Starting phenix.real_space_refine
on Thu Sep 18 10:07:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dpa_47100/09_2025/9dpa_47100.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dpa_47100/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dpa_47100/09_2025/9dpa_47100.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dpa_47100/09_2025/9dpa_47100.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dpa_47100/09_2025/9dpa_47100.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dpa_47100/09_2025/9dpa_47100.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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
          Unusual residues: {'AMP%rna3p': 1}
          Classifications: {'RNA_mixed': 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
          Unusual residues: {'AMP%rna3p': 1}
          Classifications: {'RNA_mixed': 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: 2.46, per 1000 atoms: 0.25
  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: 0.63
  Conformation dependent library (CDL) restraints added in 338.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 1.27
  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: 1.69

  Time building geometry restraints manager: 0.92 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: 13749
        2.29 -     4.58: 429
        4.58 -     6.88: 43
        6.88 -     9.17: 11
        9.17 -    11.46: 7
  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:             1.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.240
  Find NCS groups from input model:        0.160
  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:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.800
-------------------------------------------------------------------------------
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     :  0.853  11.462  14239  Z= 0.535
  Chirality :  0.053   0.528   1613
  Planarity :  0.006   0.096   1552
  Dihedral  : 20.533 170.207   4436
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 10.69
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.009   0.000   ARG A 442 
 TYR   0.021   0.001   TYR B 499 
 PHE   0.022   0.001   PHE B 340 
 TRP   0.013   0.002   TRP B 547 
 HIS   0.007   0.001   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 (10262)
  covalent geometry    : angle       0.85303 (14239)
  hydrogen bonds       : bond        0.17148 (  430)
  hydrogen bonds       : angle       7.21757 ( 1163)

*********************** 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  : 0.371 
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: 0.5877
  time to fit residues: 67.9803
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  : 0.355 
-------------------------------------------------------------------------------
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 49 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    8.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    1.4984

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.114954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.078843 restraints weight = 17116.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.43
r_work: 0.2943 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  10262  Z= 0.196
  Angle     :  0.627   8.974  14239  Z= 0.316
  Chirality :  0.040   0.235   1613
  Planarity :  0.005   0.054   1552
  Dihedral  : 19.558 163.982   2339
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 25.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.26), residues: 1007
  helix:  1.39 (0.27), residues: 372
  sheet: -0.56 (0.35), residues: 220
  loop : -1.38 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 438 
 TYR   0.029   0.001   TYR B 499 
 PHE   0.033   0.002   PHE A 340 
 TRP   0.015   0.003   TRP A 547 
 HIS   0.004   0.001   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (10262)
  covalent geometry    : angle       0.62676 (14239)
  hydrogen bonds       : bond        0.04778 (  430)
  hydrogen bonds       : angle       5.06099 ( 1163)

*********************** 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
  110 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A  217 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6786 (t-170)
REVERT: A  434 CYS cc_start: 0.8187 (t) cc_final: 0.7200 (t)
REVERT: A  442 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.7580 (ttp-170)
  outliers start: 30
  outliers final: 8
  residues processed: 105
  average time/residue: 0.5000
  time to fit residues: 56.8730
Evaluate side-chains
  77 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  368 SER
Chi-restraints excluded: chain A residue  454 VAL
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 81 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   chunk 104 optimal weight:    8.9990
   chunk 12 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 = 0.3723 r_free = 0.3723 target = 0.114673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.078459 restraints weight = 17103.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.48
r_work: 0.2937 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.1534

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= 0.172
  Angle     :  0.612   9.217  14239  Z= 0.304
  Chirality :  0.039   0.232   1613
  Planarity :  0.005   0.055   1552
  Dihedral  : 19.493 164.167   2327
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.97 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.26), residues: 1007
  helix:  1.44 (0.27), residues: 373
  sheet: -0.48 (0.35), residues: 220
  loop : -1.34 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 420 
 TYR   0.027   0.001   TYR B 499 
 PHE   0.029   0.002   PHE A 340 
 TRP   0.014   0.002   TRP A 547 
 HIS   0.003   0.001   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (10262)
  covalent geometry    : angle       0.61192 (14239)
  hydrogen bonds       : bond        0.04469 (  430)
  hydrogen bonds       : angle       4.79174 ( 1163)

