Starting phenix.real_space_refine
on Wed Mar  4 02:05:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x68_22073/03_2026/6x68_22073.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x68_22073/03_2026/6x68_22073.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x68_22073/03_2026/6x68_22073.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x68_22073/03_2026/6x68_22073.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x68_22073/03_2026/6x68_22073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x68_22073/03_2026/6x68_22073.map"
  }
  resolution = 3.66
  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=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     Zn      4      6.06       5
     P     124      5.49       5
     S      88      5.16       5
     C    6063      2.51       5
     N    1811      2.21       5
     O    2152      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10246
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "C"
      Number of atoms: 3848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3848
          Classifications: {'peptide': 478}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 25, 'TRANS': 452}
    Chain: "D"
      Number of atoms: 3848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3848
          Classifications: {'peptide': 478}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 25, 'TRANS': 452}
    Chain: "A"
      Number of atoms: 1517
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1517
          Classifications: {'DNA': 74}
          Link IDs: {'rna3p': 73}
    Chain: "B"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 1025
          Classifications: {'DNA': 50}
          Link IDs: {'rna3p': 49}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 2, ' ZN': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 1, ' ZN': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3568  SG  CYS C 559      43.876  58.830  53.085  1.00101.37           S
  ATOM   3593  SG  CYS C 562      44.008  62.320  53.323  1.00101.18           S
  ATOM   3747  SG  CYS C 582      44.083  60.658  50.274  1.00102.93           S
  ATOM   3684  SG  CYS C 574      50.264  50.434  49.266  1.00157.97           S
  ATOM   3708  SG  CYS C 577      50.090  49.390  52.178  1.00145.09           S
  ATOM   3815  SG  CYS C 590      51.546  52.352  51.479  1.00159.91           S
  ATOM   3836  SG  CYS C 593      52.626  49.806  51.000  1.00172.88           S
  ATOM   7416  SG  CYS D 559      50.389  56.078  28.512  1.00  0.00           S
  ATOM   7441  SG  CYS D 562      47.844  55.761  27.137  1.00319.64           S
  ATOM   7595  SG  CYS D 582      47.770  55.742  30.601  1.00289.96           S
  ATOM   7532  SG  CYS D 574      58.188  55.339  37.702  1.00325.15           S
  ATOM   7556  SG  CYS D 577      60.281  55.493  35.331  1.00356.83           S
  ATOM   7663  SG  CYS D 590      58.020  52.711  36.125  1.00303.36           S
  ATOM   7684  SG  CYS D 593      59.976  53.297  37.650  1.00322.51           S

  Time building chain proxies: 2.54, per 1000 atoms: 0.25
  Number of scatterers: 10246
  At special positions: 0
  Unit cell: (95.04, 90.72, 149.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      4     29.99
     Ca      4     19.99
     S      88     16.00
     P     124     15.00
     O    2152      8.00
     N    1811      7.00
     C    6063      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: 0.82
  Conformation dependent library (CDL) restraints added in 388.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 603 "
        pdb="ZN    ZN C 603 " - pdb=" SG  CYS C 582 "
        pdb="ZN    ZN C 603 " - pdb=" SG  CYS C 562 "
        pdb="ZN    ZN C 603 " - pdb=" SG  CYS C 559 "
        pdb="ZN    ZN C 603 " - pdb=" ND1 HIS C 585 "
      pdb="  ZN C 604 "
        pdb="ZN    ZN C 604 " - pdb=" SG  CYS C 577 "
        pdb="ZN    ZN C 604 " - pdb=" SG  CYS C 593 "
        pdb="ZN    ZN C 604 " - pdb=" SG  CYS C 590 "
        pdb="ZN    ZN C 604 " - pdb=" SG  CYS C 574 "
      pdb="  ZN D 602 "
        pdb="ZN    ZN D 602 " - pdb=" SG  CYS D 562 "
        pdb="ZN    ZN D 602 " - pdb=" SG  CYS D 582 "
        pdb="ZN    ZN D 602 " - pdb=" SG  CYS D 559 "
        pdb="ZN    ZN D 602 " - pdb=" ND1 HIS D 585 "
      pdb="  ZN D 603 "
        pdb="ZN    ZN D 603 " - pdb=" SG  CYS D 574 "
        pdb="ZN    ZN D 603 " - pdb=" SG  CYS D 593 "
        pdb="ZN    ZN D 603 " - pdb=" SG  CYS D 590 "
        pdb="ZN    ZN D 603 " - pdb=" SG  CYS D 577 "
      Number of angles added : 18


  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1820

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 7 sheets defined
      46.1% alpha, 11.5% beta
      52 base pairs and 103 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'C' and resid 123 through 126
    Processing helix  chain 'C' and resid 130 through 159
      removed outlier: 3.935A  pdb=" N   PHE C 138 " --> pdb=" O   CYS C 134 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   ASP C 141 " --> pdb=" O   LEU C 137 " (cutoff:3.500A)
      removed outlier: 8.287A  pdb=" N   GLU C 142 " --> pdb=" O   PHE C 138 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE C 143 " --> pdb=" O   PHE C 139 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE C 144 " --> pdb=" O   THR C 140 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA C 153 " --> pdb=" O   LYS C 149 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU C 154 " --> pdb=" O   TRP C 150 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU C 157 " --> pdb=" O   ALA C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 169
    Processing helix  chain 'C' and resid 172 through 189
    Processing helix  chain 'C' and resid 195 through 200
