Starting phenix.real_space_refine
on Thu Aug  6 15:19:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dpa_47100/08_2026/9dpa_47100.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dpa_47100/08_2026/9dpa_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_47100/08_2026/9dpa_47100.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dpa_47100/08_2026/9dpa_47100.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dpa_47100/08_2026/9dpa_47100.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dpa_47100/08_2026/9dpa_47100.cif"
  }
  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-2.2rc3-6140/lib/python3.11/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: 2.39, per 1000 atoms: 0.24
  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: 0.83
  Conformation dependent library (CDL) restraints added in 296.3 milliseconds
  

  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: 1.15
  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: 1.73

  Time building geometry restraints manager: 1.10 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: 13672
        2.29 -     4.58: 514
        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=" O2    U C  66 "
        pdb=" C2    U C  66 "
        pdb=" N3    U C  66 "
      ideal   model   delta    sigma   weight residual
     122.20  119.01    3.19 7.00e-01 2.04e+00 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: 1457
       0.106 -    0.211: 146
       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:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     11.370
  Find NCS groups from input model:        0.170
  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:7.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
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= 0.444
  Angle     :  0.876  11.462  14239  Z= 0.613
  Chirality :  0.060   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 : 10.69
  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 are 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/Z
  covalent geometry    : bond        0.00656 /  0.44 (10262)
  covalent geometry    : angle       0.87567 /  0.61 (14239)
  hydrogen bonds       : bond        0.17148 / 11.75 (  430)
  hydrogen bonds       : angle       7.21757 /  5.05 ( 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  : 0.343 
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: 0.5970
  time to fit residues: 69.1794
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  : 0.354 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 106 optimal weight:   20.0000
   chunk 38 optimal weight:    0.6980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3743 r_free = 0.3743 target = 0.115944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.080124 restraints weight = 17164.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.44
r_work: 0.2972 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10262  Z= 0.196
  Angle     :  0.609   7.583  14239  Z= 0.320
  Chirality :  0.041   0.394   1613
  Planarity :  0.005   0.056   1552
  Dihedral  : 19.694 167.426   2339
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 26.76 %
    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 are not related in a simple way.
  whole: -0.27 (0.26), residues: 1007
  helix:  1.35 (0.27), residues: 371
  sheet: -0.55 (0.35), residues: 221
  loop : -1.37 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 247 
 TYR   0.026   0.001   TYR B 499 
 PHE   0.029   0.002   PHE A 340 
 TRP   0.013   0.003   TRP B 547 
 HIS   0.004   0.001   HIS A 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.20 (10262)
  covalent geometry    : angle       0.60942 /  0.32 (14239)
  hydrogen bonds       : bond        0.05670 /  4.13 (  430)
  hydrogen bonds       : angle       5.35113 /  3.77 ( 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
  106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  406 MET cc_start: 0.8182 (ptp) cc_final: 0.7907 (ptm)
REVERT: A  434 CYS cc_start: 0.8156 (t) cc_final: 0.7144 (t)
REVERT: A  442 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7595 (ttp-170)
REVERT: B  221 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8530 (mmmm)
  outliers start: 29
  outliers final: 11
  residues processed: 99
  average time/residue: 0.4532
  time to fit residues: 48.7132
Evaluate side-chains
  81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  455 THR
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  221 LYS
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
Chi-restraints excluded: chain B residue  554 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 81 optimal weight:    0.1980
   chunk 89 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 104 optimal weight:   20.0000
   chunk 12 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3789 r_free = 0.3789 target = 0.117303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.081669 restraints weight = 17282.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.47
r_work: 0.3035 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10262  Z= 0.124
  Angle     :  0.571   8.844  14239  Z= 0.296
  Chirality :  0.040   0.399   1613
  Planarity :  0.005   0.055   1552
  Dihedral  : 19.615 165.336   2329
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 25.08 %
    Favored  : 71.35 %
  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 are not related in a simple way.
  whole: -0.13 (0.26), residues: 1007
  helix:  1.46 (0.27), residues: 372
  sheet: -0.42 (0.36), residues: 220
  loop : -1.32 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 420 
 TYR   0.023   0.001   TYR B 499 
 PHE   0.027   0.001   PHE A 340 
 TRP   0.011   0.002   TRP A 547 
 HIS   0.003   0.000   HIS A 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 (10262)
  covalent geometry    : angle       0.57142 /  0.30 (14239)
  hydrogen bonds       : bond        0.04800 /  3.54 (  430)
  hydrogen bonds       : angle       4.90833 /  3.47 ( 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
  115 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 83
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  434 CYS cc_start: 0.8111 (t) cc_final: 0.7087 (t)
REVERT: A  442 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7444 (ttp-170)
REVERT: B  141 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8862 (tppp)
  outliers start: 32
  outliers final: 8
  residues processed: 106
  average time/residue: 0.5700
  time to fit residues: 65.1674
Evaluate side-chains
  81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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  141 LYS
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0770
   chunk 105 optimal weight:   30.0000
   chunk 52 optimal weight:    5.9990
   chunk 73 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6540

