ARG cc_start: 0.8413 (ttm170) cc_final: 0.8142 (ttm170)
REVERT: B  498 ILE cc_start: 0.7906 (mm) cc_final: 0.7503 (mt)
REVERT: B  699 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7568 (mm-30)
REVERT: B  728 LYS cc_start: 0.7895 (mttp) cc_final: 0.7535 (ttmm)
  outliers start: 39
  outliers final: 32
  residues processed: 266
  average time/residue: 0.2802
  time to fit residues: 103.1243
Evaluate side-chains
  267 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 233
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 73 optimal weight:    0.1980
   chunk 87 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 125 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 127 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3703 r_free = 0.3703 target = 0.134630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.117457 restraints weight = 13868.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.13
r_work: 0.3343 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10220  Z= 0.164
  Angle     :  0.592  15.224  13896  Z= 0.286
  Chirality :  0.042   0.229   1668
  Planarity :  0.004   0.052   1730
  Dihedral  :  4.028  17.693   1376
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.18 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.24), residues: 1284
  helix:  1.96 (0.18), residues: 904
  sheet: -0.62 (0.65), residues: 54
  loop : -0.02 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  80 
 HIS   0.003   0.001   HIS B 735 
 PHE   0.027   0.002   PHE B 720 
 TYR   0.010   0.001   TYR B 550 
 ARG   0.004   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03786 (  664)
  hydrogen bonds       : angle       3.87922 ( 1950)
  covalent geometry    : bond        0.00388 (10220)
  covalent geometry    : angle       0.59160 (13896)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 243
  time to evaluate  : 1.195 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.7459 (t70) cc_final: 0.7058 (t0)
REVERT: A  240 SER cc_start: 0.8729 (m) cc_final: 0.8456 (t)
REVERT: A  293 MET cc_start: 0.7172 (ptp) cc_final: 0.6841 (ptp)
REVERT: A  309 SER cc_start: 0.8241 (t) cc_final: 0.8010 (m)
REVERT: A  334 VAL cc_start: 0.8043 (t) cc_final: 0.7798 (p)
REVERT: A  498 ILE cc_start: 0.8068 (mm) cc_final: 0.7768 (mt)
REVERT: A  662 LEU cc_start: 0.8780 (mt) cc_final: 0.8461 (mp)
REVERT: A  699 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7381 (mm-30)
REVERT: A  728 LYS cc_start: 0.7794 (mttp) cc_final: 0.7512 (mttm)
REVERT: A  730 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7680 (mp)
REVERT: A  742 LEU cc_start: 0.8339 (mt) cc_final: 0.8072 (mp)
REVERT: B  133 TYR cc_start: 0.7929 (t80) cc_final: 0.7719 (t80)
REVERT: B  309 SER cc_start: 0.8313 (t) cc_final: 0.7937 (p)
REVERT: B  334 VAL cc_start: 0.8204 (t) cc_final: 0.7867 (m)
REVERT: B  358 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7452 (mt)
REVERT: B  369 ARG cc_start: 0.8399 (ttm170) cc_final: 0.8142 (ttm170)
REVERT: B  498 ILE cc_start: 0.7904 (mm) cc_final: 0.7521 (mt)
REVERT: B  699 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7564 (mm-30)
REVERT: B  728 LYS cc_start: 0.7885 (mttp) cc_final: 0.7526 (ttmm)
  outliers start: 36
  outliers final: 32
  residues processed: 267
  average time/residue: 0.2412
  time to fit residues: 88.5736
Evaluate side-chains
  272 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 238
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  582 LYS
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  725 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9980
   chunk 59 optimal weight:    0.3980
   chunk 54 optimal weight:    0.3980
   chunk 124 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3703 r_free = 0.3703 target = 0.134710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.117488 restraints weight = 13977.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.14
r_work: 0.3342 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10220  Z= 0.162