      removed outlier: 3.838A  pdb=" N   PHE C 200 " --> pdb=" O   THR C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 224
    Processing helix  chain 'C' and resid 231 through 235
    Processing helix  chain 'C' and resid 241 through 243
      No H-bonds generated for 'chain 'C' and resid 241 through 243'
    Processing helix  chain 'C' and resid 244 through 258
      removed outlier: 4.611A  pdb=" N   LEU C 250 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASN C 258 " --> pdb=" O   GLN C 254 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 333
    Processing helix  chain 'C' and resid 334 through 337
    Processing helix  chain 'C' and resid 346 through 350
    Processing helix  chain 'C' and resid 351 through 358
    Processing helix  chain 'C' and resid 379 through 384
    Processing helix  chain 'C' and resid 433 through 443
    Processing helix  chain 'C' and resid 443 through 453
      removed outlier: 4.831A  pdb=" N   ASP C 447 " --> pdb=" O   LYS C 443 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   LEU C 449 " --> pdb=" O   GLY C 445 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 465 through 491
      removed outlier: 4.055A  pdb=" N   LEU C 469 " --> pdb=" O   TRP C 465 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 498 through 519
      removed outlier: 3.680A  pdb=" N   SER C 512 " --> pdb=" O   MET C 508 " (cutoff:3.500A)
      removed outlier: 5.447A  pdb=" N   SER C 513 " --> pdb=" O   SER C 509 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   PHE C 514 " --> pdb=" O   LEU C 510 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LYS C 517 " --> pdb=" O   SER C 513 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU C 519 " --> pdb=" O   MET C 515 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 525 through 535
    Processing helix  chain 'C' and resid 563 through 567
    Processing helix  chain 'D' and resid 123 through 126
    Processing helix  chain 'D' and resid 130 through 137
    Processing helix  chain 'D' and resid 140 through 159
      removed outlier: 4.075A  pdb=" N   ALA D 153 " --> pdb=" O   LYS D 149 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLU D 154 " --> pdb=" O   TRP D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 169
    Processing helix  chain 'D' and resid 172 through 190
    Processing helix  chain 'D' and resid 195 through 200
    Processing helix  chain 'D' and resid 213 through 224
    Processing helix  chain 'D' and resid 231 through 236
    Processing helix  chain 'D' and resid 241 through 243
      No H-bonds generated for 'chain 'D' and resid 241 through 243'
    Processing helix  chain 'D' and resid 244 through 257
      removed outlier: 3.744A  pdb=" N   GLN D 254 " --> pdb=" O   LEU D 250 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   CYS D 255 " --> pdb=" O   PHE D 251 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 323 through 333
    Processing helix  chain 'D' and resid 334 through 337
    Processing helix  chain 'D' and resid 346 through 350
      removed outlier: 3.885A  pdb=" N   THR D 350 " --> pdb=" O   ASN D 347 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 351 through 358
    Processing helix  chain 'D' and resid 379 through 384
    Processing helix  chain 'D' and resid 433 through 443
      removed outlier: 3.948A  pdb=" N   GLN D 441 " --> pdb=" O   MET D 437 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   THR D 442 " --> pdb=" O   TYR D 438 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 444 through 456
    Processing helix  chain 'D' and resid 464 through 491
      removed outlier: 3.542A  pdb=" N   ALA D 468 " --> pdb=" O   ARG D 464 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU D 470 " --> pdb=" O   PRO D 466 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE D 479 " --> pdb=" O   ASN D 475 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   PHE D 482 " --> pdb=" O   CYS D 478 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 498 through 519
      removed outlier: 5.383A  pdb=" N   SER D 513 " --> pdb=" O   SER D 509 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   PHE D 514 " --> pdb=" O   LEU D 510 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU D 519 " --> pdb=" O   MET D 515 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 525 through 536
    Processing helix  chain 'D' and resid 590 through 594
    Processing sheet with id=AA1, first strand: chain 'C' and resid 120 through 121
    Processing sheet with id=AA2, first strand: chain 'C' and resid 306 through 311
      removed outlier: 6.828A  pdb=" N   MET C 298 " --> pdb=" O   ILE C 307 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLY C 309 " --> pdb=" O   LEU C 296 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LEU C 296 " --> pdb=" O   GLY C 309 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   LYS C 294 " --> pdb=" O   PRO C 311 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU C 265 " --> pdb=" O   THR C 344 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 572 through 574
      removed outlier: 3.539A  pdb=" N   LYS C 579 " --> pdb=" O   CYS C 574 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 120 through 121
    Processing sheet with id=AA5, first strand: chain 'D' and resid 282 through 283
      removed outlier: 6.457A  pdb=" N   ASP D 300 " --> pdb=" O   MET D 306 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   MET D 306 " --> pdb=" O   ASP D 300 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 282 through 283
      removed outlier: 5.029A  pdb=" N   ILE D 367 " --> pdb=" O   SER D 419 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 572 through 573

    332 hydrogen bonds defined for protein.
