Starting phenix.real_space_refine
on Sat May 17 17:17:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dpa_47100/05_2025/9dpa_47100.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dpa_47100/05_2025/9dpa_47100.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dpa_47100/05_2025/9dpa_47100.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dpa_47100/05_2025/9dpa_47100.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dpa_47100/05_2025/9dpa_47100.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dpa_47100/05_2025/9dpa_47100.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7580 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      78      5.49       5
     S      56      5.16       5
     Na      1      4.78       5
     C    5996      2.51       5
     N    1691      2.21       5
     O    2056      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9878
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 4100
          Classifications: {'peptide': 506}
          Link IDs: {'PTRANS': 29, 'TRANS': 476}
    Chain: "B"
      Number of atoms: 4092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 4092
          Classifications: {'peptide': 505}
          Link IDs: {'PTRANS': 29, 'TRANS': 475}
    Chain: "C"
      Number of atoms: 1619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1619
          Classifications: {'RNA': 76}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 29, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 17, 'rna3p': 58}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Classifications: {'RNA': 1, 'peptide': 1}
          Modifications used: {'COO': 1, 'rna3p': 1}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Classifications: {'RNA': 1}
          Modifications used: {'rna3p': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.31, per 1000 atoms: 0.64
  Number of scatterers: 9878
  At special positions: 0
  Unit cell: (84.53, 101.65, 128.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      56     16.00
     P      78     15.00
     Na      1     11.00
     O    2056      8.00
     N    1691      7.00
     C    5996      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1898

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 9 sheets defined
      38.4% alpha, 22.4% beta
      26 base pairs and 34 stacking pairs defined.
    Time for finding SS restraints: 3.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 90
      removed outlier: 3.549A  pdb=" N   ILE A  79 " --> pdb=" O   GLN A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 165 through 174
    Processing helix  chain 'A' and resid 222 through 229
    Processing helix  chain 'A' and resid 229 through 237
    Processing helix  chain 'A' and resid 238 through 261
      removed outlier: 3.858A  pdb=" N   GLN A 242 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 311
    Processing helix  chain 'A' and resid 346 through 366
      removed outlier: 4.346A  pdb=" N   GLU A 352 " --> pdb=" O   HIS A 348 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ILE A 353 " --> pdb=" O   ASP A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 405
    Processing helix  chain 'A' and resid 410 through 414
    Processing helix  chain 'A' and resid 416 through 430
      removed outlier: 3.631A  pdb=" N   ARG A 420 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 452
      removed outlier: 3.626A  pdb=" N   LEU A 444 " --> pdb=" O   THR A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 456
    Processing helix  chain 'A' and resid 504 through 520
    Processing helix  chain 'A' and resid 530 through 539
      removed outlier: 3.545A  pdb=" N   TYR A 539 " --> pdb=" O   THR A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 559
      removed outlier: 3.856A  pdb=" N   PHE A 557 " --> pdb=" O   ARG A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 568
      removed outlier: 4.158A  pdb=" N   VAL A 567 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 90
    Processing helix  chain 'B' and resid 104 through 113
    Processing helix  chain 'B' and resid 165 through 174
    Processing helix  chain 'B' and resid 222 through 229
    Processing helix  chain 'B' and resid 229 through 237
    Processing helix  chain 'B' and resid 238 through 261
    Processing helix  chain 'B' and resid 300 through 311
    Processing helix  chain 'B' and resid 349 through 367
      removed outlier: 3.735A  pdb=" N   ILE B 353 " --> pdb=" O   ASP B 349 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU B 355 " --> pdb=" O   MET B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 404
    Processing helix  chain 'B' and resid 416 through 430
    Processing helix  chain 'B' and resid 439 through 452
      removed outlier: 3.552A  pdb=" N   LYS B 446 " --> pdb=" O   ARG B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 470
