Starting phenix.real_space_refine
on Tue Feb  3 21:37:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qxl_53437/02_2026/9qxl_53437.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qxl_53437/02_2026/9qxl_53437.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qxl_53437/02_2026/9qxl_53437.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qxl_53437/02_2026/9qxl_53437.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qxl_53437/02_2026/9qxl_53437.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qxl_53437/02_2026/9qxl_53437.cif"
  }
  resolution = 3.14
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    4437      2.51       5
     N    1199      2.21       5
     O    1267      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6947
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2170
          Classifications: {'peptide': 272}
          Link IDs: {'PTRANS': 4, 'TRANS': 267}
    Chain: "B"
      Number of atoms: 1995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1995
          Classifications: {'peptide': 244}
          Link IDs: {'PTRANS': 6, 'TRANS': 237}
    Chain: "C"
      Number of atoms: 2489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2489
          Classifications: {'peptide': 325}
          Link IDs: {'PTRANS': 5, 'TRANS': 319}
    Chain: "E"
      Number of atoms: 293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 293
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 4, 'TRANS': 34}
  Time building chain proxies: 1.32, per 1000 atoms: 0.19
  Number of scatterers: 6947
  At special positions: 0
  Unit cell: (87.77, 98.49, 125.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1267      8.00
     N    1199      7.00
     C    4437      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 441 " - pdb=" SG  CYS A 445 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 490 " - pdb=" SG  CYS A 562 " distance=2.03

