Starting phenix.real_space_refine
on Fri Feb 14 08:26:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8opq_17085/02_2025/8opq_17085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8opq_17085/02_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_17085/02_2025/8opq_17085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8opq_17085/02_2025/8opq_17085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8opq_17085/02_2025/8opq_17085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8opq_17085/02_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-5592/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: 7.29, per 1000 atoms: 0.73
  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: 2.92
  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: 1.22
  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: 3.28

  Time building geometry restraints manager: 3.31 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:             5.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     27.140
  Find NCS groups from input model:        0.330
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.850
-------------------------------------------------------------------------------
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= 0.195
  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 

*********************** 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  : 1.095 
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: 0.2597
  time to fit residues: 93.6674
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  : 1.150 
-------------------------------------------------------------------------------
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 = 0.134872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.117755 restraints weight = 13763.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.11
r_work: 0.3353 rms_B_bonded: 2.72 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= 0.390
  Angle     :  0.616  11.278  13896  Z= 0.311
  Chirality :  0.044   0.146   1668
  Planarity :  0.005   0.039   1730
  Dihedral  :  3.930  15.705   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 

*********************** 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  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6316 (tmm) cc_final: 0.5797 (tmm)
REVERT: A  102 ILE cc_start: 0.8369 (mm) cc_final: 0.8159 (tp)
REVERT: A  240 SER cc_start: 0.8671 (m) cc_final: 0.8346 (t)
REVERT: A  293 MET cc_start: 0.7142 (ptp) cc_final: 0.6845 (ptp)
REVERT: A  301 THR cc_start: 0.8247 (t) cc_final: 0.7978 (p)
REVERT: A  309 SER cc_start: 0.8151 (t) cc_final: 0.7871 (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: 0.7447 (mt)
REVERT: A  409 GLU cc_start: 0.7392 (tt0) cc_final: 0.7070 (tt0)
REVERT: A  458 ARG cc_start: 0.7345 (tpt170) cc_final: 0.7104 (ttt180)
REVERT: A  568 ASP cc_start: 0.7182 (t0) cc_final: 0.6756 (t0)
REVERT: A  698 ILE cc_start: 0.8337 (tt) cc_final: 0.8086 (tt)
REVERT: A  699 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7285 (mm-30)
REVERT: A  728 LYS cc_start: 0.7687 (mttp) cc_final: 0.7296 (mttm)
REVERT: B  293 MET cc_start: 0.6876 (ptp) cc_final: 0.6577 (ptp)
REVERT: B  309 SER cc_start: 0.8346 (t) cc_final: 0.7967 (p)
REVERT: B  334 VAL cc_start: 0.8312 (t) cc_final: 0.7971 (m)
REVERT: B  369 ARG cc_start: 0.8329 (ttm170) cc_final: 0.8126 (ttm170)
REVERT: B  498 ILE cc_start: 0.7926 (mm) cc_final: 0.7515 (mt)
REVERT: B  521 ASP cc_start: 0.7648 (t0) cc_final: 0.7358 (t0)
REVERT: B  699 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7443 (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: 0.2522
  time to fit residues: 89.8865
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  : 1.168 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 8 optimal weight:    0.1980
   chunk 111 optimal weight:    0.8980
   chunk 122 optimal weight:    0.1980
   chunk 80 optimal weight:    0.8980
   chunk 86 optimal weight:    0.0370
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.3658

-------------------------------------------------------------------------------
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 = 0.3734 r_free = 0.3734 target = 0.136994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.119635 restraints weight = 13882.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.14
r_work: 0.3374 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10220  Z= 0.191
  Angle     :  0.538  11.726  13896  Z= 0.266
  Chirality :  0.040   0.148   1668
  Planarity :  0.005   0.085   1730
  Dihedral  :  3.856  15.809   1376
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.27 %
    Favored  : 83.27 %
  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:  2.17 (0.24), residues: 1284
  helix:  2.03 (0.18), residues: 902
  sheet:  0.23 (0.70), residues: 54
  loop :  0.06 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  80 
 HIS   0.013   0.001   HIS A 708 
 PHE   0.027   0.002   PHE A 731 
 TYR   0.010   0.001   TYR B 550 
 ARG   0.012   0.000   ARG B 544 