      No H-bonds generated for 'chain 'B' and resid 468 through 470'
    Processing helix  chain 'B' and resid 504 through 522
    Processing helix  chain 'B' and resid 530 through 539
    Processing helix  chain 'B' and resid 551 through 559
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 137
      removed outlier: 5.980A  pdb=" N   ILE A 132 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ALA A 134 " --> pdb=" O   ASP A 146 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   LEU A 196 " --> pdb=" O   LYS A 153 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN A 155 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   MET A 157 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   ASN A 159 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   GLU A 202 " --> pdb=" O   ASN A 159 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLN A 185 " --> pdb=" O   TYR A 201 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   ILE A 203 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   GLY A 183 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   LEU A 205 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   ILE A 181 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265
      removed outlier: 5.856A  pdb=" N   LEU A 264 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ILE A 318 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ILE A 495 " --> pdb=" O   GLY A 550 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LEU A 488 " --> pdb=" O   ILE A 495 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   ASN A 497 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   PHE A 486 " --> pdb=" O   ASN A 497 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ARG A 392 " --> pdb=" O   PHE A 461 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272
      removed outlier: 3.720A  pdb=" N   TYR A 295 " --> pdb=" O   ASN A 272 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 373
    Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 466
    Processing sheet with id=AA6, first strand: chain 'B' and resid 126 through 137
      removed outlier: 6.262A  pdb=" N   ILE B 132 " --> pdb=" O   ARG B 148 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ALA B 134 " --> pdb=" O   ASP B 146 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   LEU B 196 " --> pdb=" O   LYS B 153 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLN B 155 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE B 198 " --> pdb=" O   GLN B 155 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   MET B 157 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   ASN B 159 " --> pdb=" O   PRO B 200 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   GLU B 202 " --> pdb=" O   ASN B 159 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   GLN B 185 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   ILE B 203 " --> pdb=" O   GLY B 183 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   GLY B 183 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ILE B 181 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 264 through 265
      removed outlier: 5.869A  pdb=" N   LEU B 264 " --> pdb=" O   TYR B 316 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   ILE B 318 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   MET B 342 " --> pdb=" O   ALA B 545 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ILE B 495 " --> pdb=" O   GLY B 550 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   GLU B 494 " --> pdb=" O   VAL B 490 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL B 490 " --> pdb=" O   GLU B 494 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   CYS B 496 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   HIS B 465 " --> pdb=" O   THR B 483 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ARG B 485 " --> pdb=" O   CYS B 463 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   CYS B 463 " --> pdb=" O   ARG B 485 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   GLU B 487 " --> pdb=" O   PHE B 461 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   PHE B 461 " --> pdb=" O   GLU B 487 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   ARG B 392 " --> pdb=" O   PHE B 461 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   CYS B 463 " --> pdb=" O   ARG B 392 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   ILE B 394 " --> pdb=" O   CYS B 463 " (cutoff:3.500A)
      removed outlier: 8.291A  pdb=" N   HIS B 465 " --> pdb=" O   ILE B 394 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 271 through 272
      removed outlier: 3.651A  pdb=" N   MET B 292 " --> pdb=" O   HIS B 287 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 370 through 373

    363 hydrogen bonds defined for protein.