  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 257.9 milliseconds
  

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1638

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      43.0% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 408 through 413
      removed outlier: 3.644A  pdb=" N   ILE A 411 " --> pdb=" O   HIS A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 452
      removed outlier: 4.117A  pdb=" N   ILE A 436 " --> pdb=" O   GLN A 432 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE A 437 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   CYS A 441 " --> pdb=" O   ILE A 437 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   ILE A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 481
      removed outlier: 3.866A  pdb=" N   ILE A 481 " --> pdb=" O   PHE A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 521
      removed outlier: 3.837A  pdb=" N   LEU A 502 " --> pdb=" O   HIS A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 551
      removed outlier: 4.283A  pdb=" N   TYR A 534 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   SER A 540 " --> pdb=" O   PHE A 536 " (cutoff:3.500A)
      Proline residue:  A 541  - end of helix
      removed outlier: 3.918A  pdb=" N   LEU A 551 " --> pdb=" O   PHE A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 556
      removed outlier: 3.766A  pdb=" N   TYR A 555 " --> pdb=" O   GLY A 552 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR A 556 " --> pdb=" O   TYR A 553 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 552 through 556'
    Processing helix  chain 'A' and resid 566 through 570
    Processing helix  chain 'A' and resid 571 through 600
      Proline residue:  A 577  - end of helix
      removed outlier: 4.014A  pdb=" N   LEU A 580 " --> pdb=" O   GLY A 576 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   PHE A 589 " --> pdb=" O   ASN A 585 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ILE A 593 " --> pdb=" O   PHE A 589 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   TYR A 594 " --> pdb=" O   GLY A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 627
      removed outlier: 4.213A  pdb=" N   ALA A 622 " --> pdb=" O   ARG A 618 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU A 623 " --> pdb=" O   GLY A 619 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   PHE A 625 " --> pdb=" O   LEU A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 630
      No H-bonds generated for 'chain 'A' and resid 628 through 630'
    Processing helix  chain 'A' and resid 631 through 640
      removed outlier: 3.522A  pdb=" N   VAL A 635 " --> pdb=" O   TRP A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 653
    Processing helix  chain 'A' and resid 655 through 665
      removed outlier: 3.545A  pdb=" N   PHE A 659 " --> pdb=" O   PHE A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 678
      removed outlier: 3.579A  pdb=" N   LEU A 678 " --> pdb=" O   GLU A 674 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 179
      removed outlier: 3.572A  pdb=" N   VAL B 177 " --> pdb=" O   LYS B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 206
      removed outlier: 3.510A  pdb=" N   ILE B 197 " --> pdb=" O   GLY B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 278
      removed outlier: 4.253A  pdb=" N   GLN B 267 " --> pdb=" O   TYR B 263 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLU B 268 " --> pdb=" O   ASN B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 304
      removed outlier: 3.593A  pdb=" N   LEU B 297 " --> pdb=" O   LYS B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 311
    Processing helix  chain 'B' and resid 312 through 318
    Processing helix  chain 'B' and resid 331 through 350
      removed outlier: 3.583A  pdb=" N   THR B 335 " --> pdb=" O   ASP B 331 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE B 348 " --> pdb=" O   GLU B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 389
    Processing helix  chain 'C' and resid 16 through 24
    Processing helix  chain 'C' and resid 28 through 33
      removed outlier: 3.677A  pdb=" N   ILE C  32 " --> pdb=" O   THR C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 36
      No H-bonds generated for 'chain 'C' and resid 34 through 36'
    Processing helix  chain 'E' and resid 34 through 39
    Processing sheet with id=AA1, first strand: chain 'B' and resid 208 through 209
      removed outlier: 3.562A  pdb=" N   LEU B 186 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA B 253 " --> pdb=" O   ARG B 183 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 50
      removed outlier: 4.009A  pdb=" N   ARG C  48 " --> pdb=" O   ILE C 337 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 57 through 62
      removed outlier: 3.929A  pdb=" N   ALA C  59 " --> pdb=" O   ALA C  72 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS C  77 " --> pdb=" O   SER C  73 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS C  90 " --> pdb=" O   ILE C  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 99 through 104
      removed outlier: 6.976A  pdb=" N   GLY C 114 " --> pdb=" O   MET C 100 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   CYS C 102 " --> pdb=" O   ALA C 112 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ALA C 112 " --> pdb=" O   CYS C 102 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   TYR C 104 " --> pdb=" O   TYR C 110 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   TYR C 110 " --> pdb=" O   TYR C 104 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   GLY C 115 " --> pdb=" O   ILE C 119 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   ILE C 119 " --> pdb=" O   GLY C 115 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ASN C 124 " --> pdb=" O   VAL C 134 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   VAL C 134 " --> pdb=" O   ASN C 124 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 145 through 151
      removed outlier: 6.925A  pdb=" N   SER C 159 " --> pdb=" O   SER C 146 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   CYS C 148 " --> pdb=" O   VAL C 157 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   VAL C 157 " --> pdb=" O   CYS C 148 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   PHE C 150 " --> pdb=" O   GLN C 155 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   GLN C 155 " --> pdb=" O   PHE C 150 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   THR C 164 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   THR C 177 " --> pdb=" O   LEU C 167 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   ASP C 169 " --> pdb=" O   GLN C 175 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLN C 175 " --> pdb=" O   ASP C 169 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 186 through 191
      removed outlier: 3.595A  pdb=" N   SER C 188 " --> pdb=" O   GLY C 201 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   SER C 206 " --> pdb=" O   ALA C 202 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   GLN C 219 " --> pdb=" O   LEU C 209 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   ASP C 211 " --> pdb=" O   CYS C 217 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   CYS C 217 " --> pdb=" O   ASP C 211 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 228 through 231
      removed outlier: 6.783A  pdb=" N   GLY C 243 " --> pdb=" O   ASN C 229 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ILE C 231 " --> pdb=" O   ALA C 241 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ALA C 241 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   SER C 244 " --> pdb=" O   THR C 248 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   THR C 248 " --> pdb=" O   SER C 244 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   CYS C 249 " --> pdb=" O   THR C 262 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   THR C 262 " --> pdb=" O   CYS C 249 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LEU C 251 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASP C 253 " --> pdb=" O   GLN C 258 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLN C 258 " --> pdb=" O   ASP C 253 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 274 through 276
      removed outlier: 3.922A  pdb=" N   SER C 274 " --> pdb=" O   GLY C 287 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ASP C 297 " --> pdb=" O   ARG C 303 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ARG C 303 " --> pdb=" O   ASP C 297 " (cutoff:3.500A)

    337 hydrogen bonds defined for protein.
    969 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.79