*********************** 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
  276 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 249
  time to evaluate  : 1.206 
Fit side-chains
REVERT: A   31 MET cc_start: 0.6314 (tmm) cc_final: 0.6038 (tmm)
REVERT: A   68 TYR cc_start: 0.7371 (t80) cc_final: 0.7156 (t80)
REVERT: A   93 ASP cc_start: 0.7446 (m-30) cc_final: 0.7188 (t0)
REVERT: A  102 ILE cc_start: 0.8265 (mm) cc_final: 0.8045 (tp)
REVERT: A  240 SER cc_start: 0.8667 (m) cc_final: 0.8291 (t)
REVERT: A  293 MET cc_start: 0.7080 (ptp) cc_final: 0.6795 (ptp)
REVERT: A  309 SER cc_start: 0.8173 (t) cc_final: 0.7919 (m)
REVERT: A  334 VAL cc_start: 0.8088 (t) cc_final: 0.7856 (p)
REVERT: A  358 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7416 (mt)
REVERT: A  458 ARG cc_start: 0.7327 (tpt170) cc_final: 0.7078 (ttt180)
REVERT: A  568 ASP cc_start: 0.7123 (t0) cc_final: 0.6686 (t0)
REVERT: A  686 LYS cc_start: 0.7732 (ttmm) cc_final: 0.7449 (mttm)
REVERT: A  698 ILE cc_start: 0.8282 (tt) cc_final: 0.8032 (tt)
REVERT: A  699 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7194 (mm-30)
REVERT: A  728 LYS cc_start: 0.7859 (mttp) cc_final: 0.7607 (mttm)
REVERT: B  133 TYR cc_start: 0.7994 (t80) cc_final: 0.7781 (t80)
REVERT: B  309 SER cc_start: 0.8318 (t) cc_final: 0.7957 (p)
REVERT: B  334 VAL cc_start: 0.8289 (t) cc_final: 0.7963 (m)
REVERT: B  358 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7462 (mt)
REVERT: B  369 ARG cc_start: 0.8393 (ttm170) cc_final: 0.8104 (ttm170)
REVERT: B  564 ARG cc_start: 0.8301 (mtt90) cc_final: 0.8082 (mtt90)
REVERT: B  699 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7464 (mm-30)
REVERT: B  728 LYS cc_start: 0.7737 (mttp) cc_final: 0.7364 (ttmm)
  outliers start: 27
  outliers final: 21
  residues processed: 263
  average time/residue: 0.2499
  time to fit residues: 89.4486
Evaluate side-chains
  257 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 234
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
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  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  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  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  719 HIS
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:    0.4980
   chunk 34 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 112 optimal weight:    0.8980
   chunk 109 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 88 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 563 GLN
B 708 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.135761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.118565 restraints weight = 13688.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.10
r_work: 0.3351 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2297

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= 0.264
  Angle     :  0.547  12.311  13896  Z= 0.272
  Chirality :  0.041   0.146   1668
  Planarity :  0.005   0.079   1730
  Dihedral  :  3.935  16.293   1376
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 15.18 %
    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:  2.04 (0.24), residues: 1284
  helix:  1.94 (0.18), residues: 908
  sheet: -0.08 (0.68), residues: 54
  loop :  0.02 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  80 
 HIS   0.015   0.001   HIS B 708 
 PHE   0.016   0.002   PHE A 731 
 TYR   0.011   0.001   TYR A 557 
 ARG   0.004   0.000   ARG B 180 

