Starting phenix.real_space_refine
on Thu Mar 13 10:53:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v1q_21015/03_2025/6v1q_21015.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v1q_21015/03_2025/6v1q_21015.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v1q_21015/03_2025/6v1q_21015.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v1q_21015/03_2025/6v1q_21015.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v1q_21015/03_2025/6v1q_21015.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v1q_21015/03_2025/6v1q_21015.cif"
  }
  resolution = 3.11
  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=   0.082
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
     Na      1      4.78       5
     C    5920      2.51       5
     N    1402      2.21       5
     O    1464      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8825
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 538, 4412
          Classifications: {'peptide': 538}
          Link IDs: {'PTRANS': 17, 'TRANS': 520}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.20, per 1000 atoms: 0.93
  Number of scatterers: 8825
  At special positions: 0
  Unit cell: (124.344, 116.808, 97.968, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     Na      1     11.00
     O    1464      8.00
     N    1402      7.00
     C    5920      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: 2.22
  Conformation dependent library (CDL) restraints added in 968.3 milliseconds
  

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 0 sheets defined
      70.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 46
    Processing helix  chain 'A' and resid 63 through 70
    Processing helix  chain 'A' and resid 71 through 88
      removed outlier: 3.641A  pdb=" N   TYR A  79 " --> pdb=" O   GLN A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 91
      No H-bonds generated for 'chain 'A' and resid 89 through 91'
    Processing helix  chain 'A' and resid 100 through 126
      removed outlier: 3.696A  pdb=" N   ILE A 107 " --> pdb=" O   ALA A 103 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLU A 108 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE A 110 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 154
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 171 through 179
      removed outlier: 3.742A  pdb=" N   LEU A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LEU A 176 " --> pdb=" O   ARG A 172 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 220
      removed outlier: 3.524A  pdb=" N   ARG A 187 " --> pdb=" O   ARG A 183 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ALA A 188 " --> pdb=" O   GLN A 184 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ILE A 192 " --> pdb=" O   ALA A 188 " (cutoff:3.500A)
      Proline residue:  A 197  - end of helix
      removed outlier: 3.976A  pdb=" N   TYR A 201 " --> pdb=" O   PRO A 197 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LEU A 205 " --> pdb=" O   TYR A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 250
      removed outlier: 3.732A  pdb=" N   PHE A 243 " --> pdb=" O   MET A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 268 through 279
      removed outlier: 3.836A  pdb=" N   PHE A 272 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 300
      removed outlier: 3.812A  pdb=" N   LEU A 288 " --> pdb=" O   MET A 284 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS A 300 " --> pdb=" O   LYS A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 320
      removed outlier: 4.862A  pdb=" N   LYS A 313 " --> pdb=" O   ALA A 309 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   PHE A 318 " --> pdb=" O   MET A 314 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   SER A 319 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 415
    Processing helix  chain 'A' and resid 420 through 432
    Processing helix  chain 'A' and resid 441 through 457
      removed outlier: 3.709A  pdb=" N   ALA A 447 " --> pdb=" O   VAL A 443 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   TRP A 449 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY A 450 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 490
      removed outlier: 3.544A  pdb=" N   THR A 483 " --> pdb=" O   ASN A 479 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE A 484 " --> pdb=" O   TRP A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 500
      removed outlier: 3.786A  pdb=" N   ILE A 495 " --> pdb=" O   PHE A 491 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LYS A 500 " --> pdb=" O   ASN A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 522
      removed outlier: 4.096A  pdb=" N   ILE A 516 " --> pdb=" O   ASP A 512 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU A 517 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LEU A 520 " --> pdb=" O   ILE A 516 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG A 521 " --> pdb=" O   LEU A 517 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU A 522 " --> pdb=" O   ARG A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 530
    Processing helix  chain 'A' and resid 543 through 568
      removed outlier: 4.197A  pdb=" N   LEU A 547 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   LEU A 554 " --> pdb=" O   GLY A 550 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU A 566 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 567 " --> pdb=" O   VAL A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 584
    Processing helix  chain 'A' and resid 589 through 593
    Processing helix  chain 'A' and resid 609 through 622