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.36: 2282
        1.36 -     1.49: 1866
        1.49 -     1.63: 2893
        1.63 -     1.76: 0
        1.76 -     1.90: 58
  Bond restraints: 7099
  Sorted by residual:
  bond pdb=" N   VAL B 367 "
       pdb=" CA  VAL B 367 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 8.04e+00
  bond pdb=" N   ASP C 322 "
       pdb=" CA  ASP C 322 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.33e-02 5.65e+03 7.28e+00
  bond pdb=" CB  CYS A 441 "
       pdb=" SG  CYS A 441 "
    ideal  model  delta    sigma   weight residual
    1.808  1.897 -0.089 3.30e-02 9.18e+02 7.21e+00
  bond pdb=" C   SER A 540 "
       pdb=" N   PRO A 541 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.28e-02 6.10e+03 3.58e+00
  bond pdb=" CB  CYS A 445 "
       pdb=" SG  CYS A 445 "
    ideal  model  delta    sigma   weight residual
    1.808  1.867 -0.059 3.30e-02 9.18e+02 3.20e+00
  ... (remaining 7094 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 9359
        2.24 -     4.48: 217
        4.48 -     6.72: 30
        6.72 -     8.96: 9
        8.96 -    11.20: 1
  Bond angle restraints: 9616
  Sorted by residual:
  angle pdb=" C   ILE A 440 "
        pdb=" N   CYS A 441 "
        pdb=" CA  CYS A 441 "
      ideal   model   delta    sigma   weight residual
     122.38  113.58    8.80 1.81e+00 3.05e-01 2.36e+01
  angle pdb=" N   ILE A 419 "
        pdb=" CA  ILE A 419 "
        pdb=" C   ILE A 419 "
      ideal   model   delta    sigma   weight residual
     110.05  105.35    4.70 1.09e+00 8.42e-01 1.86e+01
  angle pdb=" CB  GLN B 176 "
        pdb=" CG  GLN B 176 "
        pdb=" CD  GLN B 176 "
      ideal   model   delta    sigma   weight residual
     112.60  119.10   -6.50 1.70e+00 3.46e-01 1.46e+01
  angle pdb=" CA  ASP C 322 "
        pdb=" CB  ASP C 322 "
        pdb=" CG  ASP C 322 "
      ideal   model   delta    sigma   weight residual
     112.60  116.13   -3.53 1.00e+00 1.00e+00 1.25e+01
  angle pdb=" CA  LEU A 529 "
        pdb=" CB  LEU A 529 "
        pdb=" CG  LEU A 529 "
      ideal   model   delta    sigma   weight residual
     116.30  127.50  -11.20 3.50e+00 8.16e-02 1.02e+01
  ... (remaining 9611 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.04: 3882
       16.04 -    32.09: 240
       32.09 -    48.13: 22
       48.13 -    64.17: 22
       64.17 -    80.21: 3
  Dihedral angle restraints: 4169
    sinusoidal: 1625
      harmonic: 2544
  Sorted by residual:
  dihedral pdb=" CB  CYS A 490 "
           pdb=" SG  CYS A 490 "
           pdb=" SG  CYS A 562 "
           pdb=" CB  CYS A 562 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -127.05   41.05     1      1.00e+01 1.00e-02 2.36e+01
  dihedral pdb=" CA  CYS C 232 "
           pdb=" C   CYS C 232 "
           pdb=" N   PHE C 233 "
           pdb=" CA  PHE C 233 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.25   21.75     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  LEU A 442 "
           pdb=" C   LEU A 442 "
           pdb=" N   ALA A 443 "
           pdb=" CA  ALA A 443 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.31   21.69     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 4166 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 836
       0.059 -    0.119: 211
       0.119 -    0.178: 30
       0.178 -    0.237: 3
       0.237 -    0.297: 2
  Chirality restraints: 1082
  Sorted by residual:
  chirality pdb=" CB  VAL A 638 "
            pdb=" CA  VAL A 638 "
            pdb=" CG1 VAL A 638 "
            pdb=" CG2 VAL A 638 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  VAL B 367 "
            pdb=" N   VAL B 367 "
            pdb=" C   VAL B 367 "
            pdb=" CB  VAL B 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  ILE A 419 "
            pdb=" N   ILE A 419 "
            pdb=" C   ILE A 419 "
            pdb=" CB  ILE A 419 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.88e-01
  ... (remaining 1079 not shown)