*********************** 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
  277 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 233
  time to evaluate  : 1.044 
Fit side-chains
REVERT: A   31 MET cc_start: 0.6257 (tmm) cc_final: 0.6051 (tmm)
REVERT: A   93 ASP cc_start: 0.7479 (m-30) cc_final: 0.7222 (t0)
REVERT: A  240 SER cc_start: 0.8692 (m) cc_final: 0.8380 (t)
REVERT: A  293 MET cc_start: 0.7109 (ptp) cc_final: 0.6798 (ptp)
REVERT: A  309 SER cc_start: 0.8235 (t) cc_final: 0.7969 (m)
REVERT: A  334 VAL cc_start: 0.8078 (t) cc_final: 0.7838 (p)
REVERT: A  358 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7468 (mt)
REVERT: A  458 ARG cc_start: 0.7359 (tpt170) cc_final: 0.7109 (ttt180)
REVERT: A  487 LEU cc_start: 0.7798 (mp) cc_final: 0.7578 (mt)
REVERT: A  568 ASP cc_start: 0.7135 (t0) cc_final: 0.6704 (t0)
REVERT: A  662 LEU cc_start: 0.8725 (mt) cc_final: 0.8471 (mp)
REVERT: A  686 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7459 (mttm)
REVERT: A  698 ILE cc_start: 0.8331 (tt) cc_final: 0.8081 (tt)
REVERT: A  699 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7315 (mm-30)
REVERT: A  728 LYS cc_start: 0.7852 (mttp) cc_final: 0.7597 (mttm)
REVERT: B  133 TYR cc_start: 0.7959 (t80) cc_final: 0.7660 (t80)
REVERT: B  247 SER cc_start: 0.8185 (p) cc_final: 0.7930 (t)
REVERT: B  309 SER cc_start: 0.8316 (t) cc_final: 0.7958 (p)
REVERT: B  334 VAL cc_start: 0.8268 (t) cc_final: 0.7938 (m)
REVERT: B  509 GLN cc_start: 0.8501 (mt0) cc_final: 0.8268 (mt0)
REVERT: B  699 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7543 (mm-30)
REVERT: B  728 LYS cc_start: 0.7857 (mttp) cc_final: 0.7503 (ttmm)
  outliers start: 44
  outliers final: 30
  residues processed: 260
  average time/residue: 0.2405
  time to fit residues: 85.9356
Evaluate side-chains
  262 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 230
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
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  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  686 LYS
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain B residue   95 LEU
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  362 LEU
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  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:    0.9990
   chunk 80 optimal weight:    0.0870
   chunk 118 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.7160

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.133889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.116801 restraints weight = 13781.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.06
r_work: 0.3339 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10220  Z= 0.280
  Angle     :  0.552  12.956  13896  Z= 0.275
  Chirality :  0.042   0.156   1668
  Planarity :  0.004   0.048   1730
  Dihedral  :  3.988  16.612   1376
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 16.82 %
    Favored  : 79.18 %
  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:  1.97 (0.24), residues: 1284
  helix:  1.90 (0.18), residues: 908
  sheet: -0.24 (0.66), residues: 54
  loop : -0.02 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  80 
 HIS   0.011   0.001   HIS B 708 
 PHE   0.016   0.002   PHE B 121 
 TYR   0.011   0.001   TYR A 557 
 ARG   0.004   0.000   ARG A 404 

*********************** 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
  282 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 238
  time to evaluate  : 1.059 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.7460 (m-30) cc_final: 0.7257 (t0)
REVERT: A  240 SER cc_start: 0.8717 (m) cc_final: 0.8427 (t)
REVERT: A  293 MET cc_start: 0.7135 (ptp) cc_final: 0.6825 (ptp)
REVERT: A  301 THR cc_start: 0.8269 (t) cc_final: 0.8044 (p)
REVERT: A  309 SER cc_start: 0.8287 (t) cc_final: 0.8028 (m)
REVERT: A  334 VAL cc_start: 0.8041 (t) cc_final: 0.7803 (p)
REVERT: A  358 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7566 (mt)
REVERT: A  458 ARG cc_start: 0.7382 (tpt170) cc_final: 0.7120 (ttt180)
REVERT: A  498 ILE cc_start: 0.8185 (mm) cc_final: 0.7876 (mt)
REVERT: A  568 ASP cc_start: 0.7124 (t0) cc_final: 0.6725 (t0)
REVERT: A  662 LEU cc_start: 0.8758 (mt) cc_final: 0.8529 (mp)
REVERT: A  698 ILE cc_start: 0.8410 (tt) cc_final: 0.8163 (tt)
REVERT: A  699 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7406 (mm-30)
REVERT: A  728 LYS cc_start: 0.7870 (mttp) cc_final: 0.7600 (mttm)
REVERT: A  730 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7736 (mp)
REVERT: B  133 TYR cc_start: 0.7950 (t80) cc_final: 0.7686 (t80)
REVERT: B  247 SER cc_start: 0.8166 (p) cc_final: 0.7943 (t)
REVERT: B  309 SER cc_start: 0.8338 (t) cc_final: 0.7974 (p)
REVERT: B  334 VAL cc_start: 0.8209 (t) cc_final: 0.7895 (m)
REVERT: B  498 ILE cc_start: 0.8011 (mm) cc_final: 0.7635 (mt)
REVERT: B  699 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7679 (mm-30)
REVERT: B  728 LYS cc_start: 0.7865 (mttp) cc_final: 0.7530 (ttmm)
  outliers start: 44
  outliers final: 31
  residues processed: 265
  average time/residue: 0.2289
  time to fit residues: 84.0438
Evaluate side-chains
  265 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 232
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  103 MET
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  238 HIS
Chi-restraints excluded: chain B residue  240 SER
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:    0.7980
   chunk 121 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 124 optimal weight:    0.6980
   chunk 105 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 459 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 = 0.3702 r_free = 0.3702 target = 0.134612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.117505 restraints weight = 13837.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.10
r_work: 0.3333 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10220  Z= 0.299
  Angle     :  0.573  13.717  13896  Z= 0.283
  Chirality :  0.042   0.147   1668
  Planarity :  0.004   0.052   1730
  Dihedral  :  4.052  17.232   1376
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.09 %
    Favored  : 78.82 %
  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:  1.88 (0.24), residues: 1284
  helix:  1.86 (0.18), residues: 908
  sheet: -0.44 (0.64), 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 735 
 PHE   0.031   0.002   PHE B 720 
 TYR   0.014   0.002   TYR B  29 
 ARG   0.004   0.000   ARG A 538 