      removed outlier: 3.602A  pdb=" N   LEU A 616 " --> pdb=" O   SER A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 634
      removed outlier: 3.504A  pdb=" N   PHE A 633 " --> pdb=" O   LEU A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 641 through 653
      removed outlier: 3.820A  pdb=" N   PHE A 645 " --> pdb=" O   ALA A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 670
      removed outlier: 3.704A  pdb=" N   PHE A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   PHE A 668 " --> pdb=" O   ILE A 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 46
    Processing helix  chain 'B' and resid 63 through 70
    Processing helix  chain 'B' and resid 71 through 88
      removed outlier: 3.641A  pdb=" N   TYR B  79 " --> pdb=" O   GLN B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 91
      No H-bonds generated for 'chain 'B' and resid 89 through 91'
    Processing helix  chain 'B' and resid 100 through 126
      removed outlier: 3.697A  pdb=" N   ILE B 107 " --> pdb=" O   ALA B 103 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLU B 108 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE B 110 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 154
    Processing helix  chain 'B' and resid 168 through 170
      No H-bonds generated for 'chain 'B' and resid 168 through 170'
    Processing helix  chain 'B' and resid 171 through 179
      removed outlier: 3.742A  pdb=" N   LEU B 175 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LEU B 176 " --> pdb=" O   ARG B 172 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL B 177 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 220
      removed outlier: 3.524A  pdb=" N   ARG B 187 " --> pdb=" O   ARG B 183 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ALA B 188 " --> pdb=" O   GLN B 184 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ILE B 192 " --> pdb=" O   ALA B 188 " (cutoff:3.500A)
      Proline residue:  B 197  - end of helix
      removed outlier: 3.976A  pdb=" N   TYR B 201 " --> pdb=" O   PRO B 197 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LEU B 205 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 250
      removed outlier: 3.733A  pdb=" N   PHE B 243 " --> pdb=" O   MET B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 267
      No H-bonds generated for 'chain 'B' and resid 265 through 267'
    Processing helix  chain 'B' and resid 268 through 279
      removed outlier: 3.835A  pdb=" N   PHE B 272 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 300
      removed outlier: 3.813A  pdb=" N   LEU B 288 " --> pdb=" O   MET B 284 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS B 300 " --> pdb=" O   LYS B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 320
      removed outlier: 4.861A  pdb=" N   LYS B 313 " --> pdb=" O   ALA B 309 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   PHE B 318 " --> pdb=" O   MET B 314 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   SER B 319 " --> pdb=" O   CYS B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 415
    Processing helix  chain 'B' and resid 420 through 432
    Processing helix  chain 'B' and resid 441 through 457
      removed outlier: 3.709A  pdb=" N   ALA B 447 " --> pdb=" O   VAL B 443 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   TRP B 449 " --> pdb=" O   SER B 445 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLY B 450 " --> pdb=" O   ASN B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 490
      removed outlier: 3.544A  pdb=" N   THR B 483 " --> pdb=" O   ASN B 479 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE B 484 " --> pdb=" O   TRP B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 500
      removed outlier: 3.787A  pdb=" N   ILE B 495 " --> pdb=" O   PHE B 491 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LYS B 500 " --> pdb=" O   ASN B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 522
      removed outlier: 4.096A  pdb=" N   ILE B 516 " --> pdb=" O   ASP B 512 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LEU B 517 " --> pdb=" O   ILE B 513 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LEU B 520 " --> pdb=" O   ILE B 516 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG B 521 " --> pdb=" O   LEU B 517 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU B 522 " --> pdb=" O   ARG B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 530
    Processing helix  chain 'B' and resid 543 through 568
      removed outlier: 4.197A  pdb=" N   LEU B 547 " --> pdb=" O   GLY B 543 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LEU B 554 " --> pdb=" O   GLY B 550 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU B 566 " --> pdb=" O   MET B 562 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU B 567 " --> pdb=" O   VAL B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 584
    Processing helix  chain 'B' and resid 589 through 593
    Processing helix  chain 'B' and resid 609 through 622
      removed outlier: 3.602A  pdb=" N   LEU B 616 " --> pdb=" O   SER B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 634
      removed outlier: 3.504A  pdb=" N   PHE B 633 " --> pdb=" O   LEU B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 640
      No H-bonds generated for 'chain 'B' and resid 638 through 640'
    Processing helix  chain 'B' and resid 641 through 653
      removed outlier: 3.820A  pdb=" N   PHE B 645 " --> pdb=" O   ALA B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 656 through 670
      removed outlier: 3.704A  pdb=" N   PHE B 663 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   PHE B 668 " --> pdb=" O   ILE B 664 " (cutoff:3.500A)

    452 hydrogen bonds defined for protein.