  Planarity restraints: 1221
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 366 "   -0.013 2.00e-02 2.50e+03   2.70e-02 7.27e+00
        pdb=" C   ALA B 366 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ALA B 366 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   VAL B 367 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 584 "    0.013 2.00e-02 2.50e+03   2.66e-02 7.07e+00
        pdb=" C   VAL A 584 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   VAL A 584 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASN A 585 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 441 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.71e+00
        pdb=" C   CYS A 441 "    0.045 2.00e-02 2.50e+03
        pdb=" O   CYS A 441 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A 442 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1218 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 2231
        2.84 -     3.36: 5984
        3.36 -     3.87: 10796
        3.87 -     4.39: 12272
        4.39 -     4.90: 21691
  Nonbonded interactions: 52974
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 448 "
            pdb=" OH  TYR A 675 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" NH1 ARG C  48 "
            pdb=" O   THR C  49 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" OG  SER C 280 "
            pdb=" OD2 ASP E  48 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" O   SER B 261 "
            pdb=" NZ  LYS B 300 "
     model   vdw
     2.416 3.120
  nonbonded pdb=" OE1 GLN B 160 "
            pdb=" OG1 THR C  85 "
     model   vdw
     2.424 3.040
  ... (remaining 52969 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             4.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.550
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
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      :  0.004   0.089   7101  Z= 0.221
  Angle     :  0.840  11.201   9620  Z= 0.468
  Chirality :  0.053   0.297   1082
  Planarity :  0.007   0.062   1221
  Dihedral  : 11.382  80.214   2525
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  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: -1.37 (0.25), residues: 872
  helix: -0.54 (0.24), residues: 343
  sheet:  0.07 (0.39), residues: 174
  loop : -1.69 (0.28), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 202 
 TYR   0.017   0.002   TYR A 676 
 PHE   0.030   0.003   PHE C 198 
 TRP   0.026   0.002   TRP A 563 
 HIS   0.011   0.002   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 7099)
  covalent geometry    : angle       0.83638 ( 9616)
  SS BOND              : bond        0.00871 (    2)
  SS BOND              : angle       3.88974 (    4)
  hydrogen bonds       : bond        0.15574 (  337)
  hydrogen bonds       : angle       5.91430 (  969)

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  451 PHE cc_start: 0.8076 (t80) cc_final: 0.7749 (t80)
REVERT: A  553 TYR cc_start: 0.6837 (p90) cc_final: 0.6220 (t80)
REVERT: A  554 ARG cc_start: 0.7903 (ptt-90) cc_final: 0.7575 (ptt90)
REVERT: B  161 ARG cc_start: 0.6758 (mtt-85) cc_final: 0.6352 (mtm180)
REVERT: B  168 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7284 (mt-10)
REVERT: B  283 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7585 (mtp-110)
REVERT: C   58 TYR cc_start: 0.8212 (m-10) cc_final: 0.7430 (m-80)
REVERT: C  196 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7868 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0816
  time to fit residues: 11.4147
Evaluate side-chains
  75 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    2.2124

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
A 599 HIS
** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  87 ASN
C 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.135037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.093352 restraints weight = 9646.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 3.38
r_work: 0.2928 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.097   7101  Z= 0.285
  Angle     :  0.680  11.124   9620  Z= 0.373
  Chirality :  0.048   0.137   1082
  Planarity :  0.005   0.045   1221
  Dihedral  :  4.488  19.085    956
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.64 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  5.87 %
    Favored  : 92.66 %
  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: -0.47 (0.27), residues: 872
  helix:  0.93 (0.27), residues: 345
  sheet: -0.29 (0.39), residues: 169
  loop : -1.55 (0.29), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 342 
 TYR   0.026   0.002   TYR C 104 
 PHE   0.022   0.003   PHE B 248 
 TRP   0.014   0.002   TRP C 331 
 HIS   0.012   0.002   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00706 ( 7099)
  covalent geometry    : angle       0.67319 ( 9616)
  SS BOND              : bond        0.03692 (    2)
  SS BOND              : angle       4.69061 (    4)
  hydrogen bonds       : bond        0.08080 (  337)
  hydrogen bonds       : angle       4.53697 (  969)

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  553 TYR cc_start: 0.7326 (p90) cc_final: 0.6588 (t80)
REVERT: B  161 ARG cc_start: 0.7189 (mtt-85) cc_final: 0.6608 (mtm110)
  outliers start: 11
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0843
  time to fit residues: 8.5053
Evaluate side-chains
  72 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  188 SER
Chi-restraints excluded: chain C residue  258 GLN
Chi-restraints excluded: chain C residue  321 ASP
Chi-restraints excluded: chain E residue   30 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 52 optimal weight:    6.9990
   chunk 71 optimal weight:    0.2980
   chunk 3 optimal weight:    0.5980
   chunk 72 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 73 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** B 230 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 = 0.3733 r_free = 0.3733 target = 0.139941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.098760 restraints weight = 9374.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 3.33
r_work: 0.3034 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.074   7101  Z= 0.109
  Angle     :  0.489  10.793   9620  Z= 0.273
  Chirality :  0.041   0.148   1082
  Planarity :  0.003   0.036   1221
  Dihedral  :  3.917  20.607    956
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  7.08 %
    Favored  : 91.99 %
  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:  0.25 (0.28), residues: 872
  helix:  1.77 (0.28), residues: 348
  sheet: -0.24 (0.39), residues: 169
  loop : -1.26 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 202 
 TYR   0.009   0.001   TYR B 339 
 PHE   0.014   0.001   PHE B 376 
 TRP   0.010   0.001   TRP A 507 
 HIS   0.004   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 7099)
  covalent geometry    : angle       0.48235 ( 9616)
  SS BOND              : bond        0.02174 (    2)
  SS BOND              : angle       4.11283 (    4)
  hydrogen bonds       : bond        0.05160 (  337)
  hydrogen bonds       : angle       4.01691 (  969)