*********************** 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
  285 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 240
  time to evaluate  : 1.104 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.7525 (m-30) cc_final: 0.7303 (t0)
REVERT: A  240 SER cc_start: 0.8729 (m) cc_final: 0.8431 (t)
REVERT: A  293 MET cc_start: 0.7178 (ptp) cc_final: 0.6862 (ptp)
REVERT: A  301 THR cc_start: 0.8285 (t) cc_final: 0.8054 (p)
REVERT: A  309 SER cc_start: 0.8281 (t) cc_final: 0.8025 (m)
REVERT: A  334 VAL cc_start: 0.8057 (t) cc_final: 0.7810 (p)
REVERT: A  458 ARG cc_start: 0.7354 (tpt170) cc_final: 0.7102 (ttt180)
REVERT: A  498 ILE cc_start: 0.8079 (mm) cc_final: 0.7786 (mt)
REVERT: A  568 ASP cc_start: 0.7136 (t0) cc_final: 0.6722 (t0)
REVERT: A  662 LEU cc_start: 0.8776 (mt) cc_final: 0.8465 (mp)
REVERT: A  686 LYS cc_start: 0.7854 (mttp) cc_final: 0.7652 (mttm)
REVERT: A  699 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7404 (mm-30)
REVERT: A  728 LYS cc_start: 0.7850 (mttp) cc_final: 0.7562 (mttm)
REVERT: B  133 TYR cc_start: 0.7924 (t80) cc_final: 0.7678 (t80)
REVERT: B  309 SER cc_start: 0.8350 (t) cc_final: 0.7971 (p)
REVERT: B  334 VAL cc_start: 0.8190 (t) cc_final: 0.7854 (m)
REVERT: B  369 ARG cc_start: 0.8428 (ttm170) cc_final: 0.8189 (ttm170)
REVERT: B  498 ILE cc_start: 0.7922 (mm) cc_final: 0.7551 (mt)
REVERT: B  509 GLN cc_start: 0.8503 (mt0) cc_final: 0.8273 (mt0)
REVERT: B  699 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7642 (mm-30)
REVERT: B  728 LYS cc_start: 0.7879 (mttp) cc_final: 0.7527 (ttmm)
  outliers start: 45
  outliers final: 37
  residues processed: 268
  average time/residue: 0.2470
  time to fit residues: 90.8279
Evaluate side-chains
  271 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 234
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
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  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  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:    3.9990
   chunk 117 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 84 optimal weight:    0.2980
   chunk 10 optimal weight:    0.4980
   chunk 107 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.7582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.133534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.116523 restraints weight = 13969.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.08
r_work: 0.3332 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10220  Z= 0.294
  Angle     :  0.576  14.434  13896  Z= 0.283
  Chirality :  0.042   0.171   1668
  Planarity :  0.004   0.053   1730
  Dihedral  :  4.082  17.917   1376
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.45 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.24), residues: 1284
  helix:  1.87 (0.18), residues: 904
  sheet: -0.64 (0.64), residues: 54
  loop : -0.08 (0.36), residues: 326

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   0.031   0.002   PHE B 720 
 TYR   0.014   0.001   TYR B  29 
 ARG   0.004   0.000   ARG B 544 