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3791 r_free = 0.3791 target = 0.117205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.081603 restraints weight = 17336.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.50
r_work: 0.3035 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.1365

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= 0.124
  Angle     :  0.568   8.754  14239  Z= 0.294
  Chirality :  0.039   0.400   1613
  Planarity :  0.005   0.056   1552
  Dihedral  : 19.570 165.468   2327
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 25.98 %
    Favored  : 71.35 %
  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 are not related in a simple way.
  whole: -0.06 (0.26), residues: 1007
  helix:  1.53 (0.27), residues: 373
  sheet: -0.36 (0.36), residues: 220
  loop : -1.31 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 420 
 TYR   0.023   0.001   TYR B 499 
 PHE   0.025   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/Z
  covalent geometry    : bond        0.00280 /  0.12 (10262)
  covalent geometry    : angle       0.56777 /  0.29 (14239)
  hydrogen bonds       : bond        0.04614 /  3.40 (  430)
  hydrogen bonds       : angle       4.76117 /  3.38 ( 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
  101 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A  434 CYS cc_start: 0.8116 (t) cc_final: 0.7088 (t)
REVERT: A  442 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7616 (ttp-170)
REVERT: B   74 ASN cc_start: 0.8669 (p0) cc_final: 0.8418 (p0)
  outliers start: 24
  outliers final: 10
  residues processed: 94
  average time/residue: 0.4282
  time to fit residues: 43.7787
Evaluate side-chains
  80 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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  499 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 106 optimal weight:   20.0000
   chunk 103 optimal weight:   10.0000
   chunk 57 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3736 r_free = 0.3736 target = 0.113925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.077888 restraints weight = 17435.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.46
r_work: 0.2959 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  10262  Z= 0.255
  Angle     :  0.637   8.730  14239  Z= 0.330
  Chirality :  0.042   0.412   1613
  Planarity :  0.005   0.056   1552
  Dihedral  : 19.563 167.329   2327
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  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 are not related in a simple way.
  whole: -0.20 (0.26), residues: 1007
  helix:  1.46 (0.27), residues: 370
  sheet: -0.41 (0.36), residues: 220
  loop : -1.45 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 178 
 TYR   0.028   0.002   TYR B 499 
 PHE   0.032   0.002   PHE A 340 
 TRP   0.019   0.003   TRP A 547 
 HIS   0.003   0.001   HIS B 114 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00598 /  0.26 (10262)
  covalent geometry    : angle       0.63701 /  0.33 (14239)
  hydrogen bonds       : bond        0.05213 /  3.75 (  430)
  hydrogen bonds       : angle       4.83555 /  3.42 ( 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: 34
    poor density    : 77
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  395 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7892 (t0)
REVERT: A  434 CYS cc_start: 0.8316 (t) cc_final: 0.7231 (t)
REVERT: A  442 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7776 (ttm110)
REVERT: B  119 ASP cc_start: 0.7507 (p0) cc_final: 0.7296 (p0)
REVERT: B  141 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8814 (tppp)
REVERT: B  396 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7675 (tmm)
  outliers start: 34
  outliers final: 13
  residues processed: 100
  average time/residue: 0.4909
  time to fit residues: 53.3819
Evaluate side-chains
  87 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
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  395 ASN
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue  141 LYS
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  361 MET
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  396 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 15 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0870
   chunk 77 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 98 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5558

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3787 r_free = 0.3787 target = 0.116368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.081571 restraints weight = 17389.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.43
r_work: 0.3012 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1615