    1302 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.21

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1286
        1.28 -     1.41: 2510
        1.41 -     1.54: 5151
        1.54 -     1.67: 43
        1.67 -     1.81: 66
  Bond restraints: 9056
  Sorted by residual:
  bond pdb=" CA  PRO A 135 "
       pdb=" C   PRO A 135 "
    ideal  model  delta    sigma   weight residual
    1.516  1.411  0.105 1.42e-02 4.96e+03 5.51e+01
  bond pdb=" CA  PRO B 135 "
       pdb=" C   PRO B 135 "
    ideal  model  delta    sigma   weight residual
    1.516  1.411  0.105 1.42e-02 4.96e+03 5.48e+01
  bond pdb=" C   ASP B 134 "
       pdb=" O   ASP B 134 "
    ideal  model  delta    sigma   weight residual
    1.237  1.142  0.095 1.29e-02 6.01e+03 5.43e+01
  bond pdb=" C   ASP A 134 "
       pdb=" O   ASP A 134 "
    ideal  model  delta    sigma   weight residual
    1.237  1.143  0.095 1.29e-02 6.01e+03 5.37e+01
  bond pdb=" N   LYS B 133 "
       pdb=" CA  LYS B 133 "
    ideal  model  delta    sigma   weight residual
    1.456  1.364  0.093 1.33e-02 5.65e+03 4.85e+01
  ... (remaining 9051 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.00: 12070
        3.00 -     5.99: 192
        5.99 -     8.99: 32
        8.99 -    11.99: 10
       11.99 -    14.99: 6
  Bond angle restraints: 12310
  Sorted by residual:
  angle pdb=" C   ILE A 459 "
        pdb=" N   LEU A 460 "
        pdb=" CA  LEU A 460 "
      ideal   model   delta    sigma   weight residual
     121.83  135.59  -13.76 1.48e+00 4.57e-01 8.64e+01
  angle pdb=" C   ILE B 459 "
        pdb=" N   LEU B 460 "
        pdb=" CA  LEU B 460 "
      ideal   model   delta    sigma   weight residual
     121.83  135.58  -13.75 1.48e+00 4.57e-01 8.63e+01
  angle pdb=" N   TYR B 262 "
        pdb=" CA  TYR B 262 "
        pdb=" C   TYR B 262 "
      ideal   model   delta    sigma   weight residual
     114.75  105.22    9.53 1.26e+00 6.30e-01 5.72e+01
  angle pdb=" N   TYR A 262 "
        pdb=" CA  TYR A 262 "
        pdb=" C   TYR A 262 "
      ideal   model   delta    sigma   weight residual
     114.75  105.25    9.50 1.26e+00 6.30e-01 5.68e+01
  angle pdb=" CA  ILE B 459 "
        pdb=" C   ILE B 459 "
        pdb=" N   LEU B 460 "
      ideal   model   delta    sigma   weight residual
     116.60  105.71   10.89 1.45e+00 4.76e-01 5.64e+01
  ... (remaining 12305 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 4513
       17.64 -    35.29: 577
       35.29 -    52.93: 152
       52.93 -    70.57: 26
       70.57 -    88.22: 10
  Dihedral angle restraints: 5278
    sinusoidal: 2072
      harmonic: 3206
  Sorted by residual:
  dihedral pdb=" CA  LYS A 541 "
           pdb=" C   LYS A 541 "
           pdb=" N   ILE A 542 "
           pdb=" CA  ILE A 542 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.46  -48.54     0      5.00e+00 4.00e-02 9.42e+01
  dihedral pdb=" CA  LYS B 541 "
           pdb=" C   LYS B 541 "
           pdb=" N   ILE B 542 "
           pdb=" CA  ILE B 542 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.50  -48.50     0      5.00e+00 4.00e-02 9.41e+01
  dihedral pdb=" C   LEU A 457 "
           pdb=" N   LEU A 457 "
           pdb=" CA  LEU A 457 "
           pdb=" CB  LEU A 457 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -143.97   21.37     0      2.50e+00 1.60e-01 7.31e+01
  ... (remaining 5275 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.179: 1438
       0.179 -    0.357: 6
       0.357 -    0.536: 2
       0.536 -    0.715: 2
       0.715 -    0.893: 4
  Chirality restraints: 1452
  Sorted by residual:
  chirality pdb=" CG  LEU B 461 "
            pdb=" CB  LEU B 461 "
            pdb=" CD1 LEU B 461 "
            pdb=" CD2 LEU B 461 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.70   -0.89 2.00e-01 2.50e+01 1.99e+01
  chirality pdb=" CG  LEU A 461 "
            pdb=" CB  LEU A 461 "
            pdb=" CD1 LEU A 461 "
            pdb=" CD2 LEU A 461 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.70   -0.89 2.00e-01 2.50e+01 1.99e+01
  chirality pdb=" CA  LEU A 457 "
            pdb=" N   LEU A 457 "
            pdb=" C   LEU A 457 "
            pdb=" CB  LEU A 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.64    0.87 2.00e-01 2.50e+01 1.91e+01
  ... (remaining 1449 not shown)

  Planarity restraints: 1482
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 224 "    1.051 9.50e-02 1.11e+02   4.71e-01 1.34e+02
        pdb=" NE  ARG A 224 "   -0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 224 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 224 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 224 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 224 "   -1.051 9.50e-02 1.11e+02   4.71e-01 1.34e+02
        pdb=" NE  ARG B 224 "    0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 224 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 224 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 224 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 456 "   -0.038 2.00e-02 2.50e+03   7.23e-02 5.22e+01