*********************** 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
  282 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 237
  time to evaluate  : 1.241 
Fit side-chains
REVERT: A   31 MET cc_start: 0.6217 (tmm) cc_final: 0.5868 (tmm)
REVERT: A  240 SER cc_start: 0.8741 (m) cc_final: 0.8457 (t)
REVERT: A  293 MET cc_start: 0.7201 (ptp) cc_final: 0.6871 (ptp)
REVERT: A  301 THR cc_start: 0.8305 (t) cc_final: 0.8092 (p)
REVERT: A  309 SER cc_start: 0.8324 (t) cc_final: 0.8078 (m)
REVERT: A  334 VAL cc_start: 0.8028 (t) cc_final: 0.7783 (p)
REVERT: A  498 ILE cc_start: 0.8171 (mm) cc_final: 0.7874 (mt)
REVERT: A  568 ASP cc_start: 0.7132 (t0) cc_final: 0.6754 (t0)
REVERT: A  662 LEU cc_start: 0.8756 (mt) cc_final: 0.8468 (mp)
REVERT: A  686 LYS cc_start: 0.7928 (mttp) cc_final: 0.7725 (mttm)
REVERT: A  699 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7486 (mm-30)
REVERT: A  728 LYS cc_start: 0.7810 (mttp) cc_final: 0.7540 (mttm)
REVERT: A  742 LEU cc_start: 0.8374 (mt) cc_final: 0.8102 (mp)
REVERT: B  133 TYR cc_start: 0.7935 (t80) cc_final: 0.7667 (t80)
REVERT: B  293 MET cc_start: 0.6920 (ptp) cc_final: 0.6620 (ptp)
REVERT: B  309 SER cc_start: 0.8354 (t) cc_final: 0.7975 (p)
REVERT: B  334 VAL cc_start: 0.8188 (t) cc_final: 0.7863 (m)
REVERT: B  369 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8222 (ttm170)
REVERT: B  498 ILE cc_start: 0.7989 (mm) cc_final: 0.7622 (mt)
REVERT: B  699 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7673 (mm-30)
REVERT: B  728 LYS cc_start: 0.7877 (mttp) cc_final: 0.7541 (ttmm)
  outliers start: 45
  outliers final: 41
  residues processed: 264
  average time/residue: 0.2423
  time to fit residues: 88.3218
Evaluate side-chains
  272 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 231
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
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  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  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  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 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  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  725 ILE
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:    0.7980
   chunk 109 optimal weight:    0.9980
   chunk 113 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 75 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 116 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 81 optimal weight:    0.9990
   chunk 70 optimal weight:    0.1980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 202 HIS
A 370 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.133594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.116568 restraints weight = 13946.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.09
r_work: 0.3342 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10220  Z= 0.234
  Angle     :  0.562  14.961  13896  Z= 0.275
  Chirality :  0.041   0.151   1668
  Planarity :  0.004   0.052   1730
  Dihedral  :  4.015  17.692   1376
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 18.00 %
    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:  2.01 (0.24), residues: 1284
  helix:  1.99 (0.18), residues: 904
  sheet: -0.74 (0.63), residues: 54
  loop : -0.08 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  80 
 HIS   0.002   0.000   HIS B 512 
 PHE   0.027   0.001   PHE B 720 
 TYR   0.012   0.001   TYR B  29 
 ARG   0.004   0.000   ARG B 180 