  Angle     :  0.589  15.353  13896  Z= 0.286
  Chirality :  0.042   0.168   1668
  Planarity :  0.004   0.052   1730
  Dihedral  :  4.035  18.141   1376
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.55 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.24), residues: 1284
  helix:  1.94 (0.18), residues: 904
  sheet: -0.56 (0.66), residues: 54
  loop :  0.00 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  80 
 HIS   0.002   0.000   HIS B 512 
 PHE   0.033   0.002   PHE B 720 
 TYR   0.011   0.001   TYR A 550 
 ARG   0.004   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03750 (  664)
  hydrogen bonds       : angle       3.87888 ( 1950)
  covalent geometry    : bond        0.00380 (10220)
  covalent geometry    : angle       0.58916 (13896)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 238
  time to evaluate  : 1.036 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.7455 (t70) cc_final: 0.7050 (t0)
REVERT: A  102 ILE cc_start: 0.8325 (mm) cc_final: 0.8097 (tp)
REVERT: A  240 SER cc_start: 0.8730 (m) cc_final: 0.8429 (t)
REVERT: A  293 MET cc_start: 0.7172 (ptp) cc_final: 0.6843 (ptp)
REVERT: A  309 SER cc_start: 0.8245 (t) cc_final: 0.8022 (m)
REVERT: A  334 VAL cc_start: 0.8056 (t) cc_final: 0.7801 (p)
REVERT: A  498 ILE cc_start: 0.8076 (mm) cc_final: 0.7775 (mt)
REVERT: A  662 LEU cc_start: 0.8785 (mt) cc_final: 0.8479 (mp)
REVERT: A  699 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7392 (mm-30)
REVERT: A  728 LYS cc_start: 0.7782 (mttp) cc_final: 0.7489 (mttm)
REVERT: A  730 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7687 (mp)
REVERT: A  742 LEU cc_start: 0.8341 (mt) cc_final: 0.8076 (mp)
REVERT: B  133 TYR cc_start: 0.7926 (t80) cc_final: 0.7707 (t80)
REVERT: B  309 SER cc_start: 0.8306 (t) cc_final: 0.7922 (p)
REVERT: B  334 VAL cc_start: 0.8196 (t) cc_final: 0.7858 (m)
REVERT: B  358 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7464 (mt)
REVERT: B  369 ARG cc_start: 0.8391 (ttm170) cc_final: 0.8150 (ttm170)
REVERT: B  498 ILE cc_start: 0.7905 (mm) cc_final: 0.7515 (mt)
REVERT: B  699 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7567 (mm-30)
REVERT: B  728 LYS cc_start: 0.7900 (mttp) cc_final: 0.7540 (ttmm)
  outliers start: 36
  outliers final: 30
  residues processed: 260
  average time/residue: 0.2326
  time to fit residues: 83.1800
Evaluate side-chains
  268 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 236
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  582 LYS
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  725 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 119 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0670
   chunk 32 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0980
   chunk 103 optimal weight:    0.7980
   chunk 81 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.135526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.118249 restraints weight = 13838.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.13
r_work: 0.3346 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10220  Z= 0.138
  Angle     :  0.579  15.393  13896  Z= 0.279
  Chirality :  0.041   0.163   1668
  Planarity :  0.004   0.052   1730
  Dihedral  :  3.988  17.657   1376
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.09 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.24), residues: 1284
  helix:  2.02 (0.18), residues: 904
  sheet: -0.52 (0.66), residues: 54
  loop :  0.06 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  80 
 HIS   0.002   0.000   HIS B 512 
 PHE   0.031   0.001   PHE B 720 
 TYR   0.011   0.001   TYR A 550 
 ARG   0.003   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 (  664)
  hydrogen bonds       : angle       3.83588 ( 1950)
  covalent geometry    : bond        0.00320 (10220)
  covalent geometry    : angle       0.57906 (13896)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5762.73 seconds
wall clock time: 101 minutes 43.72 seconds (6103.72 seconds total)