    1053 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      67 hydrogen bonds
      110 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      34 stacking parallelities
  Total time for adding SS restraints: 3.70

  Time building geometry restraints manager: 2.94 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2635
        1.33 -     1.46: 2404
        1.46 -     1.58: 4974
        1.58 -     1.70: 153
        1.70 -     1.82: 96
  Bond restraints: 10262
  Sorted by residual:
  bond pdb=" C   LYS A 370 "
       pdb=" N   VAL A 371 "
    ideal  model  delta    sigma   weight residual
    1.331  1.243  0.088 1.32e-02 5.74e+03 4.47e+01
  bond pdb=" C   MET B 527 "
       pdb=" N   PHE B 528 "
    ideal  model  delta    sigma   weight residual
    1.329  1.438 -0.109 1.76e-02 3.23e+03 3.85e+01
  bond pdb=" C   PHE B 335 "
       pdb=" N   THR B 336 "
    ideal  model  delta    sigma   weight residual
    1.329  1.413 -0.084 1.43e-02 4.89e+03 3.45e+01
  bond pdb=" C4  AMP B 602 "
       pdb=" C5  AMP B 602 "
    ideal  model  delta    sigma   weight residual
    1.490  1.379  0.111 2.00e-02 2.50e+03 3.09e+01
  bond pdb=" C4  AMP A 601 "
       pdb=" C5  AMP A 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.99e+01
  ... (remaining 10257 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 13762
        2.29 -     4.58: 424
        4.58 -     6.88: 40
        6.88 -     9.17: 8
        9.17 -    11.46: 5
  Bond angle restraints: 14239
  Sorted by residual:
  angle pdb=" C   GLY B 186 "
        pdb=" N   ASN B 187 "
        pdb=" CA  ASN B 187 "
      ideal   model   delta    sigma   weight residual
     120.94  131.32  -10.38 1.90e+00 2.77e-01 2.98e+01
  angle pdb=" O   MET B 527 "
        pdb=" C   MET B 527 "
        pdb=" N   PHE B 528 "
      ideal   model   delta    sigma   weight residual
     122.68  128.75   -6.07 1.17e+00 7.31e-01 2.69e+01
  angle pdb=" O   ARG A 420 "
        pdb=" C   ARG A 420 "
        pdb=" N   LYS A 421 "
      ideal   model   delta    sigma   weight residual
     122.12  127.28   -5.16 1.06e+00 8.90e-01 2.37e+01
  angle pdb=" N   PRO B 436 "
        pdb=" CA  PRO B 436 "
        pdb=" C   PRO B 436 "
      ideal   model   delta    sigma   weight residual
     110.70  116.45   -5.75 1.22e+00 6.72e-01 2.22e+01
  angle pdb=" C   LYS A 370 "
        pdb=" N   VAL A 371 "
        pdb=" CA  VAL A 371 "
      ideal   model   delta    sigma   weight residual
     122.99  129.31   -6.32 1.39e+00 5.18e-01 2.07e+01
  ... (remaining 14234 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.04: 5893
       34.04 -    68.08: 397
       68.08 -   102.12: 39
      102.12 -   136.17: 2
      136.17 -   170.21: 3
  Dihedral angle restraints: 6334
    sinusoidal: 3383
      harmonic: 2951
  Sorted by residual:
  dihedral pdb=" O4'   U C  66 "
           pdb=" C1'   U C  66 "
           pdb=" N1    U C  66 "
           pdb=" C2    U C  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -4.39 -155.61     1      1.50e+01 4.44e-03 8.15e+01
  dihedral pdb=" C5' AMP B 602 "
           pdb=" O5' AMP B 602 "
           pdb=" P   AMP B 602 "
           pdb=" O3P AMP B 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -171.93  111.93     1      2.00e+01 2.50e-03 3.30e+01
  dihedral pdb=" CA  TYR A 499 "
           pdb=" C   TYR A 499 "
           pdb=" N   THR A 500 "
           pdb=" CA  THR A 500 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.64   21.36     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 6331 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1516
       0.106 -    0.211: 87
       0.211 -    0.317: 8
       0.317 -    0.422: 0
       0.422 -    0.528: 2
  Chirality restraints: 1613
  Sorted by residual:
  chirality pdb=" P     C C  48 "
            pdb=" OP1   C C  48 "
            pdb=" OP2   C C  48 "
            pdb=" O5'   C C  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.94   -0.53 2.00e-01 2.50e+01 6.97e+00
  chirality pdb=" P     U C  47 "
            pdb=" OP1   U C  47 "
            pdb=" OP2   U C  47 "
            pdb=" O5'   U C  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.87   -0.46 2.00e-01 2.50e+01 5.37e+00
  chirality pdb=" C3'   U C  47 "
            pdb=" C4'   U C  47 "
            pdb=" O3'   U C  47 "
            pdb=" C2'   U C  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.48   -0.27 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 1610 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 528 "   -0.013 2.00e-02 2.50e+03   2.65e-02 7.02e+00
        pdb=" C   PHE B 528 "    0.046 2.00e-02 2.50e+03