    906 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      129 hydrogen bonds
      258 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      103 stacking parallelities
  Total time for adding SS restraints: 1.96

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2084
        1.33 -     1.45: 3323
        1.45 -     1.58: 4912
        1.58 -     1.71: 247
        1.71 -     1.83: 136
  Bond restraints: 10702
  Sorted by residual:
  bond pdb=" O3'  DA A  33 "
       pdb=" P    DT A  34 "
    ideal  model  delta    sigma   weight residual
    1.607  1.516  0.091 1.50e-02 4.44e+03 3.72e+01
  bond pdb=" N   SER D 289 "
       pdb=" CA  SER D 289 "
    ideal  model  delta    sigma   weight residual
    1.458  1.392  0.066 1.19e-02 7.06e+03 3.10e+01
  bond pdb=" N   ASN C 384 "
       pdb=" CA  ASN C 384 "
    ideal  model  delta    sigma   weight residual
    1.454  1.392  0.061 1.23e-02 6.61e+03 2.47e+01
  bond pdb=" CA  ASN C 384 "
       pdb=" C   ASN C 384 "
    ideal  model  delta    sigma   weight residual
    1.523  1.465  0.058 1.21e-02 6.83e+03 2.33e+01
  bond pdb=" C4'  DT A  34 "
       pdb=" C3'  DT A  34 "
    ideal  model  delta    sigma   weight residual
    1.523  1.617 -0.094 2.00e-02 2.50e+03 2.23e+01
  ... (remaining 10697 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.39: 14542
        4.39 -     8.79: 399
        8.79 -    13.18: 25
       13.18 -    17.58: 3
       17.58 -    21.97: 1
  Bond angle restraints: 14970
  Sorted by residual:
  angle pdb=" CA  ASN C 384 "
        pdb=" C   ASN C 384 "
        pdb=" N   SER C 385 "
      ideal   model   delta    sigma   weight residual
     115.36   93.39   21.97 1.56e+00 4.11e-01 1.98e+02
  angle pdb=" N   VAL C 552 "
        pdb=" CA  VAL C 552 "
        pdb=" C   VAL C 552 "
      ideal   model   delta    sigma   weight residual
     113.47  101.80   11.67 1.01e+00 9.80e-01 1.33e+02
  angle pdb=" N   ASN C 384 "
        pdb=" CA  ASN C 384 "
        pdb=" C   ASN C 384 "
      ideal   model   delta    sigma   weight residual
     109.85  125.80  -15.95 1.58e+00 4.01e-01 1.02e+02
  angle pdb=" CA  ASN C 384 "
        pdb=" C   ASN C 384 "
        pdb=" O   ASN C 384 "
      ideal   model   delta    sigma   weight residual
     121.46  132.88  -11.42 1.17e+00 7.31e-01 9.53e+01
  angle pdb=" CA  ARG D 315 "
        pdb=" C   ARG D 315 "
        pdb=" N   GLY D 316 "
      ideal   model   delta    sigma   weight residual
     116.84  100.98   15.86 1.71e+00 3.42e-01 8.60e+01
  ... (remaining 14965 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.95: 5681
       33.95 -    67.90: 571
       67.90 -   101.85: 6
      101.85 -   135.80: 0
      135.80 -   169.75: 2
  Dihedral angle restraints: 6260
    sinusoidal: 3444
      harmonic: 2816
  Sorted by residual:
  dihedral pdb=" C   PRO D 408 "
           pdb=" N   PRO D 408 "
           pdb=" CA  PRO D 408 "
           pdb=" CB  PRO D 408 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -107.37  -13.33     0      2.50e+00 1.60e-01 2.84e+01
  dihedral pdb=" C   TYR D 527 "
           pdb=" N   TYR D 527 "
           pdb=" CA  TYR D 527 "
           pdb=" CB  TYR D 527 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.50  -12.10     0      2.50e+00 1.60e-01 2.34e+01
  dihedral pdb=" C   PRO C 541 "
           pdb=" N   PRO C 541 "
           pdb=" CA  PRO C 541 "
           pdb=" CB  PRO C 541 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -108.72  -11.98     0      2.50e+00 1.60e-01 2.29e+01
  ... (remaining 6257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1311
       0.098 -    0.196: 290
       0.196 -    0.294: 44
       0.294 -    0.393: 10
       0.393 -    0.491: 3
  Chirality restraints: 1658
  Sorted by residual:
  chirality pdb=" CA  ASN C 384 "
            pdb=" N   ASN C 384 "
            pdb=" C   ASN C 384 "
            pdb=" CB  ASN C 384 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.02e+00
  chirality pdb=" CA  PRO D 551 "
            pdb=" N   PRO D 551 "
            pdb=" C   PRO D 551 "
            pdb=" CB  PRO D 551 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.31    0.41 2.00e-01 2.50e+01 4.12e+00
  chirality pdb=" CA  PRO D 410 "
            pdb=" N   PRO D 410 "
            pdb=" C   PRO D 410 "
            pdb=" CB  PRO D 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.32    0.40 2.00e-01 2.50e+01 3.92e+00
  ... (remaining 1655 not shown)

  Planarity restraints: 1472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 594 "   -0.034 2.00e-02 2.50e+03   6.58e-02 4.33e+01
        pdb=" C   PHE D 594 "    0.114 2.00e-02 2.50e+03
        pdb=" O   PHE D 594 "   -0.041 2.00e-02 2.50e+03