*********************** 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
  112 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 78
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
REVERT: A  217 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.7044 (t-170)
REVERT: A  434 CYS cc_start: 0.8255 (t) cc_final: 0.7281 (t)
REVERT: A  442 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7568 (ttp-110)
  outliers start: 34
  outliers final: 10
  residues processed: 105
  average time/residue: 0.5679
  time to fit residues: 64.4668
Evaluate side-chains
  79 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  271 MET
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  434 CYS
Chi-restraints excluded: chain B residue  499 TYR
Chi-restraints excluded: chain B residue  529 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 105 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.116225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.080500 restraints weight = 17395.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 2.46
r_work: 0.3000 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10262  Z= 0.138
  Angle     :  0.605  11.024  14239  Z= 0.298
  Chirality :  0.039   0.228   1613
  Planarity :  0.005   0.054   1552
  Dihedral  : 19.437 163.838   2327
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 25.20 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.26), residues: 1007
  helix:  1.53 (0.27), residues: 373
  sheet: -0.41 (0.35), residues: 220
  loop : -1.35 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 297 
 TYR   0.024   0.001   TYR B 499 
 PHE   0.027   0.001   PHE A 340 
 TRP   0.013   0.002   TRP A 547 
 HIS   0.002   0.000   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (10262)
  covalent geometry    : angle       0.60483 (14239)
  hydrogen bonds       : bond        0.04132 (  430)
  hydrogen bonds       : angle       4.58633 ( 1163)

*********************** 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
  105 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  406 MET cc_start: 0.8450 (ptp) cc_final: 0.8216 (ptm)
REVERT: A  434 CYS cc_start: 0.8220 (t) cc_final: 0.7246 (t)
REVERT: A  442 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7537 (ttp-170)
REVERT: B  406 MET cc_start: 0.5632 (pmm) cc_final: 0.5233 (pp-130)
REVERT: B  421 LYS cc_start: 0.9198 (mmmt) cc_final: 0.8972 (mmmt)
  outliers start: 24
  outliers final: 10
  residues processed: 98
  average time/residue: 0.5840
  time to fit residues: 61.8625
Evaluate side-chains
  81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
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  434 CYS
Chi-restraints excluded: chain B residue  499 TYR
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  554 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 106 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
B 497 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.112521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.076454 restraints weight = 17453.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 2.45
r_work: 0.2924 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050  10262  Z= 0.327
  Angle     :  0.701   9.603  14239  Z= 0.351
  Chirality :  0.043   0.260   1613
  Planarity :  0.005   0.053   1552
  Dihedral  : 19.535 166.687   2327
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 24.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.26), residues: 1007
  helix:  1.36 (0.26), residues: 369
  sheet: -0.53 (0.36), residues: 217
  loop : -1.48 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 420 
 TYR   0.033   0.002   TYR B 499 
 PHE   0.035   0.002   PHE A 340 
 TRP   0.017   0.003   TRP A 547 
 HIS   0.003   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00772 (10262)
  covalent geometry    : angle       0.70076 (14239)
  hydrogen bonds       : bond        0.05279 (  430)
  hydrogen bonds       : angle       4.92462 ( 1163)

*********************** 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
  111 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 76
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  395 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7964 (t0)
REVERT: A  442 ARG cc_start: 0.8107 (ttp-110) cc_final: 0.7497 (ttp-170)
REVERT: B  141 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (tppp)
REVERT: B  421 LYS cc_start: 0.9227 (mmmt) cc_final: 0.9017 (mmmt)
  outliers start: 35
  outliers final: 10
  residues processed: 103
  average time/residue: 0.5679
  time to fit residues: 63.2007
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  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain B residue  141 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  499 TYR
Chi-restraints excluded: chain B residue  554 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 38 optimal weight:    0.2980
   chunk 77 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 98 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.115173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.079663 restraints weight = 17406.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.46
r_work: 0.3006 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10262  Z= 0.125
  Angle     :  0.617  10.533  14239  Z= 0.303
  Chirality :  0.039   0.297   1613
  Planarity :  0.005   0.055   1552
  Dihedral  : 19.426 163.471   2327
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 26.64 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.26), residues: 1007
  helix:  1.52 (0.26), residues: 373
  sheet: -0.44 (0.36), residues: 220
  loop : -1.39 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 420 
 TYR   0.023   0.001   TYR B 499 
 PHE   0.024   0.001   PHE B 340 
 TRP   0.014   0.002   TRP A 547 
 HIS   0.003   0.000   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10262)
  covalent geometry    : angle       0.61716 (14239)
  hydrogen bonds       : bond        0.04085 (  430)
  hydrogen bonds       : angle       4.56346 ( 1163)