        pdb=" O   PHE B 528 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ILE B 529 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 241 "    0.214 9.50e-02 1.11e+02   9.57e-02 5.63e+00
        pdb=" NE  ARG B 241 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 241 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 241 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 241 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 260 "    0.011 2.00e-02 2.50e+03   2.23e-02 4.98e+00
        pdb=" CD  GLU A 260 "   -0.039 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 260 "    0.014 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 260 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 827
        2.74 -     3.28: 9754
        3.28 -     3.82: 17661
        3.82 -     4.36: 21245
        4.36 -     4.90: 34765
  Nonbonded interactions: 84252
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 109 "
            pdb=" OG  SER A 113 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OH  TYR B 286 "
            pdb=" OD1 ASP B 291 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OH  TYR A 286 "
            pdb=" OD1 ASP A 291 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   LEU A 413 "
            pdb=" OG1 THR A 416 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O2'   G C  65 "
            pdb=" OP1   U C  66 "
     model   vdw
     2.261 3.040
  ... (remaining 84247 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 72 through 576 or resid 601))
  selection = (chain 'B' and (resid 72 through 576 or resid 602))
}

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:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     28.010
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
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      :  0.007   0.111  10262  Z= 0.435
  Angle     :  0.830  11.462  14239  Z= 0.533
  Chirality :  0.054   0.528   1613
  Planarity :  0.006   0.096   1552
  Dihedral  : 20.536 170.207   4436
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 26.53 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.26), residues: 1007
  helix:  1.01 (0.28), residues: 356
  sheet: -0.84 (0.35), residues: 225
  loop : -1.35 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 547 
 HIS   0.007   0.001   HIS A 465 
 PHE   0.022   0.001   PHE B 340 
 TYR   0.021   0.001   TYR B 499 
 ARG   0.009   0.000   ARG A 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17148 (  430)
  hydrogen bonds       : angle       7.21757 ( 1163)
  covalent geometry    : bond        0.00653 (10262)
  covalent geometry    : angle       0.82952 (14239)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A  434 CYS cc_start: 0.8269 (t) cc_final: 0.7325 (t)
REVERT: A  442 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7314 (ttp-170)
REVERT: A  451 PHE cc_start: 0.8402 (m-80) cc_final: 0.7973 (m-80)
  outliers start: 14
  outliers final: 10
  residues processed: 108
  average time/residue: 1.2083
  time to fit residues: 140.3529
Evaluate side-chains
  82 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  552 ASP
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  554 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0980
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
A 217 HIS
B 237 ASN
** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.117203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.081575 restraints weight = 16948.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.42
r_work: 0.2994 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10262  Z= 0.136
  Angle     :  0.591   8.618  14239  Z= 0.300
  Chirality :  0.038   0.232   1613
  Planarity :  0.005   0.055   1552
  Dihedral  : 19.578 163.277   2339
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 25.53 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.26), residues: 1007
  helix:  1.49 (0.27), residues: 372
  sheet: -0.46 (0.35), residues: 220
  loop : -1.32 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 547 
 HIS   0.004   0.001   HIS A 465 
 PHE   0.029   0.002   PHE A 340 
 TYR   0.027   0.001   TYR B 499 
 ARG   0.003   0.000   ARG A 438 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  430)
  hydrogen bonds       : angle       4.97325 ( 1163)
  covalent geometry    : bond        0.00308 (10262)
  covalent geometry    : angle       0.59067 (14239)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 85
  time to evaluate  : 0.999 
Fit side-chains
REVERT: A  406 MET cc_start: 0.8272 (ptp) cc_final: 0.7994 (ptm)