        pdb=" OXT PHE D 594 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 594 "   -0.030 2.00e-02 2.50e+03   5.78e-02 3.34e+01
        pdb=" C   PHE C 594 "    0.100 2.00e-02 2.50e+03
        pdb=" O   PHE C 594 "   -0.035 2.00e-02 2.50e+03
        pdb=" OXT PHE C 594 "   -0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 507 "   -0.061 2.00e-02 2.50e+03   3.40e-02 2.31e+01
        pdb=" CG  TYR D 507 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 507 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 507 "    0.038 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 507 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 507 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 507 "   -0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR D 507 "   -0.046 2.00e-02 2.50e+03
  ... (remaining 1469 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.30: 9
        2.30 -     2.95: 4458
        2.95 -     3.60: 13893
        3.60 -     4.25: 25472
        4.25 -     4.90: 37684
  Nonbonded interactions: 81516
  Sorted by model distance:
  nonbonded pdb=" OP1  DT A  -3 "
            pdb="CA    CA A 101 "
     model   vdw
     1.652 2.510
  nonbonded pdb=" OD2 ASP D 346 "
            pdb="CA    CA A 101 "
     model   vdw
     1.905 2.510
  nonbonded pdb=" OD2 ASP C 218 "
            pdb="CA    CA C 602 "
     model   vdw
     2.030 2.510
  nonbonded pdb=" OD2 ASP C 346 "
            pdb="CA    CA C 601 "
     model   vdw
     2.075 2.510
  nonbonded pdb=" OP1  DT B  -3 "
            pdb="CA    CA C 601 "
     model   vdw
     2.105 2.510
  ... (remaining 81511 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 'C' and (resid 117 through 601 or resid 603))
  selection = (chain 'D' and (resid 117 through 601 or resid 603))
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.920
  Find NCS groups from input model:        0.140
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
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      :  0.019   0.619  10718  Z= 0.930
  Angle     :  1.797  24.715  14988  Z= 1.198
  Chirality :  0.087   0.491   1658
  Planarity :  0.005   0.066   1472
  Dihedral  : 21.014 169.750   4440
  Min Nonbonded Distance : 1.652

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.52 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  6.90 %
    Favored  : 92.53 %
  Cbeta Deviations :  1.10 %
  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: -0.38 (0.26), residues: 952
  helix: -1.14 (0.24), residues: 366
  sheet:  1.50 (0.50), residues: 108
  loop :  0.25 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 526 
 TYR   0.061   0.010   TYR D 507 
 PHE   0.031   0.006   PHE D 349 
 TRP   0.040   0.009   TRP C 465 
 HIS   0.009   0.003   HIS C 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.01201 (10702)
  covalent geometry    : angle       1.74392 (14970)
  hydrogen bonds       : bond        0.22798 (  459)
  hydrogen bonds       : angle       6.46602 ( 1164)
  metal coordination   : bond        0.39325 (   16)
  metal coordination   : angle      12.67705 (   18)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  359 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 354
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  191 ASP cc_start: 0.7915 (p0) cc_final: 0.7481 (p0)
REVERT: C  228 ASP cc_start: 0.7858 (t0) cc_final: 0.7624 (t70)
REVERT: C  413 MET cc_start: 0.6567 (mpp) cc_final: 0.6334 (mpp)
REVERT: C  462 THR cc_start: 0.7971 (t) cc_final: 0.7696 (p)
REVERT: D  206 MET cc_start: 0.8437 (mmm) cc_final: 0.8207 (mmt)
  outliers start: 5
  outliers final: 1
  residues processed: 357
  average time/residue: 0.1208
  time to fit residues: 57.6749
Evaluate side-chains
  224 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  179 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
C 357 ASN
C 440 ASN
C 441 GLN
C 571 ASN
D 253 HIS
D 264 HIS
D 347 ASN
D 531 ASN
D 538 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.146233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.111232 restraints weight = 18168.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.115144 restraints weight = 7956.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.117528 restraints weight = 4926.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.118913 restraints weight = 3760.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.119642 restraints weight = 3260.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  10718  Z= 0.208
  Angle     :  0.819   9.089  14988  Z= 0.451
  Chirality :  0.045   0.169   1658
  Planarity :  0.005   0.049   1472
  Dihedral  : 24.403 163.184   2456
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.21 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.65 %