        pdb=" C   MET A 456 "    0.125 2.00e-02 2.50e+03
        pdb=" O   MET A 456 "   -0.046 2.00e-02 2.50e+03
        pdb=" N   LEU A 457 "   -0.041 2.00e-02 2.50e+03
  ... (remaining 1479 not shown)

  Histogram of nonbonded interaction distances:
        1.40 -     2.10: 10
        2.10 -     2.80: 2776
        2.80 -     3.50: 12517
        3.50 -     4.20: 21187
        4.20 -     4.90: 36947
  Nonbonded interactions: 73437
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 224 "
            pdb=" OE1 GLU B 440 "
     model   vdw
     1.396 3.120
  nonbonded pdb=" OE1 GLU A 440 "
            pdb=" NH2 ARG B 224 "
     model   vdw
     1.396 3.120
  nonbonded pdb=" NZ  LYS A 219 "
            pdb=" OD2 ASP B 438 "
     model   vdw
     1.777 3.120
  nonbonded pdb=" OD2 ASP A 438 "
            pdb=" NZ  LYS B 219 "
     model   vdw
     1.786 3.120
  nonbonded pdb=" NZ  LYS A 223 "
            pdb=" OE2 GLU B 439 "
     model   vdw
     1.852 3.120
  ... (remaining 73432 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 34 through 672)
  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:             1.260
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.810
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.105   9056  Z= 0.534
  Angle     :  1.007  14.986  12310  Z= 0.596
  Chirality :  0.073   0.893   1452
  Planarity :  0.018   0.471   1482
  Dihedral  : 17.131  88.216   3198
  Min Nonbonded Distance : 1.396

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  9.40 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  7.48 %
    Allowed  : 18.14 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.58 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.86 (0.21), residues: 1064
  helix: -2.97 (0.15), residues: 686
  sheet:  None (None), residues: 0
  loop : -3.44 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 626 
 HIS   0.003   0.001   HIS B 121 
 PHE   0.010   0.001   PHE B 420 
 TYR   0.015   0.002   TYR B 163 
 ARG   0.004   0.000   ARG B 531 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 77
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5619 (ttmt)
REVERT: A  441 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8610 (p0)
REVERT: A  541 LYS cc_start: 0.2714 (OUTLIER) cc_final: 0.2039 (mmtt)
REVERT: A  546 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8202 (tp)
REVERT: B  223 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5662 (ttmt)
REVERT: B  441 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8481 (p0)
REVERT: B  541 LYS cc_start: 0.2774 (OUTLIER) cc_final: 0.2056 (mmtt)
REVERT: B  546 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8294 (tp)
  outliers start: 73
  outliers final: 35
  residues processed: 146
  average time/residue: 0.2101
  time to fit residues: 42.6187
Evaluate side-chains
  100 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 57
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  223 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  310 LYS
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  315 CYS
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  441 ASN
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  532 PHE
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  546 ILE
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  149 ILE
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  223 LYS
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  310 LYS
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  315 CYS
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  441 ASN
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  532 PHE
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  546 ILE
Chi-restraints excluded: chain B residue  587 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
A 263 ASN
A 279 ASN
A 649 HIS
A 658 ASN
B 194 ASN
B 263 ASN
B 279 ASN
** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 649 HIS
B 658 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.064492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.055856 restraints weight = 44773.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 3.62
r_work: 0.3168 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9056  Z= 0.195
  Angle     :  0.705  10.625  12310  Z= 0.369
  Chirality :  0.044   0.153   1452
  Planarity :  0.005   0.043   1482
  Dihedral  :  9.704  57.018   1274
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 19.88 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -2.81 (0.25), residues: 1064
  helix: -1.31 (0.19), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.74 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 478 
 HIS   0.003   0.001   HIS B  71 
 PHE   0.020   0.001   PHE A 560 
 TYR   0.014   0.001   TYR A 424 
 ARG   0.005   0.000   ARG B 169 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 70