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  547 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7654 (t80)
REVERT: A  553 TYR cc_start: 0.7244 (p90) cc_final: 0.6654 (t80)
REVERT: B  161 ARG cc_start: 0.7142 (mtt-85) cc_final: 0.6687 (mtm110)
REVERT: C   58 TYR cc_start: 0.8634 (m-80) cc_final: 0.7623 (m-80)
REVERT: E   38 MET cc_start: 0.7977 (mpp) cc_final: 0.7624 (mmp)
  outliers start: 7
  outliers final: 4
  residues processed: 81
  average time/residue: 0.1024
  time to fit residues: 10.9225
Evaluate side-chains
  75 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain C residue   54 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0770
   chunk 23 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.7538

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

Flipped N/Q/H residues before XYZ refinement:
** B 230 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 = 0.3715 r_free = 0.3715 target = 0.138553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.096940 restraints weight = 9543.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 3.36
r_work: 0.3013 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   7101  Z= 0.124
  Angle     :  0.486  10.829   9620  Z= 0.269
  Chirality :  0.041   0.145   1082
  Planarity :  0.003   0.035   1221
  Dihedral  :  3.807  23.581    956
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  9.08 %
    Favored  : 89.85 %
  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:  0.46 (0.28), residues: 872
  helix:  2.00 (0.28), residues: 354
  sheet: -0.22 (0.39), residues: 175
  loop : -1.24 (0.30), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 202 
 TYR   0.010   0.001   TYR C 104 
 PHE   0.013   0.001   PHE C 198 
 TRP   0.011   0.001   TRP A 507 
 HIS   0.005   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7099)
  covalent geometry    : angle       0.47903 ( 9616)
  SS BOND              : bond        0.02174 (    2)
  SS BOND              : angle       3.90777 (    4)
  hydrogen bonds       : bond        0.05265 (  337)
  hydrogen bonds       : angle       3.98899 (  969)

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A  547 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7629 (t80)
REVERT: A  553 TYR cc_start: 0.7303 (p90) cc_final: 0.6668 (t80)
REVERT: A  675 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7169 (t80)
REVERT: B  161 ARG cc_start: 0.7130 (mtt-85) cc_final: 0.6658 (mtm110)
REVERT: C   58 TYR cc_start: 0.8694 (m-80) cc_final: 0.7655 (m-80)
REVERT: E   38 MET cc_start: 0.7871 (mpp) cc_final: 0.7543 (mmp)
  outliers start: 8
  outliers final: 5
  residues processed: 73
  average time/residue: 0.0845
  time to fit residues: 8.2004
Evaluate side-chains
  75 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  675 TYR
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   97 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0170
   chunk 5 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.0024

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

Flipped N/Q/H residues before XYZ refinement:
B 160 GLN
** B 230 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 = 0.3706 r_free = 0.3706 target = 0.138002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.096251 restraints weight = 9606.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 3.40
r_work: 0.2998 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   7101  Z= 0.146
  Angle     :  0.503  11.028   9620  Z= 0.278
  Chirality :  0.042   0.138   1082
  Planarity :  0.003   0.035   1221
  Dihedral  :  3.801  19.399    956
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  8.81 %
    Favored  : 89.72 %
  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:  0.60 (0.29), residues: 872
  helix:  2.09 (0.28), residues: 355
  sheet: -0.10 (0.39), residues: 180
  loop : -1.18 (0.31), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 554 
 TYR   0.011   0.001   TYR C 104 
 PHE   0.013   0.001   PHE C 198 
 TRP   0.010   0.001   TRP A 507 
 HIS   0.006   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7099)
  covalent geometry    : angle       0.49638 ( 9616)
  SS BOND              : bond        0.02414 (    2)
  SS BOND              : angle       3.91964 (    4)
  hydrogen bonds       : bond        0.05701 (  337)
  hydrogen bonds       : angle       3.98083 (  969)