*********************** 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
  290 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 245
  time to evaluate  : 1.124 
Fit side-chains
REVERT: A  240 SER cc_start: 0.8725 (m) cc_final: 0.8458 (t)
REVERT: A  293 MET cc_start: 0.7154 (ptp) cc_final: 0.6824 (ptp)
REVERT: A  301 THR cc_start: 0.8263 (t) cc_final: 0.8056 (p)
REVERT: A  309 SER cc_start: 0.8258 (t) cc_final: 0.8019 (m)
REVERT: A  334 VAL cc_start: 0.8033 (t) cc_final: 0.7783 (p)
REVERT: A  498 ILE cc_start: 0.8096 (mm) cc_final: 0.7796 (mt)
REVERT: A  662 LEU cc_start: 0.8758 (mt) cc_final: 0.8457 (mp)
REVERT: A  699 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7400 (mm-30)
REVERT: A  728 LYS cc_start: 0.7813 (mttp) cc_final: 0.7532 (mttm)
REVERT: A  730 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7684 (mp)
REVERT: A  742 LEU cc_start: 0.8340 (mt) cc_final: 0.8074 (mp)
REVERT: B  133 TYR cc_start: 0.7926 (t80) cc_final: 0.7706 (t80)
REVERT: B  293 MET cc_start: 0.6883 (ptp) cc_final: 0.6577 (ptp)
REVERT: B  309 SER cc_start: 0.8336 (t) cc_final: 0.7958 (p)
REVERT: B  334 VAL cc_start: 0.8198 (t) cc_final: 0.7865 (m)
REVERT: B  369 ARG cc_start: 0.8414 (ttm170) cc_final: 0.8202 (ttm170)
REVERT: B  498 ILE cc_start: 0.7942 (mm) cc_final: 0.7564 (mt)
REVERT: B  699 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7619 (mm-30)
REVERT: B  728 LYS cc_start: 0.7883 (mttp) cc_final: 0.7530 (ttmm)
  outliers start: 45
  outliers final: 34
  residues processed: 273
  average time/residue: 0.2393
  time to fit residues: 89.7229
Evaluate side-chains
  273 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 238
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
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  277 LEU
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  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  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  345 VAL
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  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
Chi-restraints excluded: chain B residue  726 THR
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:    0.0870
   chunk 87 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 125 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0970
   chunk 127 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.5556

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

Flipped N/Q/H residues before XYZ refinement:
B 509 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.133439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.116375 restraints weight = 13915.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.09
r_work: 0.3341 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10220  Z= 0.240
  Angle     :  0.576  15.276  13896  Z= 0.280
  Chirality :  0.041   0.186   1668
  Planarity :  0.004   0.054   1730
  Dihedral  :  4.018  17.875   1376
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.27 %
    Favored  : 77.82 %
  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:  2.00 (0.24), residues: 1284
  helix:  1.96 (0.18), residues: 904
  sheet: -0.68 (0.63), 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   0.000   HIS B 735 
 PHE   0.027   0.001   PHE B 720 
 TYR   0.010   0.001   TYR B 550 
 ARG   0.007   0.000   ARG B 544 

*********************** 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
  290 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 247
  time to evaluate  : 1.196 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.7403 (t70) cc_final: 0.7149 (t0)
REVERT: A  240 SER cc_start: 0.8728 (m) cc_final: 0.8433 (t)
REVERT: A  293 MET cc_start: 0.7159 (ptp) cc_final: 0.6834 (ptp)
REVERT: A  301 THR cc_start: 0.8252 (t) cc_final: 0.8046 (p)
REVERT: A  309 SER cc_start: 0.8240 (t) cc_final: 0.8004 (m)
REVERT: A  334 VAL cc_start: 0.8036 (t) cc_final: 0.7791 (p)
REVERT: A  498 ILE cc_start: 0.8080 (mm) cc_final: 0.7780 (mt)
REVERT: A  662 LEU cc_start: 0.8756 (mt) cc_final: 0.8457 (mp)
REVERT: A  699 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7391 (mm-30)
REVERT: A  728 LYS cc_start: 0.7824 (mttp) cc_final: 0.7545 (mttm)
REVERT: A  730 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7659 (mp)
REVERT: A  742 LEU cc_start: 0.8342 (mt) cc_final: 0.8071 (mp)
REVERT: B  133 TYR cc_start: 0.7910 (t80) cc_final: 0.7670 (t80)
REVERT: B  293 MET cc_start: 0.6899 (ptp) cc_final: 0.6613 (ptp)
REVERT: B  309 SER cc_start: 0.8332 (t) cc_final: 0.7949 (p)
REVERT: B  334 VAL cc_start: 0.8193 (t) cc_final: 0.7864 (m)
REVERT: B  369 ARG cc_start: 0.8402 (ttm170) cc_final: 0.8197 (ttm170)
REVERT: B  498 ILE cc_start: 0.7939 (mm) cc_final: 0.7553 (mt)
REVERT: B  699 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7619 (mm-30)
REVERT: B  728 LYS cc_start: 0.7892 (mttp) cc_final: 0.7540 (ttmm)
  outliers start: 43
  outliers final: 38
  residues processed: 273
  average time/residue: 0.2363
  time to fit residues: 89.1335
Evaluate side-chains
  283 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 244
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
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  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  424 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  444 VAL
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  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  345 VAL
Chi-restraints excluded: chain B residue  360 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  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
Chi-restraints excluded: chain B residue  726 THR
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:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 115 optimal weight:    0.5980
   chunk 59 optimal weight:    0.4980
   chunk 54 optimal weight:    0.9990
   chunk 124 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 48 optimal weight:    0.1980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3707 r_free = 0.3707 target = 0.134995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.117737 restraints weight = 13983.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.14
r_work: 0.3347 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10220  Z= 0.237
  Angle     :  0.579  15.437  13896  Z= 0.281
  Chirality :  0.042   0.233   1668
  Planarity :  0.004   0.053   1730
  Dihedral  :  4.004  17.838   1376
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.73 %
    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:  2.01 (0.24), residues: 1284
  helix:  1.96 (0.18), residues: 904
  sheet: -0.61 (0.64), residues: 54
  loop : -0.00 (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   0.033   0.002   PHE B 720 
 TYR   0.010   0.001   TYR A 550 
 ARG   0.006   0.000   ARG B 544 