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= 0.119
  Angle     :  0.579   8.701  14239  Z= 0.298
  Chirality :  0.040   0.403   1613
  Planarity :  0.005   0.054   1552
  Dihedral  : 19.561 165.566   2327
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  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 are not related in a simple way.
  whole: -0.13 (0.26), residues: 1007
  helix:  1.49 (0.27), residues: 373
  sheet: -0.38 (0.36), residues: 220
  loop : -1.38 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 420 
 TYR   0.023   0.001   TYR B 499 
 PHE   0.027   0.001   PHE A 340 
 TRP   0.012   0.002   TRP A 547 
 HIS   0.002   0.000   HIS B 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 (10262)
  covalent geometry    : angle       0.57909 /  0.30 (14239)
  hydrogen bonds       : bond        0.04554 /  3.38 (  430)
  hydrogen bonds       : angle       4.61901 /  3.27 ( 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
  102 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  434 CYS cc_start: 0.8223 (t) cc_final: 0.7224 (t)
REVERT: A  442 ARG cc_start: 0.8006 (ttp-110) cc_final: 0.7448 (ttp-170)
REVERT: B   74 ASN cc_start: 0.8720 (p0) cc_final: 0.8490 (p0)
REVERT: B  141 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8795 (tppp)
REVERT: B  146 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7924 (t0)
REVERT: B  271 MET cc_start: 0.8865 (mtp) cc_final: 0.8628 (mtm)
REVERT: B  396 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7745 (tmm)
REVERT: B  406 MET cc_start: 0.5571 (pmm) cc_final: 0.5123 (pp-130)
  outliers start: 24
  outliers final: 10
  residues processed: 95
  average time/residue: 0.5141
  time to fit residues: 52.7847
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  : 0.333 
-------------------------------------------------------------------------------
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  141 LYS
Chi-restraints excluded: chain B residue  146 ASP
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  396 MET
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 2 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 86 optimal weight:    9.9990
   chunk 75 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3770 r_free = 0.3770 target = 0.116405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.079904 restraints weight = 17471.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.55
r_work: 0.2997 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.1689

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= 0.141
  Angle     :  0.598   9.753  14239  Z= 0.305
  Chirality :  0.040   0.403   1613
  Planarity :  0.005   0.056   1552
  Dihedral  : 19.518 165.818   2327
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 27.54 %
    Favored  : 69.90 %
  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 are not related in a simple way.
  whole: -0.11 (0.26), residues: 1007
  helix:  1.52 (0.27), residues: 373
  sheet: -0.35 (0.36), residues: 220
  loop : -1.39 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 420 
 TYR   0.023   0.001   TYR B 499 
 PHE   0.030   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/Z
  covalent geometry    : bond        0.00326 /  0.14 (10262)
  covalent geometry    : angle       0.59832 /  0.30 (14239)
  hydrogen bonds       : bond        0.04566 /  3.35 (  430)
  hydrogen bonds       : angle       4.59059 /  3.26 ( 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
  98 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  434 CYS cc_start: 0.8213 (t) cc_final: 0.7206 (t)
REVERT: A  442 ARG cc_start: 0.7931 (ttp-110) cc_final: 0.7420 (ttp-170)
REVERT: B  141 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8781 (tppp)
REVERT: B  396 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7676 (tmm)
  outliers start: 23
  outliers final: 12
  residues processed: 89
  average time/residue: 0.5327
  time to fit residues: 51.1523
Evaluate side-chains
  84 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  454 VAL
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  396 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 106 optimal weight:   20.0000
   chunk 97 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 86 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 95 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 101 optimal weight:   20.0000
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3777 r_free = 0.3777 target = 0.116902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.080287 restraints weight = 17384.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.55
r_work: 0.3001 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.1736

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= 0.136
  Angle     :  0.592   9.247  14239  Z= 0.303
  Chirality :  0.040   0.403   1613
  Planarity :  0.005   0.055   1552
  Dihedral  : 19.514 165.763   2327
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 27.98 %
    Favored  : 69.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.26), residues: 1007
  helix:  1.54 (0.27), residues: 373
  sheet: -0.35 (0.36), residues: 220
  loop : -1.38 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 420 
 TYR   0.023   0.001   TYR B 499 
 PHE   0.028   0.001   PHE A 340 
 TRP   0.013   0.002   TRP A 547 
 HIS   0.003   0.000   HIS A 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 (10262)
  covalent geometry    : angle       0.59157 /  0.30 (14239)
  hydrogen bonds       : bond        0.04473 /  3.28 (  430)
  hydrogen bonds       : angle       4.54014 /  3.22 ( 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
  96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  217 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6659 (t-170)
REVERT: A  434 CYS cc_start: 0.8213 (t) cc_final: 0.7188 (t)
REVERT: A  442 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7425 (ttp-170)
REVERT: B   74 ASN cc_start: 0.8740 (p0) cc_final: 0.8518 (p0)
REVERT: B   88 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8894 (ttmt)
REVERT: B  141 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8740 (tppp)
REVERT: B  396 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7661 (tmm)
REVERT: B  406 MET cc_start: 0.5725 (pmm) cc_final: 0.5401 (pp-130)
  outliers start: 23
  outliers final: 10
  residues processed: 88
  average time/residue: 0.5517
  time to fit residues: 52.6093
Evaluate side-chains
  84 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue   88 LYS
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  396 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 22 optimal weight:    0.0670
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 86 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0470
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.4616

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3793 r_free = 0.3793 target = 0.117458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.081429 restraints weight = 17379.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.52
r_work: 0.3031 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.1801