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  547 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7637 (t80)
REVERT: A  553 TYR cc_start: 0.7367 (p90) cc_final: 0.6639 (t80)
REVERT: A  554 ARG cc_start: 0.8291 (ptt-90) cc_final: 0.8060 (ptt90)
REVERT: A  675 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7184 (t80)
REVERT: A  676 TYR cc_start: 0.8124 (t80) cc_final: 0.7308 (m-10)
REVERT: B  161 ARG cc_start: 0.7160 (mtt-85) cc_final: 0.6735 (mtm180)
REVERT: C   58 TYR cc_start: 0.8720 (m-80) cc_final: 0.7653 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0864
  time to fit residues: 8.9140
Evaluate side-chains
  83 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  675 TYR
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  188 SER
Chi-restraints excluded: chain C residue  233 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 64 optimal weight:    0.0030
   chunk 81 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.3196

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

Flipped N/Q/H residues before XYZ refinement:
** B 230 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 = 0.3680 r_free = 0.3680 target = 0.135879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.094199 restraints weight = 9593.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 3.38
r_work: 0.2942 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   7101  Z= 0.178
  Angle     :  0.542  10.987   9620  Z= 0.299
  Chirality :  0.043   0.161   1082
  Planarity :  0.003   0.035   1221
  Dihedral  :  3.946  18.774    956
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.98 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  8.68 %
    Favored  : 89.19 %
  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:  0.58 (0.29), residues: 872
  helix:  2.07 (0.28), residues: 353
  sheet: -0.01 (0.39), residues: 178
  loop : -1.23 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 554 
 TYR   0.013   0.001   TYR C 104 
 PHE   0.014   0.002   PHE C 240 
 TRP   0.010   0.001   TRP A 507 
 HIS   0.007   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 7099)
  covalent geometry    : angle       0.53566 ( 9616)
  SS BOND              : bond        0.02728 (    2)
  SS BOND              : angle       4.21986 (    4)
  hydrogen bonds       : bond        0.06361 (  337)
  hydrogen bonds       : angle       4.06516 (  969)

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  547 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7590 (t80)
REVERT: A  553 TYR cc_start: 0.7436 (p90) cc_final: 0.6624 (t80)
REVERT: A  675 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7321 (t80)
REVERT: A  676 TYR cc_start: 0.8231 (t80) cc_final: 0.7366 (m-10)
REVERT: B  161 ARG cc_start: 0.7099 (mtt-85) cc_final: 0.6531 (mtm110)
REVERT: C   58 TYR cc_start: 0.8729 (m-80) cc_final: 0.7605 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0686
  time to fit residues: 7.5271
Evaluate side-chains
  83 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  675 TYR
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  188 SER
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain C residue  317 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0170
   chunk 20 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 62 optimal weight:    0.1980
   chunk 15 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.4218

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

Flipped N/Q/H residues before XYZ refinement:
A 408 HIS
** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.139706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.098327 restraints weight = 9441.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 3.36
r_work: 0.3024 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.067   7101  Z= 0.099
  Angle     :  0.458  10.711   9620  Z= 0.254
  Chirality :  0.040   0.144   1082
  Planarity :  0.003   0.032   1221
  Dihedral  :  3.638  20.568    956
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  9.21 %
    Favored  : 89.19 %
  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:  0.95 (0.29), residues: 872
  helix:  2.41 (0.28), residues: 356
  sheet:  0.14 (0.40), residues: 173
  loop : -1.06 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 554 
 TYR   0.009   0.001   TYR B 339 
 PHE   0.012   0.001   PHE C 291 
 TRP   0.010   0.001   TRP C 296 
 HIS   0.004   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 7099)
  covalent geometry    : angle       0.45160 ( 9616)
  SS BOND              : bond        0.01913 (    2)
  SS BOND              : angle       3.76881 (    4)
  hydrogen bonds       : bond        0.04492 (  337)
  hydrogen bonds       : angle       3.80463 (  969)