REVERT: A  434 CYS cc_start: 0.8075 (t) cc_final: 0.7067 (t)
REVERT: A  442 ARG cc_start: 0.8084 (ttp-110) cc_final: 0.7716 (ttp-170)
REVERT: A  569 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9100 (mt)
  outliers start: 27
  outliers final: 8
  residues processed: 106
  average time/residue: 1.0859
  time to fit residues: 124.6396
Evaluate side-chains
  78 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain B residue  124 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  499 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 101 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** B 465 HIS ** 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 = 0.3723 r_free = 0.3723 target = 0.114612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.078414 restraints weight = 17268.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 2.44
r_work: 0.2938 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10262  Z= 0.180
  Angle     :  0.602   9.370  14239  Z= 0.303
  Chirality :  0.039   0.231   1613
  Planarity :  0.005   0.055   1552
  Dihedral  : 19.546 164.666   2327
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.20 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.26), residues: 1007
  helix:  1.48 (0.26), residues: 373
  sheet: -0.47 (0.35), residues: 220
  loop : -1.33 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A 547 
 HIS   0.002   0.001   HIS A 215 
 PHE   0.030   0.002   PHE A 340 
 TYR   0.027   0.001   TYR B 499 
 ARG   0.003   0.000   ARG B 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04522 (  430)
  hydrogen bonds       : angle       4.77881 ( 1163)
  covalent geometry    : bond        0.00418 (10262)
  covalent geometry    : angle       0.60218 (14239)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 81
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: A  396 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.8030 (ttp)
REVERT: A  434 CYS cc_start: 0.8255 (t) cc_final: 0.7387 (t)
REVERT: A  442 ARG cc_start: 0.8058 (ttp-110) cc_final: 0.7755 (ttm170)
  outliers start: 33
  outliers final: 9
  residues processed: 108
  average time/residue: 1.1668
  time to fit residues: 136.3489
Evaluate side-chains
  79 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  499 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 465 HIS ** 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 = 0.3785 r_free = 0.3785 target = 0.117134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.081532 restraints weight = 17242.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.49
r_work: 0.3025 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10262  Z= 0.122
  Angle     :  0.586  10.582  14239  Z= 0.292
  Chirality :  0.038   0.226   1613
  Planarity :  0.005   0.056   1552
  Dihedral  : 19.474 163.477   2327
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 25.53 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.26), residues: 1007
  helix:  1.58 (0.27), residues: 373
  sheet: -0.41 (0.36), residues: 220
  loop : -1.30 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 547 
 HIS   0.002   0.000   HIS A 476 
 PHE   0.025   0.001   PHE A 340 
 TYR   0.022   0.001   TYR B 499 
 ARG   0.002   0.000   ARG A 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03945 (  430)
  hydrogen bonds       : angle       4.51490 ( 1163)
  covalent geometry    : bond        0.00276 (10262)
  covalent geometry    : angle       0.58560 (14239)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  406 MET cc_start: 0.8503 (ptp) cc_final: 0.8277 (ptm)
REVERT: A  434 CYS cc_start: 0.8106 (t) cc_final: 0.7121 (t)
REVERT: A  442 ARG cc_start: 0.7965 (ttp-110) cc_final: 0.7748 (ttm110)
REVERT: B  161 ARG cc_start: 0.8453 (mtm180) cc_final: 0.8064 (mtm180)
REVERT: B  396 MET cc_start: 0.7820 (tmt) cc_final: 0.7612 (tmm)
REVERT: B  421 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8956 (mmmt)
  outliers start: 23
  outliers final: 11
  residues processed: 102
  average time/residue: 1.0912
  time to fit residues: 121.0733
Evaluate side-chains
  84 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue  124 ILE
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  499 TYR
Chi-restraints excluded: chain B residue  529 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 106 optimal weight:   10.0000
   chunk 96 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 217 HIS
** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.116501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.080740 restraints weight = 17299.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.45
r_work: 0.3008 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10262  Z= 0.145