*********************** 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
  105 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A  395 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7893 (t0)
REVERT: A  434 CYS cc_start: 0.8144 (t) cc_final: 0.7327 (t)
REVERT: A  442 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7571 (ttm-80)
REVERT: B  141 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8680 (tppp)
REVERT: B  406 MET cc_start: 0.5627 (pmm) cc_final: 0.5261 (pp-130)
  outliers start: 24
  outliers final: 9
  residues processed: 101
  average time/residue: 0.5241
  time to fit residues: 57.3570
Evaluate side-chains
  83 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain B residue  141 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  499 TYR
Chi-restraints excluded: chain B residue  554 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0000
   chunk 2 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 75 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.115400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.079572 restraints weight = 17477.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.47
r_work: 0.2990 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10262  Z= 0.161
  Angle     :  0.643  11.655  14239  Z= 0.314
  Chirality :  0.040   0.332   1613
  Planarity :  0.005   0.054   1552
  Dihedral  : 19.403 164.633   2327
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 27.87 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.26), residues: 1007
  helix:  1.51 (0.26), residues: 373
  sheet: -0.40 (0.36), residues: 220
  loop : -1.34 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 420 
 TYR   0.024   0.001   TYR B 499 
 PHE   0.027   0.002   PHE A 340 
 TRP   0.016   0.003   TRP B 547 
 HIS   0.002   0.000   HIS B 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (10262)
  covalent geometry    : angle       0.64270 (14239)
  hydrogen bonds       : bond        0.04235 (  430)
  hydrogen bonds       : angle       4.55503 ( 1163)

*********************** 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
  95 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  141 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.7995 (mmmm)
REVERT: A  434 CYS cc_start: 0.8174 (t) cc_final: 0.7448 (t)
REVERT: A  442 ARG cc_start: 0.8087 (ttp-110) cc_final: 0.7655 (ttm110)
REVERT: B  141 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8699 (tppp)
  outliers start: 18
  outliers final: 11
  residues processed: 91
  average time/residue: 0.5939
  time to fit residues: 58.1832
Evaluate side-chains
  83 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LYS
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  124 ILE
Chi-restraints excluded: chain B residue  141 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  499 TYR
Chi-restraints excluded: chain B residue  554 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 106 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 95 optimal weight:    7.9990
   chunk 63 optimal weight:    0.6980
   chunk 101 optimal weight:   10.0000
   chunk 76 optimal weight:    0.7980
   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 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 = 0.3768 r_free = 0.3768 target = 0.115747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.079627 restraints weight = 17436.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.51
r_work: 0.3000 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10262  Z= 0.134
  Angle     :  0.644  12.196  14239  Z= 0.312
  Chirality :  0.040   0.353   1613
  Planarity :  0.005   0.055   1552
  Dihedral  : 19.373 164.063   2327
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 27.31 %
    Favored  : 70.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.26), residues: 1007
  helix:  1.55 (0.26), residues: 373
  sheet: -0.37 (0.36), residues: 219
  loop : -1.30 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 420 
 TYR   0.021   0.001   TYR B 499 
 PHE   0.026   0.001   PHE A 340 
 TRP   0.014   0.003   TRP A 547 
 HIS   0.003   0.000   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10262)
  covalent geometry    : angle       0.64439 (14239)
  hydrogen bonds       : bond        0.04037 (  430)
  hydrogen bonds       : angle       4.49535 ( 1163)