    Favored  : 78.62 %
  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:  0.41 (0.27), residues: 952
  helix:  0.50 (0.28), residues: 361
  sheet:  1.30 (0.50), residues: 110
  loop : -0.04 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 169 
 TYR   0.017   0.002   TYR D 439 
 PHE   0.042   0.002   PHE C 241 
 TRP   0.010   0.002   TRP D 150 
 HIS   0.003   0.001   HIS D 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (10702)
  covalent geometry    : angle       0.80752 (14970)
  hydrogen bonds       : bond        0.06670 (  459)
  hydrogen bonds       : angle       4.65156 ( 1164)
  metal coordination   : bond        0.01136 (   16)
  metal coordination   : angle       4.05062 (   18)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 241
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8807 (m-80) cc_final: 0.8389 (m-80)
REVERT: C  154 GLU cc_start: 0.8313 (mp0) cc_final: 0.8100 (mp0)
REVERT: C  182 ILE cc_start: 0.9067 (mm) cc_final: 0.8862 (mm)
REVERT: C  257 GLN cc_start: 0.8333 (mm110) cc_final: 0.8039 (tm-30)
REVERT: C  413 MET cc_start: 0.5669 (mpp) cc_final: 0.5204 (mpp)
REVERT: C  430 THR cc_start: 0.8766 (t) cc_final: 0.8557 (p)
REVERT: C  440 ASN cc_start: 0.8404 (m-40) cc_final: 0.8159 (m110)
REVERT: C  452 MET cc_start: 0.9115 (mtt) cc_final: 0.8869 (mtp)
REVERT: C  565 LYS cc_start: 0.8547 (mtmt) cc_final: 0.8092 (mmtp)
REVERT: D  146 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7678 (mt-10)
REVERT: D  214 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7301 (ttp-170)
REVERT: D  331 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8223 (tm-30)
REVERT: D  332 LEU cc_start: 0.8672 (mm) cc_final: 0.8231 (mm)
REVERT: D  372 ARG cc_start: 0.7689 (mtt90) cc_final: 0.7487 (mtm-85)
REVERT: D  394 MET cc_start: 0.6782 (mtp) cc_final: 0.6542 (ttm)
REVERT: D  536 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8024 (tp)
REVERT: D  569 LYS cc_start: 0.6631 (mttt) cc_final: 0.5400 (tmtt)
  outliers start: 33
  outliers final: 22
  residues processed: 259
  average time/residue: 0.1036
  time to fit residues: 37.4567
Evaluate side-chains
  236 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 213
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  254 GLN
Chi-restraints excluded: chain C residue  299 CYS
Chi-restraints excluded: chain C residue  343 ILE
Chi-restraints excluded: chain C residue  465 TRP
Chi-restraints excluded: chain D residue  171 THR
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  179 PHE
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  211 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  256 ILE
Chi-restraints excluded: chain D residue  280 PHE
Chi-restraints excluded: chain D residue  286 ASN
Chi-restraints excluded: chain D residue  315 ARG
Chi-restraints excluded: chain D residue  351 SER
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  454 SER
Chi-restraints excluded: chain D residue  527 TYR
Chi-restraints excluded: chain D residue  536 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 73 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
C 571 ASN
D 347 ASN
D 434 GLN
D 440 ASN
D 538 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.146154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.111729 restraints weight = 18572.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.115508 restraints weight = 8387.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.117872 restraints weight = 5279.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.119049 restraints weight = 4048.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.119987 restraints weight = 3541.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10718  Z= 0.163
  Angle     :  0.708   7.534  14988  Z= 0.391
  Chirality :  0.041   0.144   1658
  Planarity :  0.005   0.046   1472
  Dihedral  : 24.541 158.271   2456
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.84 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.46 %
    Favored  : 77.38 %
  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:  0.37 (0.28), residues: 952
  helix:  0.89 (0.28), residues: 364
  sheet:  1.02 (0.51), residues: 112
  loop : -0.39 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 337 
 TYR   0.021   0.001   TYR D 439 
 PHE   0.053   0.002   PHE C 241 
 TRP   0.007   0.001   TRP D 150 
 HIS   0.002   0.001   HIS D 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (10702)
  covalent geometry    : angle       0.70018 (14970)
  hydrogen bonds       : bond        0.05078 (  459)
  hydrogen bonds       : angle       4.22361 ( 1164)
  metal coordination   : bond        0.00780 (   16)