  Angle     :  0.592   9.923  14239  Z= 0.295
  Chirality :  0.039   0.282   1613
  Planarity :  0.005   0.056   1552
  Dihedral  : 19.472 164.564   2327
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 26.31 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.26), residues: 1007
  helix:  1.61 (0.27), residues: 373
  sheet: -0.39 (0.36), residues: 220
  loop : -1.32 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 547 
 HIS   0.002   0.000   HIS B 120 
 PHE   0.027   0.001   PHE A 340 
 TYR   0.022   0.001   TYR B 499 
 ARG   0.007   0.000   ARG B 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04079 (  430)
  hydrogen bonds       : angle       4.50002 ( 1163)
  covalent geometry    : bond        0.00335 (10262)
  covalent geometry    : angle       0.59233 (14239)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A  434 CYS cc_start: 0.7955 (t) cc_final: 0.7089 (t)
REVERT: A  442 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7861 (ttm110)
REVERT: B  406 MET cc_start: 0.5700 (pmm) cc_final: 0.5304 (pp-130)
  outliers start: 28
  outliers final: 12
  residues processed: 101
  average time/residue: 1.1110
  time to fit residues: 121.7430
Evaluate side-chains
  83 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue  124 ILE
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  499 TYR
Chi-restraints excluded: chain B residue  529 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 95 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 29 optimal weight:    0.1980
   chunk 74 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 217 HIS
** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.114430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.078422 restraints weight = 17450.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.49
r_work: 0.2972 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10262  Z= 0.185
  Angle     :  0.621   9.828  14239  Z= 0.309
  Chirality :  0.040   0.300   1613
  Planarity :  0.005   0.057   1552
  Dihedral  : 19.501 164.942   2327
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 26.76 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.26), residues: 1007
  helix:  1.57 (0.26), residues: 373
  sheet: -0.46 (0.36), residues: 222
  loop : -1.35 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 547 
 HIS   0.003   0.001   HIS A 217 
 PHE   0.028   0.002   PHE A 340 
 TYR   0.024   0.001   TYR B 499 
 ARG   0.002   0.000   ARG B 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04320 (  430)
  hydrogen bonds       : angle       4.56887 ( 1163)
  covalent geometry    : bond        0.00431 (10262)
  covalent geometry    : angle       0.62095 (14239)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 1.256 
Fit side-chains
REVERT: A  434 CYS cc_start: 0.8015 (t) cc_final: 0.7167 (t)
REVERT: A  442 ARG cc_start: 0.8220 (ttp-110) cc_final: 0.7683 (ttm-80)
REVERT: B   74 ASN cc_start: 0.8799 (p0) cc_final: 0.8586 (p0)
REVERT: B   88 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8996 (ttmt)
REVERT: B  161 ARG cc_start: 0.8472 (mtm180) cc_final: 0.8015 (mtm180)
REVERT: B  420 ARG cc_start: 0.8826 (tmm160) cc_final: 0.8393 (tmt-80)
  outliers start: 27
  outliers final: 12
  residues processed: 95
  average time/residue: 1.1674
  time to fit residues: 120.1549
Evaluate side-chains
  87 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue   88 LYS
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  499 TYR
Chi-restraints excluded: chain B residue  529 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 31 optimal weight:    0.2980
   chunk 61 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 465 HIS ** 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 = 0.3782 r_free = 0.3782 target = 0.117164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.081360 restraints weight = 17512.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.47
r_work: 0.3020 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10262  Z= 0.122
  Angle     :  0.598  11.436  14239  Z= 0.295
  Chirality :  0.039   0.325   1613
  Planarity :  0.005   0.057   1552
  Dihedral  : 19.482 163.917   2327
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 28.43 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.26), residues: 1007
  helix:  1.62 (0.27), residues: 373
  sheet: -0.34 (0.36), residues: 219
  loop : -1.33 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 547 
 HIS   0.009   0.000   HIS A 217 
 PHE   0.024   0.001   PHE A 340 
 TYR   0.021   0.001   TYR B 499 