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= 0.116
  Angle     :  0.598  10.390  14239  Z= 0.303
  Chirality :  0.039   0.400   1613
  Planarity :  0.005   0.056   1552
  Dihedral  : 19.493 165.358   2327
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 28.54 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.26), residues: 1007
  helix:  1.54 (0.27), residues: 373
  sheet: -0.32 (0.36), residues: 219
  loop : -1.39 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 420 
 TYR   0.021   0.001   TYR B 499 
 PHE   0.027   0.001   PHE A 340 
 TRP   0.011   0.002   TRP A 547 
 HIS   0.007   0.000   HIS A 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 (10262)
  covalent geometry    : angle       0.59765 /  0.30 (14239)
  hydrogen bonds       : bond        0.04296 /  3.16 (  430)
  hydrogen bonds       : angle       4.48666 /  3.18 ( 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
  96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  406 MET cc_start: 0.7851 (ptm) cc_final: 0.6827 (ppp)
REVERT: A  434 CYS cc_start: 0.8167 (t) cc_final: 0.7632 (t)
REVERT: A  442 ARG cc_start: 0.7878 (ttp-110) cc_final: 0.7417 (ttp-170)
REVERT: B   74 ASN cc_start: 0.8770 (p0) cc_final: 0.8559 (p0)
REVERT: B   88 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8877 (ttmt)
REVERT: B  141 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8770 (tppp)
REVERT: B  396 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7685 (tmm)
REVERT: B  406 MET cc_start: 0.5720 (pmm) cc_final: 0.5231 (pp-130)
  outliers start: 17
  outliers final: 8
  residues processed: 91
  average time/residue: 0.5841
  time to fit residues: 57.3090
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  : 0.343 
-------------------------------------------------------------------------------
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  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  396 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 105 optimal weight:   30.0000
   chunk 27 optimal weight:    2.9990
   chunk 99 optimal weight:    0.1980
   chunk 102 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 103 optimal weight:   10.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.4186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3766 r_free = 0.3766 target = 0.116098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.079245 restraints weight = 17279.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.54
r_work: 0.2986 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.1848

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= 0.186
  Angle     :  0.645  15.875  14239  Z= 0.324
  Chirality :  0.041   0.406   1613
  Planarity :  0.005   0.056   1552
  Dihedral  : 19.491 166.494   2327
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 28.99 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.26), residues: 1007
  helix:  1.49 (0.26), residues: 373
  sheet: -0.27 (0.36), residues: 220
  loop : -1.38 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 420 
 TYR   0.024   0.001   TYR B 499 
 PHE   0.029   0.002   PHE A 340 
 TRP   0.015   0.002   TRP A 547 
 HIS   0.004   0.001   HIS A 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.19 (10262)
  covalent geometry    : angle       0.64548 /  0.32 (14239)
  hydrogen bonds       : bond        0.04603 /  3.35 (  430)
  hydrogen bonds       : angle       4.56691 /  3.24 ( 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
  86 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  406 MET cc_start: 0.7839 (ptm) cc_final: 0.6913 (ppp)
REVERT: A  421 LYS cc_start: 0.9280 (mmmm) cc_final: 0.8961 (mmmt)
REVERT: A  434 CYS cc_start: 0.8052 (t) cc_final: 0.7256 (t)
REVERT: A  442 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7363 (ttp-170)
REVERT: B   74 ASN cc_start: 0.8788 (p0) cc_final: 0.8574 (p0)
REVERT: B  141 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8777 (tppp)
REVERT: B  396 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7655 (tmm)
REVERT: B  406 MET cc_start: 0.5599 (pmm) cc_final: 0.5123 (pp-130)
  outliers start: 13
  outliers final: 8
  residues processed: 81
  average time/residue: 0.5683
  time to fit residues: 49.8575
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  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 VAL
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  396 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0870
   chunk 46 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0040
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.4770

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3787 r_free = 0.3787 target = 0.117363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.081060 restraints weight = 17408.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.50
r_work: 0.3026 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10262  Z= 0.119
  Angle     :  0.626  14.030  14239  Z= 0.312
  Chirality :  0.040   0.401   1613
  Planarity :  0.005   0.056   1552
  Dihedral  : 19.496 165.501   2327
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 29.10 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.26), residues: 1007
  helix:  1.55 (0.26), residues: 373
  sheet: -0.30 (0.36), residues: 220
  loop : -1.35 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 420 
 TYR   0.022   0.001   TYR B 499 
 PHE   0.027   0.001   PHE A 340 
 TRP   0.016   0.002   TRP B 547 
 HIS   0.004   0.000   HIS A 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 (10262)
  covalent geometry    : angle       0.62632 /  0.31 (14239)
  hydrogen bonds       : bond        0.04289 /  3.16 (  430)
  hydrogen bonds       : angle       4.49663 /  3.19 ( 1163)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2465.72 seconds
wall clock time: 42 minutes 58.21 seconds (2578.21 seconds total)