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 GLN cc_start: 0.8494 (mp-120) cc_final: 0.8232 (mm110)
REVERT: A  547 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7563 (t80)
REVERT: A  553 TYR cc_start: 0.7326 (p90) cc_final: 0.6631 (t80)
REVERT: A  554 ARG cc_start: 0.8298 (ptt-90) cc_final: 0.8039 (ptt90)
REVERT: A  675 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7353 (t80)
REVERT: A  676 TYR cc_start: 0.8157 (t80) cc_final: 0.7284 (m-10)
REVERT: B  161 ARG cc_start: 0.7058 (mtt-85) cc_final: 0.6507 (mtm110)
REVERT: C   58 TYR cc_start: 0.8711 (m-80) cc_final: 0.7604 (m-80)
REVERT: E   38 MET cc_start: 0.7717 (mpp) cc_final: 0.7226 (mmp)
  outliers start: 12
  outliers final: 9
  residues processed: 83
  average time/residue: 0.0789
  time to fit residues: 8.6906
Evaluate side-chains
  79 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  675 TYR
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  188 SER
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  317 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 4 optimal weight:    0.0070
   chunk 64 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0370
   chunk 15 optimal weight:    0.1980
   chunk 78 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.140223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.098853 restraints weight = 9509.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 3.38
r_work: 0.3042 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.064   7101  Z= 0.099
  Angle     :  0.459  10.850   9620  Z= 0.254
  Chirality :  0.040   0.142   1082
  Planarity :  0.003   0.032   1221
  Dihedral  :  3.560  20.173    956
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 10.41 %
    Favored  : 87.98 %
  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:  1.10 (0.29), residues: 872
  helix:  2.59 (0.28), residues: 356
  sheet:  0.11 (0.40), residues: 175
  loop : -0.98 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 554 
 TYR   0.010   0.001   TYR C 123 
 PHE   0.015   0.001   PHE C 291 
 TRP   0.009   0.001   TRP A 507 
 HIS   0.004   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 7099)
  covalent geometry    : angle       0.45334 ( 9616)
  SS BOND              : bond        0.01850 (    2)
  SS BOND              : angle       3.60419 (    4)
  hydrogen bonds       : bond        0.04336 (  337)
  hydrogen bonds       : angle       3.76254 (  969)

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 GLN cc_start: 0.8501 (mp-120) cc_final: 0.8265 (mm110)
REVERT: A  547 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7597 (t80)
REVERT: A  553 TYR cc_start: 0.7355 (p90) cc_final: 0.6698 (t80)
REVERT: A  675 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7245 (t80)
REVERT: A  676 TYR cc_start: 0.8070 (t80) cc_final: 0.7211 (m-10)
REVERT: B  161 ARG cc_start: 0.7082 (mtt-85) cc_final: 0.6532 (mtm110)
REVERT: C   58 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.7674 (m-80)
REVERT: E   38 MET cc_start: 0.7728 (mpp) cc_final: 0.7260 (mmp)
  outliers start: 12
  outliers final: 8
  residues processed: 81
  average time/residue: 0.0687
  time to fit residues: 7.4540
Evaluate side-chains
  85 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  675 TYR
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  188 SER
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain C residue  317 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 39 optimal weight:    0.3980
   chunk 72 optimal weight:    0.9990
   chunk 66 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 230 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 = 0.3716 r_free = 0.3716 target = 0.138647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.097312 restraints weight = 9455.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 3.34
r_work: 0.3027 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   7101  Z= 0.124
  Angle     :  0.512  13.593   9620  Z= 0.278
  Chirality :  0.041   0.138   1082
  Planarity :  0.003   0.032   1221
  Dihedral  :  3.674  22.581    956
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.29 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  9.88 %
    Favored  : 88.12 %
  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 are not related in a simple way.
  whole:  1.05 (0.29), residues: 872
  helix:  2.54 (0.28), residues: 356
  sheet:  0.12 (0.39), residues: 178
  loop : -1.04 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 374 
 TYR   0.009   0.001   TYR B 339 
 PHE   0.014   0.001   PHE C 291 
 TRP   0.010   0.001   TRP A 507 
 HIS   0.005   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7099)
  covalent geometry    : angle       0.50428 ( 9616)
  SS BOND              : bond        0.02057 (    2)
  SS BOND              : angle       4.24083 (    4)
  hydrogen bonds       : bond        0.04929 (  337)
  hydrogen bonds       : angle       3.93099 (  969)