 ARG   0.002   0.000   ARG B 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03937 (  430)
  hydrogen bonds       : angle       4.44577 ( 1163)
  covalent geometry    : bond        0.00278 (10262)
  covalent geometry    : angle       0.59762 (14239)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A  434 CYS cc_start: 0.7930 (t) cc_final: 0.7095 (t)
REVERT: A  442 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7691 (ttm110)
REVERT: B   88 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8867 (ttmt)
REVERT: B  161 ARG cc_start: 0.8479 (mtm180) cc_final: 0.7955 (mtm180)
REVERT: B  420 ARG cc_start: 0.8753 (tmm160) cc_final: 0.8427 (mmm160)
  outliers start: 18
  outliers final: 8
  residues processed: 95
  average time/residue: 1.2349
  time to fit residues: 126.4610
Evaluate side-chains
  79 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue   88 LYS
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  499 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 88 optimal weight:    0.0670
   chunk 74 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 101 optimal weight:   10.0000
   chunk 102 optimal weight:    5.9990
   chunk 71 optimal weight:    0.5980
   chunk 33 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A 217 HIS
** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.116391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.080451 restraints weight = 17300.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 2.45
r_work: 0.2941 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10262  Z= 0.121
  Angle     :  0.624  11.611  14239  Z= 0.305
  Chirality :  0.039   0.347   1613
  Planarity :  0.005   0.057   1552
  Dihedral  : 19.461 163.944   2327
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 28.87 %
    Favored  : 69.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.26), residues: 1007
  helix:  1.66 (0.27), residues: 373
  sheet: -0.31 (0.36), residues: 219
  loop : -1.26 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 547 
 HIS   0.002   0.000   HIS A 476 
 PHE   0.027   0.001   PHE A 340 
 TYR   0.020   0.001   TYR B 499 
 ARG   0.002   0.000   ARG B 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  430)
  hydrogen bonds       : angle       4.41949 ( 1163)
  covalent geometry    : bond        0.00274 (10262)
  covalent geometry    : angle       0.62380 (14239)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.928 
Fit side-chains
REVERT: A  433 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8487 (tm-30)
REVERT: A  442 ARG cc_start: 0.7989 (ttp-110) cc_final: 0.7642 (ttm110)
REVERT: B  161 ARG cc_start: 0.8566 (mtm180) cc_final: 0.8005 (mtm180)
REVERT: B  355 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8562 (tt0)
REVERT: B  420 ARG cc_start: 0.8753 (tmm160) cc_final: 0.8466 (mmm160)
  outliers start: 19
  outliers final: 9
  residues processed: 89
  average time/residue: 1.1627
  time to fit residues: 111.9441
Evaluate side-chains
  83 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  499 TYR
Chi-restraints excluded: chain B residue  554 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 98 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0040
   chunk 17 optimal weight:    1.9990
   chunk 102 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.9398

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

Flipped N/Q/H residues before XYZ refinement:
A 497 ASN
** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.115855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.079730 restraints weight = 17254.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 2.44
r_work: 0.2926 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10262  Z= 0.144
  Angle     :  0.637  12.223  14239  Z= 0.312
  Chirality :  0.040   0.349   1613
  Planarity :  0.005   0.057   1552
  Dihedral  : 19.459 164.436   2327
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 28.43 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.26), residues: 1007
  helix:  1.63 (0.26), residues: 373
  sheet: -0.26 (0.37), residues: 220
  loop : -1.22 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 547 
 HIS   0.004   0.000   HIS A 465 
 PHE   0.029   0.002   PHE A 340 
 TYR   0.020   0.001   TYR B 499 
 ARG   0.002   0.000   ARG A 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04043 (  430)
  hydrogen bonds       : angle       4.45597 ( 1163)
  covalent geometry    : bond        0.00334 (10262)
  covalent geometry    : angle       0.63657 (14239)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 1.064 
Fit side-chains