********************** 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
  283 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 242
  time to evaluate  : 1.069 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.7450 (t70) cc_final: 0.7074 (t0)
REVERT: A  102 ILE cc_start: 0.8333 (mm) cc_final: 0.8078 (tp)
REVERT: A  240 SER cc_start: 0.8721 (m) cc_final: 0.8457 (t)
REVERT: A  293 MET cc_start: 0.7157 (ptp) cc_final: 0.6824 (ptp)
REVERT: A  301 THR cc_start: 0.8226 (t) cc_final: 0.8025 (p)
REVERT: A  309 SER cc_start: 0.8230 (t) cc_final: 0.8000 (m)
REVERT: A  334 VAL cc_start: 0.8060 (t) cc_final: 0.7804 (p)
REVERT: A  498 ILE cc_start: 0.8073 (mm) cc_final: 0.7780 (mt)
REVERT: A  662 LEU cc_start: 0.8753 (mt) cc_final: 0.8456 (mp)
REVERT: A  699 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7392 (mm-30)
REVERT: A  728 LYS cc_start: 0.7833 (mttp) cc_final: 0.7546 (mttm)
REVERT: A  730 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7655 (mp)
REVERT: A  742 LEU cc_start: 0.8335 (mt) cc_final: 0.8064 (mp)
REVERT: B  209 TYR cc_start: 0.8178 (m-10) cc_final: 0.7948 (m-10)
REVERT: B  293 MET cc_start: 0.6879 (ptp) cc_final: 0.6588 (ptp)
REVERT: B  309 SER cc_start: 0.8313 (t) cc_final: 0.7932 (p)
REVERT: B  334 VAL cc_start: 0.8193 (t) cc_final: 0.7860 (m)
REVERT: B  498 ILE cc_start: 0.7908 (mm) cc_final: 0.7520 (mt)
REVERT: B  699 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7618 (mm-30)
REVERT: B  728 LYS cc_start: 0.7899 (mttp) cc_final: 0.7549 (ttmm)
  outliers start: 41
  outliers final: 35
  residues processed: 267
  average time/residue: 0.2346
  time to fit residues: 86.4011
Evaluate side-chains
  275 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 239
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
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  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  424 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  444 VAL
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  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  345 VAL
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  401 SER
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
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 119 optimal weight:    0.0010
   chunk 56 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 107 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 81 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0270
   overall best weight:    0.3844

-------------------------------------------------------------------------------
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 = 0.3705 r_free = 0.3705 target = 0.134691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.117587 restraints weight = 13898.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.09
r_work: 0.3361 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10220  Z= 0.205
  Angle     :  0.579  15.545  13896  Z= 0.280
  Chirality :  0.041   0.230   1668
  Planarity :  0.004   0.053   1730
  Dihedral  :  3.960  17.316   1376
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.00 %
    Favored  : 77.73 %
  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:  2.10 (0.24), residues: 1284
  helix:  2.01 (0.18), residues: 904
  sheet: -0.47 (0.65), residues: 54
  loop :  0.05 (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 735 
 PHE   0.039   0.002   PHE B 571 
 TYR   0.010   0.001   TYR A 550 
 ARG   0.007   0.000   ARG B 544 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5007.69 seconds
wall clock time: 90 minutes 40.31 seconds (5440.31 seconds total)