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 MET cc_start: 0.9130 (ttp) cc_final: 0.8901 (ttp)
REVERT: A  647 ILE cc_start: 0.9720 (mt) cc_final: 0.9510 (pt)
REVERT: B  461 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.4925 (tp)
REVERT: B  565 MET cc_start: 0.8861 (ptp) cc_final: 0.8559 (ptp)
REVERT: B  647 ILE cc_start: 0.9732 (mt) cc_final: 0.9480 (pt)
  outliers start: 56
  outliers final: 20
  residues processed: 118
  average time/residue: 0.1890
  time to fit residues: 32.2724
Evaluate side-chains
  83 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  310 LYS
Chi-restraints excluded: chain A residue  315 CYS
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain B residue  149 ILE
Chi-restraints excluded: chain B residue  259 MET
Chi-restraints excluded: chain B residue  315 CYS
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  506 THR
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  664 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   chunk 87 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0370
   overall best weight:    1.1664

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 ASN
** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.064472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.055768 restraints weight = 46689.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 3.65
r_work: 0.3173 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9056  Z= 0.200
  Angle     :  0.656   8.557  12310  Z= 0.346
  Chirality :  0.044   0.245   1452
  Planarity :  0.003   0.023   1482
  Dihedral  :  7.198  54.840   1200
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 21.00 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 (0.26), residues: 1064
  helix: -0.60 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -2.63 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 626 
 HIS   0.002   0.001   HIS B 501 
 PHE   0.017   0.001   PHE B 560 
 TYR   0.024   0.001   TYR B 201 
 ARG   0.005   0.000   ARG B 531 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 61
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8278 (t0)
REVERT: A  151 MET cc_start: 0.9143 (ttp) cc_final: 0.8877 (ttp)
REVERT: A  573 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.9010 (pm20)
REVERT: A  647 ILE cc_start: 0.9717 (mt) cc_final: 0.9473 (pt)
REVERT: B   70 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8345 (t0)
REVERT: B  461 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.5988 (tp)
REVERT: B  573 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.9021 (pm20)
REVERT: B  647 ILE cc_start: 0.9728 (mt) cc_final: 0.9452 (pt)
  outliers start: 31
  outliers final: 14
  residues processed: 86
  average time/residue: 0.1866
  time to fit residues: 23.8470
Evaluate side-chains
  73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  506 THR
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  664 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 73 optimal weight:    0.8980
   chunk 78 optimal weight:    5.9990
   chunk 92 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0570
   overall best weight:    1.3904

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

Flipped N/Q/H residues before XYZ refinement:
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.063784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.055028 restraints weight = 46601.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 3.73
r_work: 0.3162 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9056  Z= 0.205
  Angle     :  0.648   8.866  12310  Z= 0.337
  Chirality :  0.043   0.229   1452
  Planarity :  0.003   0.021   1482
  Dihedral  :  6.577  49.079   1188
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.39 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.61 (0.26), residues: 1064
  helix: -0.30 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.46 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 626 
 HIS   0.003   0.001   HIS B  71 
 PHE   0.016   0.001   PHE A 560 
 TYR   0.021   0.001   TYR B 201 
 ARG   0.003   0.000   ARG A 531 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 59
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 MET cc_start: 0.9137 (ttp) cc_final: 0.8884 (ttp)
REVERT: A  562 MET cc_start: 0.9517 (mmp) cc_final: 0.9199 (mmp)
REVERT: A  647 ILE cc_start: 0.9733 (mt) cc_final: 0.9469 (pt)
REVERT: B  201 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.7095 (m-80)
REVERT: B  562 MET cc_start: 0.9506 (mmp) cc_final: 0.9129 (mmp)
REVERT: B  647 ILE cc_start: 0.9741 (mt) cc_final: 0.9468 (pt)
  outliers start: 37
  outliers final: 20
  residues processed: 90
  average time/residue: 0.1842
  time to fit residues: 24.8773
Evaluate side-chains
  75 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  506 THR
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  664 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 33 optimal weight:    0.1980