REVERT: A  407 LYS cc_start: 0.9376 (tppp) cc_final: 0.9080 (tppp)
REVERT: A  433 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8480 (tm-30)
REVERT: A  442 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7573 (ttm110)
REVERT: A  499 TYR cc_start: 0.8333 (m-80) cc_final: 0.8074 (m-80)
REVERT: B  161 ARG cc_start: 0.8570 (mtm180) cc_final: 0.8012 (mtm180)
REVERT: B  355 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8542 (tt0)
REVERT: B  420 ARG cc_start: 0.8740 (tmm160) cc_final: 0.8465 (mmm160)
  outliers start: 18
  outliers final: 10
  residues processed: 88
  average time/residue: 1.1647
  time to fit residues: 110.6813
Evaluate side-chains
  85 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  499 TYR
Chi-restraints excluded: chain B residue  554 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 102 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0970
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 465 HIS ** 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 = 0.3717 r_free = 0.3717 target = 0.115698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.079917 restraints weight = 17250.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 2.43
r_work: 0.2925 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10262  Z= 0.138
  Angle     :  0.637  12.257  14239  Z= 0.312
  Chirality :  0.040   0.349   1613
  Planarity :  0.005   0.057   1552
  Dihedral  : 19.454 164.162   2327
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 28.54 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.26), residues: 1007
  helix:  1.61 (0.26), residues: 373
  sheet: -0.23 (0.37), residues: 220
  loop : -1.21 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 547 
 HIS   0.003   0.000   HIS A 465 
 PHE   0.029   0.001   PHE A 340 
 TYR   0.019   0.001   TYR B 499 
 ARG   0.003   0.000   ARG A 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04052 (  430)
  hydrogen bonds       : angle       4.46950 ( 1163)
  covalent geometry    : bond        0.00320 (10262)
  covalent geometry    : angle       0.63693 (14239)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 1.010 
Fit side-chains
REVERT: A  433 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8483 (tm-30)
REVERT: A  442 ARG cc_start: 0.7911 (ttp-110) cc_final: 0.7531 (ttm110)
REVERT: A  453 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8125 (pm20)
REVERT: A  499 TYR cc_start: 0.8332 (m-80) cc_final: 0.8047 (m-80)
REVERT: B  161 ARG cc_start: 0.8564 (mtm180) cc_final: 0.8022 (mtm180)
REVERT: B  355 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8550 (tt0)
REVERT: B  420 ARG cc_start: 0.8790 (tmm160) cc_final: 0.8486 (mmm160)
  outliers start: 16
  outliers final: 10
  residues processed: 89
  average time/residue: 1.2275
  time to fit residues: 118.0374
Evaluate side-chains
  86 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  453 GLU
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  434 CYS
Chi-restraints excluded: chain B residue  479 LYS
Chi-restraints excluded: chain B residue  499 TYR
Chi-restraints excluded: chain B residue  554 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0050
   chunk 17 optimal weight:    1.9990
   chunk 77 optimal weight:    0.2980
   chunk 75 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
** B 465 HIS ** 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 = 0.3734 r_free = 0.3734 target = 0.116961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.081171 restraints weight = 17238.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.43
r_work: 0.2959 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10262  Z= 0.121
  Angle     :  0.649  12.302  14239  Z= 0.316
  Chirality :  0.039   0.353   1613
  Planarity :  0.005   0.057   1552
  Dihedral  : 19.424 163.649   2327
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 29.21 %
    Favored  : 69.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.26), residues: 1007
  helix:  1.65 (0.26), residues: 373
  sheet: -0.22 (0.37), residues: 219
  loop : -1.18 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 547 
 HIS   0.003   0.000   HIS A 465 
 PHE   0.027   0.001   PHE A 340 
 TYR   0.017   0.001   TYR B 499 
 ARG   0.003   0.000   ARG A 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03887 (  430)
  hydrogen bonds       : angle       4.41910 ( 1163)
  covalent geometry    : bond        0.00279 (10262)
  covalent geometry    : angle       0.64893 (14239)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5142.38 seconds
wall clock time: 89 minutes 43.99 seconds (5383.99 seconds total)