  metal coordination   : angle       3.13961 (   18)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 240
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 ILE cc_start: 0.9191 (mm) cc_final: 0.8915 (mm)
REVERT: C  185 MET cc_start: 0.8811 (tpp) cc_final: 0.8356 (tpp)
REVERT: C  310 MET cc_start: 0.7564 (ptp) cc_final: 0.7297 (ptp)
REVERT: C  356 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8520 (mtmm)
REVERT: C  388 ARG cc_start: 0.8616 (mtp85) cc_final: 0.8166 (ttm-80)
REVERT: C  413 MET cc_start: 0.5808 (mpp) cc_final: 0.5362 (mpp)
REVERT: C  430 THR cc_start: 0.8719 (t) cc_final: 0.8477 (p)
REVERT: C  437 MET cc_start: 0.8685 (mmm) cc_final: 0.8209 (mmt)
REVERT: C  440 ASN cc_start: 0.8711 (m-40) cc_final: 0.8242 (m110)
REVERT: C  456 MET cc_start: 0.8011 (mtm) cc_final: 0.7768 (ttm)
REVERT: C  565 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8255 (mmtp)
REVERT: C  589 MET cc_start: 0.7033 (mpt) cc_final: 0.6714 (mpt)
REVERT: D  146 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7606 (mt-10)
REVERT: D  189 ARG cc_start: 0.7928 (mmt90) cc_final: 0.7476 (mtt90)
REVERT: D  229 LYS cc_start: 0.9022 (pttm) cc_final: 0.8713 (mmtm)
REVERT: D  264 HIS cc_start: 0.8645 (m-70) cc_final: 0.8129 (m90)
REVERT: D  286 ASN cc_start: 0.8141 (m-40) cc_final: 0.7845 (p0)
REVERT: D  331 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8129 (tm-30)
REVERT: D  332 LEU cc_start: 0.8572 (mm) cc_final: 0.7864 (mm)
REVERT: D  372 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7634 (mtm-85)
REVERT: D  515 MET cc_start: 0.9089 (mtp) cc_final: 0.8860 (mtm)
REVERT: D  536 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8006 (tp)
REVERT: D  569 LYS cc_start: 0.6706 (mttt) cc_final: 0.5499 (tmtt)
REVERT: D  589 MET cc_start: 0.8261 (mtp) cc_final: 0.7920 (mtm)
  outliers start: 28
  outliers final: 16
  residues processed: 258
  average time/residue: 0.0943
  time to fit residues: 34.6308
Evaluate side-chains
  231 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 213
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  254 GLN
Chi-restraints excluded: chain C residue  343 ILE
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  435 MET
Chi-restraints excluded: chain D residue  211 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  280 PHE
Chi-restraints excluded: chain D residue  351 SER
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  454 SER
Chi-restraints excluded: chain D residue  527 TYR
Chi-restraints excluded: chain D residue  536 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 94 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   chunk 10 optimal weight:    0.6980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 475 ASN
C 571 ASN
D 254 GLN
** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 538 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.146312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.111485 restraints weight = 18999.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.115221 restraints weight = 8572.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.117612 restraints weight = 5430.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.118812 restraints weight = 4171.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.119662 restraints weight = 3656.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10718  Z= 0.155
  Angle     :  0.682   6.666  14988  Z= 0.374
  Chirality :  0.041   0.198   1658
  Planarity :  0.005   0.048   1472
  Dihedral  : 24.350 161.541   2454
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.36 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.27 %
    Favored  : 75.45 %
  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:  0.37 (0.28), residues: 952
  helix:  1.13 (0.28), residues: 360
  sheet:  1.01 (0.52), residues: 112
  loop : -0.60 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 567 
 TYR   0.015   0.001   TYR D 439 
 PHE   0.039   0.002   PHE C 241 
 TRP   0.022   0.002   TRP C 465 
 HIS   0.001   0.000   HIS D 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10702)
  covalent geometry    : angle       0.67620 (14970)
  hydrogen bonds       : bond        0.04513 (  459)
  hydrogen bonds       : angle       4.01400 ( 1164)
  metal coordination   : bond        0.00600 (   16)
  metal coordination   : angle       2.74942 (   18)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 232
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 ILE cc_start: 0.9223 (mm) cc_final: 0.8945 (mm)
REVERT: C  221 ILE cc_start: 0.9496 (tp) cc_final: 0.9282 (tp)
REVERT: C  310 MET cc_start: 0.7637 (ptp) cc_final: 0.7347 (ptp)