   chunk 63 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0010
   chunk 93 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 625 GLN
B  70 ASN
** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 625 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.065526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.056664 restraints weight = 45627.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 3.72
r_work: 0.3214 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9056  Z= 0.150
  Angle     :  0.612   7.429  12310  Z= 0.316
  Chirality :  0.042   0.193   1452
  Planarity :  0.003   0.021   1482
  Dihedral  :  6.003  45.913   1184
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.72 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.48 (0.27), residues: 1064
  helix: -0.12 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -2.68 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 626 
 HIS   0.002   0.001   HIS B 649 
 PHE   0.016   0.001   PHE A 560 
 TYR   0.016   0.001   TYR A 424 
 ARG   0.003   0.000   ARG A 531 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8599 (pt0)
REVERT: A  151 MET cc_start: 0.9133 (ttp) cc_final: 0.8876 (ttp)
REVERT: A  201 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6957 (m-10)
REVERT: A  461 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.5554 (tt)
REVERT: A  573 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.9043 (pm20)
REVERT: A  647 ILE cc_start: 0.9728 (mt) cc_final: 0.9467 (pt)
REVERT: B   70 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8276 (t0)
REVERT: B  201 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.7106 (m-80)
REVERT: B  461 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6297 (tt)
REVERT: B  573 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.9055 (pm20)
REVERT: B  647 ILE cc_start: 0.9737 (mt) cc_final: 0.9462 (pt)
  outliers start: 29
  outliers final: 8
  residues processed: 101
  average time/residue: 0.2174
  time to fit residues: 31.7057
Evaluate side-chains
  78 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 1.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 GLU
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  664 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0070
   chunk 44 optimal weight:    0.0270
   chunk 93 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7660

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.065186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.056616 restraints weight = 45517.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 3.69
r_work: 0.3213 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9056  Z= 0.165
  Angle     :  0.616   7.944  12310  Z= 0.318
  Chirality :  0.042   0.171   1452
  Planarity :  0.003   0.024   1482
  Dihedral  :  5.528  44.545   1176
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.16 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.30 (0.27), residues: 1064
  helix:  0.08 (0.21), residues: 698
  sheet:  None (None), residues: 0
  loop : -2.73 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 478 
 HIS   0.004   0.001   HIS A 649 
 PHE   0.015   0.001   PHE B 560 
 TYR   0.016   0.001   TYR B 201 
 ARG   0.006   0.000   ARG A 518 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 64
  time to evaluate  : 1.363 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8467 (t0)
REVERT: A   74 MET cc_start: 0.8664 (mmm) cc_final: 0.8138 (mpp)
REVERT: A  151 MET cc_start: 0.9118 (ttp) cc_final: 0.8899 (ttp)
REVERT: A  201 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.7142 (m-10)
REVERT: A  461 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.5793 (tt)
REVERT: A  573 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.9050 (pm20)
REVERT: A  647 ILE cc_start: 0.9737 (mt) cc_final: 0.9446 (pt)
REVERT: B   74 MET cc_start: 0.8661 (mmm) cc_final: 0.8162 (mpp)
REVERT: B  201 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7343 (m-80)
REVERT: B  461 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6146 (tt)
REVERT: B  562 MET cc_start: 0.9492 (mmp) cc_final: 0.9178 (mmp)
REVERT: B  573 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.9060 (pm20)
REVERT: B  647 ILE cc_start: 0.9737 (mt) cc_final: 0.9440 (pt)
REVERT: B  655 ILE cc_start: 0.9559 (OUTLIER) cc_final: 0.9256 (mp)
  outliers start: 29
  outliers final: 10
  residues processed: 89
  average time/residue: 0.1983
  time to fit residues: 27.0329
Evaluate side-chains
  78 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  664 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 37 optimal weight:    8.9990
   chunk 96 optimal weight:    0.4980
   chunk 53 optimal weight:   10.0000
   chunk 34 optimal weight:    0.4980
   chunk 93 optimal weight:    0.5980
   chunk 19 optimal weight:    8.9990
   chunk 91 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
B  70 ASN
** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.064991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.056395 restraints weight = 45912.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 3.67
r_work: 0.3203 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9056  Z= 0.188
  Angle     :  0.635   8.204  12310  Z= 0.326
  Chirality :  0.043   0.223   1452
  Planarity :  0.003   0.027   1482
  Dihedral  :  5.493  43.759   1176
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.67 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.16 (0.27), residues: 1064
  helix:  0.13 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -2.56 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 626 
 HIS   0.004   0.001   HIS A  71 
 PHE   0.014   0.001   PHE B 560 
 TYR   0.017   0.001   TYR B 201 
 ARG   0.005   0.000   ARG A 518 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 64
  time to evaluate  : 1.132 
Fit side-chains
REVERT: A   70 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8203 (t0)
REVERT: A   74 MET cc_start: 0.8705 (mmm) cc_final: 0.8189 (mpp)
REVERT: A  151 MET cc_start: 0.9110 (ttp) cc_final: 0.8893 (ttp)
REVERT: A  201 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.7179 (m-10)
REVERT: A  461 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6106 (tt)
REVERT: A  573 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.9023 (pm20)
REVERT: A  647 ILE cc_start: 0.9742 (mt) cc_final: 0.9463 (pt)
REVERT: B   70 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8337 (t0)
REVERT: B   74 MET cc_start: 0.8677 (mmm) cc_final: 0.8165 (mpp)
REVERT: B  201 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.7225 (m-10)
REVERT: B  461 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6251 (tt)
REVERT: B  573 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.9024 (pm20)
REVERT: B  647 ILE cc_start: 0.9751 (mt) cc_final: 0.9472 (pt)
  outliers start: 32
  outliers final: 10
  residues processed: 93
  average time/residue: 0.2445
  time to fit residues: 34.7863
Evaluate side-chains
  76 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  664 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 43 optimal weight:    0.0970
   chunk 26 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 625 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.065472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.056589 restraints weight = 46521.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.76
r_work: 0.3207 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9056  Z= 0.165
  Angle     :  0.636   8.450  12310  Z= 0.322
  Chirality :  0.043   0.203   1452
  Planarity :  0.003   0.027   1482
  Dihedral  :  5.461  42.893   1176
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 24.69 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.07 (0.27), residues: 1064
  helix:  0.19 (0.20), residues: 700
  sheet:  None (None), residues: 0
  loop : -2.50 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 626 
 HIS   0.005   0.001   HIS A  71 
 PHE   0.015   0.001   PHE B 560 
 TYR   0.016   0.001   TYR B 201 
 ARG   0.003   0.000   ARG A 518 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 62
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A   74 MET cc_start: 0.8695 (mmm) cc_final: 0.8172 (mpp)
REVERT: A  151 MET cc_start: 0.9101 (ttp) cc_final: 0.8891 (ttp)
REVERT: A  201 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.7200 (m-10)
REVERT: A  461 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6029 (tt)
REVERT: A  573 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.9050 (pm20)
REVERT: A  647 ILE cc_start: 0.9739 (mt) cc_final: 0.9466 (pt)
REVERT: B   74 MET cc_start: 0.8690 (mmm) cc_final: 0.8178 (mpp)
REVERT: B  201 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.7226 (m-10)
REVERT: B  461 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6190 (tt)
REVERT: B  573 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.9048 (pm20)
REVERT: B  647 ILE cc_start: 0.9748 (mt) cc_final: 0.9474 (pt)
  outliers start: 26
  outliers final: 14
  residues processed: 84
  average time/residue: 0.1576
  time to fit residues: 21.0192
Evaluate side-chains
  79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  149 ILE
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  664 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0270
   chunk 33 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
A 608 ASN
B  70 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.066099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.057161 restraints weight = 46157.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 3.84
r_work: 0.3228 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9056  Z= 0.153
  Angle     :  0.628   8.787  12310  Z= 0.315
  Chirality :  0.042   0.177   1452
  Planarity :  0.003   0.028   1482
  Dihedral  :  5.320  41.227   1176
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 25.61 %