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 GLN cc_start: 0.8579 (mp-120) cc_final: 0.8334 (mm110)
REVERT: A  547 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7611 (t80)
REVERT: A  553 TYR cc_start: 0.7366 (p90) cc_final: 0.6699 (t80)
REVERT: A  675 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7183 (t80)
REVERT: A  676 TYR cc_start: 0.8026 (t80) cc_final: 0.7203 (m-10)
REVERT: B  161 ARG cc_start: 0.7134 (mtt-85) cc_final: 0.6590 (mtm110)
REVERT: B  191 ASN cc_start: 0.8093 (t0) cc_final: 0.7829 (t0)
REVERT: C   58 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.7678 (m-80)
REVERT: C  133 ARG cc_start: 0.7139 (ptt180) cc_final: 0.6734 (ptm160)
REVERT: E   38 MET cc_start: 0.7729 (mpp) cc_final: 0.7261 (mmp)
  outliers start: 15
  outliers final: 12
  residues processed: 83
  average time/residue: 0.0783
  time to fit residues: 8.5259
Evaluate side-chains
  86 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  675 TYR
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain C residue   46 THR
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  188 SER
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  321 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 67 optimal weight:    8.9990
   chunk 75 optimal weight:    0.0970
   chunk 23 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 69 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 530 HIS
** B 230 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 = 0.3733 r_free = 0.3733 target = 0.140430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.098861 restraints weight = 9489.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 3.38
r_work: 0.3017 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   7101  Z= 0.113
  Angle     :  0.502  13.117   9620  Z= 0.272
  Chirality :  0.041   0.137   1082
  Planarity :  0.003   0.032   1221
  Dihedral  :  3.661  20.969    956
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.06 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.15 %
    Favored  : 87.85 %
  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:  1.13 (0.29), residues: 872
  helix:  2.65 (0.28), residues: 354
  sheet:  0.15 (0.40), residues: 175
  loop : -1.00 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 554 
 TYR   0.010   0.001   TYR C 123 
 PHE   0.019   0.001   PHE A 452 
 TRP   0.009   0.001   TRP A 507 
 HIS   0.004   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7099)
  covalent geometry    : angle       0.49504 ( 9616)
  SS BOND              : bond        0.01935 (    2)
  SS BOND              : angle       4.16164 (    4)
  hydrogen bonds       : bond        0.04645 (  337)
  hydrogen bonds       : angle       3.90145 (  969)

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 GLN cc_start: 0.8492 (mp-120) cc_final: 0.8248 (mm-40)
REVERT: A  547 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7578 (t80)
REVERT: A  553 TYR cc_start: 0.7339 (p90) cc_final: 0.6606 (t80)
REVERT: A  675 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7241 (t80)
REVERT: B  161 ARG cc_start: 0.7063 (mtt-85) cc_final: 0.6517 (mtm110)
REVERT: B  191 ASN cc_start: 0.8102 (t0) cc_final: 0.7827 (t0)
REVERT: C   58 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.7626 (m-80)
REVERT: C  133 ARG cc_start: 0.7160 (ptt180) cc_final: 0.6728 (ptm160)
REVERT: E   38 MET cc_start: 0.7643 (mpp) cc_final: 0.7163 (mmp)
  outliers start: 15
  outliers final: 9
  residues processed: 84
  average time/residue: 0.0905
  time to fit residues: 10.0017
Evaluate side-chains
  85 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  675 TYR
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain C residue   46 THR
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  188 SER
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain C residue  317 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   chunk 46 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 530 HIS
** B 230 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 = 0.3696 r_free = 0.3696 target = 0.136984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.095510 restraints weight = 9436.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 3.33
r_work: 0.2976 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   7101  Z= 0.146
  Angle     :  0.528  13.491   9620  Z= 0.290
  Chirality :  0.042   0.137   1082
  Planarity :  0.003   0.033   1221
  Dihedral  :  3.826  20.702    956
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.87 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  9.88 %
    Favored  : 88.38 %
  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:  1.02 (0.29), residues: 872
  helix:  2.51 (0.28), residues: 355
  sheet:  0.13 (0.39), residues: 178
  loop : -1.05 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 374 
 TYR   0.010   0.001   TYR C 104 
 PHE   0.018   0.001   PHE A 452 
 TRP   0.010   0.001   TRP A 507 
 HIS   0.006   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7099)
  covalent geometry    : angle       0.52160 ( 9616)
  SS BOND              : bond        0.02361 (    2)
  SS BOND              : angle       4.15835 (    4)
  hydrogen bonds       : bond        0.05566 (  337)
  hydrogen bonds       : angle       4.02807 (  969)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1594.89 seconds
wall clock time: 27 minutes 59.77 seconds (1679.77 seconds total)