REVERT: C  356 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8489 (mtmm)
REVERT: C  413 MET cc_start: 0.5620 (mpp) cc_final: 0.5136 (mpp)
REVERT: C  430 THR cc_start: 0.8763 (t) cc_final: 0.8518 (p)
REVERT: C  437 MET cc_start: 0.8732 (mmm) cc_final: 0.8238 (mmt)
REVERT: C  440 ASN cc_start: 0.8767 (m-40) cc_final: 0.8182 (m110)
REVERT: C  565 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8259 (mmtp)
REVERT: C  589 MET cc_start: 0.6762 (mpt) cc_final: 0.6466 (mpt)
REVERT: D  189 ARG cc_start: 0.7975 (mmt90) cc_final: 0.7515 (mtt90)
REVERT: D  191 ASP cc_start: 0.8878 (p0) cc_final: 0.8647 (p0)
REVERT: D  206 MET cc_start: 0.8548 (mmt) cc_final: 0.8106 (tpp)
REVERT: D  218 ASP cc_start: 0.8655 (m-30) cc_final: 0.8370 (m-30)
REVERT: D  286 ASN cc_start: 0.8097 (m-40) cc_final: 0.7828 (p0)
REVERT: D  297 MET cc_start: 0.8973 (ttm) cc_final: 0.8759 (mtp)
REVERT: D  332 LEU cc_start: 0.8633 (mm) cc_final: 0.8277 (mm)
REVERT: D  515 MET cc_start: 0.9092 (mtp) cc_final: 0.8852 (mtm)
REVERT: D  536 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8056 (tp)
REVERT: D  569 LYS cc_start: 0.6630 (mttt) cc_final: 0.5447 (tmtt)
REVERT: D  589 MET cc_start: 0.8108 (mtp) cc_final: 0.7570 (mtm)
  outliers start: 29
  outliers final: 19
  residues processed: 246
  average time/residue: 0.0898
  time to fit residues: 31.6896
Evaluate side-chains
  225 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 204
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  435 MET
Chi-restraints excluded: chain C residue  580 VAL
Chi-restraints excluded: chain D residue  171 THR
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  211 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  267 ILE
Chi-restraints excluded: chain D residue  271 LEU
Chi-restraints excluded: chain D residue  324 LEU
Chi-restraints excluded: chain D residue  351 SER
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  453 CYS
Chi-restraints excluded: chain D residue  454 SER
Chi-restraints excluded: chain D residue  523 THR
Chi-restraints excluded: chain D residue  536 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 89 optimal weight:   20.0000
   chunk 61 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 105 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 571 ASN
D 254 GLN
** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 538 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.144860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.110236 restraints weight = 18752.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.113895 restraints weight = 8529.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.116156 restraints weight = 5410.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.117498 restraints weight = 4199.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.118153 restraints weight = 3647.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.4735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10718  Z= 0.163
  Angle     :  0.673   7.630  14988  Z= 0.367
  Chirality :  0.040   0.167   1658
  Planarity :  0.005   0.049   1472
  Dihedral  : 24.374 161.264   2454
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.38 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.41 (0.28), residues: 952
  helix:  1.21 (0.28), residues: 363
  sheet:  0.78 (0.51), residues: 115
  loop : -0.56 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 222 
 TYR   0.013   0.001   TYR D 439 
 PHE   0.046   0.002   PHE C 241 
 TRP   0.008   0.001   TRP C 465 
 HIS   0.002   0.000   HIS C 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (10702)
  covalent geometry    : angle       0.66604 (14970)
  hydrogen bonds       : bond        0.04593 (  459)
  hydrogen bonds       : angle       3.96819 ( 1164)
  metal coordination   : bond        0.00690 (   16)
  metal coordination   : angle       2.93436 (   18)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 214
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  297 MET cc_start: 0.8535 (mtm) cc_final: 0.8313 (mtp)
REVERT: C  310 MET cc_start: 0.7661 (ptp) cc_final: 0.7441 (ptp)
REVERT: C  356 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8485 (mtmm)
REVERT: C  413 MET cc_start: 0.5615 (mpp) cc_final: 0.4763 (mpp)
REVERT: C  437 MET cc_start: 0.8793 (mmm) cc_final: 0.8265 (mmt)
REVERT: C  440 ASN cc_start: 0.8955 (m-40) cc_final: 0.8460 (m110)
REVERT: C  565 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8282 (mmtp)
REVERT: D  169 ARG cc_start: 0.7461 (mtm110) cc_final: 0.7159 (ptp-110)
REVERT: D  206 MET cc_start: 0.8499 (mmt) cc_final: 0.8268 (mmt)
REVERT: D  218 ASP cc_start: 0.8666 (m-30) cc_final: 0.8376 (m-30)
REVERT: D  277 ARG cc_start: 0.8195 (mtm110) cc_final: 0.7876 (mtm110)