    Favored  : 71.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.04 (0.27), residues: 1064
  helix:  0.21 (0.20), residues: 714
  sheet:  None (None), residues: 0
  loop : -2.55 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 626 
 HIS   0.003   0.001   HIS A 649 
 PHE   0.013   0.001   PHE A 560 
 TYR   0.015   0.001   TYR B 201 
 ARG   0.003   0.000   ARG A 166 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A   70 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8359 (t0)
REVERT: A   74 MET cc_start: 0.8699 (mmm) cc_final: 0.8183 (mpp)
REVERT: A  186 ARG cc_start: 0.8590 (ptt90) cc_final: 0.7944 (tpt170)
REVERT: A  201 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.7194 (m-10)
REVERT: A  461 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.5958 (tt)
REVERT: A  573 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9031 (pm20)
REVERT: A  647 ILE cc_start: 0.9741 (mt) cc_final: 0.9474 (pt)
REVERT: A  655 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9245 (mp)
REVERT: B   70 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8237 (t0)
REVERT: B   74 MET cc_start: 0.8680 (mmm) cc_final: 0.8160 (mpp)
REVERT: B  201 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7236 (m-10)
REVERT: B  461 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.5956 (tt)
REVERT: B  573 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.9050 (pm20)
REVERT: B  647 ILE cc_start: 0.9747 (mt) cc_final: 0.9462 (pt)
REVERT: B  670 VAL cc_start: 0.9234 (t) cc_final: 0.9014 (m)
  outliers start: 24
  outliers final: 11
  residues processed: 87
  average time/residue: 0.1620
  time to fit residues: 22.1121
Evaluate side-chains
  81 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  149 ILE
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  664 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 100 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.064807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.055993 restraints weight = 46309.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 3.73
r_work: 0.3185 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9056  Z= 0.215
  Angle     :  0.663   9.142  12310  Z= 0.334
  Chirality :  0.043   0.204   1452
  Planarity :  0.003   0.026   1482
  Dihedral  :  5.386  40.854   1176
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 25.82 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.27), residues: 1064
  helix:  0.23 (0.20), residues: 714
  sheet:  None (None), residues: 0
  loop : -2.46 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 480 
 HIS   0.005   0.001   HIS B  71 
 PHE   0.013   0.001   PHE B 560 
 TYR   0.018   0.001   TYR B 201 
 ARG   0.003   0.000   ARG A 518 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.998 
Fit side-chains
REVERT: A   70 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8303 (t0)
REVERT: A  201 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7206 (m-10)
REVERT: A  562 MET cc_start: 0.9398 (mmp) cc_final: 0.8943 (mmp)
REVERT: A  573 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8996 (pm20)
REVERT: A  647 ILE cc_start: 0.9754 (mt) cc_final: 0.9447 (pt)
REVERT: A  655 ILE cc_start: 0.9549 (pt) cc_final: 0.9279 (mp)
REVERT: B  201 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7243 (m-10)
REVERT: B  562 MET cc_start: 0.9362 (mmp) cc_final: 0.8895 (mmp)
REVERT: B  573 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.9058 (pm20)
REVERT: B  647 ILE cc_start: 0.9759 (mt) cc_final: 0.9475 (pt)
  outliers start: 23
  outliers final: 14
  residues processed: 75
  average time/residue: 0.1580
  time to fit residues: 18.4987
Evaluate side-chains
  75 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  149 ILE
Chi-restraints excluded: chain B residue  201 TYR
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  655 ILE
Chi-restraints excluded: chain B residue  664 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0670
   chunk 35 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.065680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.056851 restraints weight = 46100.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 3.75
r_work: 0.3217 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9056  Z= 0.163
  Angle     :  0.650   9.348  12310  Z= 0.324
  Chirality :  0.043   0.187   1452
  Planarity :  0.003   0.025   1482
  Dihedral  :  5.334  41.053   1176
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 25.92 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.27), residues: 1064
  helix:  0.26 (0.21), residues: 714
  sheet:  None (None), residues: 0
  loop : -2.45 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 626 
 HIS   0.003   0.001   HIS A 649 
 PHE   0.013   0.001   PHE B 560 
 TYR   0.015   0.001   TYR B 201 
 ARG   0.003   0.000   ARG A 518 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3868.52 seconds
wall clock time: 68 minutes 15.89 seconds (4095.89 seconds total)