*********************** 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
  102 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A  141 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8063 (mmmm)
REVERT: A  314 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8605 (mtt90)
REVERT: A  434 CYS cc_start: 0.8107 (t) cc_final: 0.7288 (t)
REVERT: A  442 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7792 (ttp-110)
REVERT: B  141 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8763 (tppp)
REVERT: B  406 MET cc_start: 0.5626 (pmm) cc_final: 0.5403 (pp-130)
  outliers start: 24
  outliers final: 10
  residues processed: 96
  average time/residue: 0.6054
  time to fit residues: 62.7240
Evaluate side-chains
  85 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue  124 ILE
Chi-restraints excluded: chain B residue  141 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  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 22 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.115927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.079327 restraints weight = 17535.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.56
r_work: 0.2976 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10262  Z= 0.177
  Angle     :  0.666  12.347  14239  Z= 0.326
  Chirality :  0.041   0.346   1613
  Planarity :  0.005   0.055   1552
  Dihedral  : 19.384 164.976   2327
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 27.87 %
    Favored  : 69.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.26), residues: 1007
  helix:  1.50 (0.26), residues: 373
  sheet: -0.46 (0.36), residues: 222
  loop : -1.29 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 438 
 TYR   0.023   0.001   TYR B 499 
 PHE   0.030   0.002   PHE A 340 
 TRP   0.013   0.003   TRP A 547 
 HIS   0.003   0.000   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (10262)
  covalent geometry    : angle       0.66613 (14239)
  hydrogen bonds       : bond        0.04330 (  430)
  hydrogen bonds       : angle       4.57282 ( 1163)

*********************** 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
  99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  141 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8022 (mmmm)
REVERT: A  407 LYS cc_start: 0.9404 (tppp) cc_final: 0.9182 (tppt)
REVERT: A  433 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8437 (tm-30)
REVERT: A  434 CYS cc_start: 0.8195 (t) cc_final: 0.7868 (t)
REVERT: A  442 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7712 (ttp-110)
REVERT: B  141 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8757 (tppp)
REVERT: B  406 MET cc_start: 0.5703 (pmm) cc_final: 0.5494 (pp-130)
  outliers start: 21
  outliers final: 11
  residues processed: 94
  average time/residue: 0.6185
  time to fit residues: 62.5531
Evaluate side-chains
  88 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain B residue  141 LYS
Chi-restraints excluded: chain B residue  198 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  434 CYS
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 44 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 105 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0870
   chunk 102 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 103 optimal weight:    5.9990
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.8160

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.115080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.079429 restraints weight = 17046.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 2.37
r_work: 0.2949 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10262  Z= 0.140
  Angle     :  0.670  13.152  14239  Z= 0.326
  Chirality :  0.040   0.346   1613
  Planarity :  0.005   0.055   1552
  Dihedral  : 19.362 164.264   2327
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 28.65 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.26), residues: 1007
  helix:  1.53 (0.26), residues: 373
  sheet: -0.35 (0.37), residues: 219
  loop : -1.29 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 420 
 TYR   0.021   0.001   TYR B 499 
 PHE   0.029   0.001   PHE A 340 
 TRP   0.016   0.003   TRP B 547 
 HIS   0.004   0.000   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (10262)
  covalent geometry    : angle       0.66964 (14239)
  hydrogen bonds       : bond        0.04124 (  430)
  hydrogen bonds       : angle       4.53032 ( 1163)

********************** 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: 15
    poor density    : 76
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A  141 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7866 (mmmm)
REVERT: A  314 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8584 (mtt90)
REVERT: A  433 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8446 (tm-30)
REVERT: A  434 CYS cc_start: 0.8162 (t) cc_final: 0.7806 (t)
REVERT: A  442 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7585 (ttm110)
REVERT: B  141 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8682 (tppp)
  outliers start: 15
  outliers final: 9
  residues processed: 88
  average time/residue: 0.6253
  time to fit residues: 59.1120
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  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue  141 LYS
Chi-restraints excluded: chain B residue  198 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  434 CYS
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:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.113106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.076846 restraints weight = 17256.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.40
r_work: 0.2892 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10262  Z= 0.221
  Angle     :  0.704  12.470  14239  Z= 0.345
  Chirality :  0.042   0.347   1613
  Planarity :  0.005   0.055   1552
  Dihedral  : 19.400 165.673   2327
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 28.65 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.26), residues: 1007
  helix:  1.44 (0.26), residues: 372
  sheet: -0.39 (0.37), residues: 217
  loop : -1.33 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 420 
 TYR   0.025   0.002   TYR B 499 
 PHE   0.033   0.002   PHE A 340 
 TRP   0.016   0.003   TRP B 547 
 HIS   0.005   0.001   HIS A 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 (10262)
  covalent geometry    : angle       0.70350 (14239)
  hydrogen bonds       : bond        0.04655 (  430)
  hydrogen bonds       : angle       4.66741 ( 1163)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2649.38 seconds
wall clock time: 46 minutes 3.75 seconds (2763.75 seconds total)