REVERT: D  286 ASN cc_start: 0.8057 (m-40) cc_final: 0.7827 (p0)
REVERT: D  297 MET cc_start: 0.8941 (ttm) cc_final: 0.8591 (mtp)
REVERT: D  310 MET cc_start: 0.7118 (mtp) cc_final: 0.6914 (mtp)
REVERT: D  332 LEU cc_start: 0.8713 (mm) cc_final: 0.8400 (mm)
REVERT: D  456 MET cc_start: 0.8670 (mmt) cc_final: 0.8274 (mmt)
REVERT: D  515 MET cc_start: 0.9169 (mtp) cc_final: 0.8891 (mtm)
REVERT: D  536 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8193 (tp)
REVERT: D  569 LYS cc_start: 0.6556 (mttt) cc_final: 0.5546 (tmtt)
REVERT: D  581 ILE cc_start: 0.5377 (pt) cc_final: 0.5110 (pt)
  outliers start: 30
  outliers final: 22
  residues processed: 229
  average time/residue: 0.0868
  time to fit residues: 29.0138
Evaluate side-chains
  227 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 203
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  139 PHE
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  256 ILE
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  435 MET
Chi-restraints excluded: chain C residue  580 VAL
Chi-restraints excluded: chain D residue  171 THR
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  211 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  267 ILE
Chi-restraints excluded: chain D residue  271 LEU
Chi-restraints excluded: chain D residue  351 SER
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  453 CYS
Chi-restraints excluded: chain D residue  454 SER
Chi-restraints excluded: chain D residue  523 THR
Chi-restraints excluded: chain D residue  527 TYR
Chi-restraints excluded: chain D residue  536 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 72 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 64 optimal weight:    0.0870
   overall best weight:    1.9964

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

Flipped N/Q/H residues before XYZ refinement:
C 257 GLN
C 286 ASN
D 254 GLN
D 264 HIS
** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 538 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.142807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.107660 restraints weight = 19253.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.111307 restraints weight = 8785.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.113516 restraints weight = 5611.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.114647 restraints weight = 4375.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.115536 restraints weight = 3857.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.4960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10718  Z= 0.180
  Angle     :  0.692   9.616  14988  Z= 0.374
  Chirality :  0.041   0.145   1658
  Planarity :  0.005   0.049   1472
  Dihedral  : 24.392 160.884   2454
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 20.14 %
    Favored  : 75.68 %
  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:  0.36 (0.28), residues: 952
  helix:  1.42 (0.29), residues: 354
  sheet:  0.60 (0.49), residues: 115
  loop : -0.74 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 372 
 TYR   0.013   0.001   TYR D 561 
 PHE   0.034   0.002   PHE C 241 
 TRP   0.011   0.001   TRP C 465 
 HIS   0.001   0.000   HIS D 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (10702)
  covalent geometry    : angle       0.68281 (14970)
  hydrogen bonds       : bond        0.04978 (  459)
  hydrogen bonds       : angle       4.01833 ( 1164)
  metal coordination   : bond        0.00724 (   16)
  metal coordination   : angle       3.27173 (   18)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 216
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  312 TYR cc_start: 0.8830 (t80) cc_final: 0.8462 (t80)
REVERT: C  356 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8505 (mtmm)
REVERT: C  413 MET cc_start: 0.5655 (mpp) cc_final: 0.4832 (mpp)
REVERT: C  437 MET cc_start: 0.8786 (mmm) cc_final: 0.8273 (mmt)
REVERT: C  440 ASN cc_start: 0.9070 (m-40) cc_final: 0.8621 (m110)
REVERT: C  467 MET cc_start: 0.7422 (mmm) cc_final: 0.6952 (mmm)
REVERT: C  565 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8297 (mmtp)
REVERT: D  169 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7370 (ptp90)
REVERT: D  218 ASP cc_start: 0.8596 (m-30) cc_final: 0.8231 (m-30)
REVERT: D  277 ARG cc_start: 0.8362 (mtm110) cc_final: 0.7989 (mtm110)
REVERT: D  297 MET cc_start: 0.8967 (ttm) cc_final: 0.8532 (mtp)
REVERT: D  332 LEU cc_start: 0.8841 (mm) cc_final: 0.8620 (mm)
REVERT: D  372 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7487 (mmt180)
REVERT: D  374 ASN cc_start: 0.8412 (p0) cc_final: 0.8181 (t0)
REVERT: D  414 VAL cc_start: 0.6383 (OUTLIER) cc_final: 0.6156 (p)
REVERT: D  515 MET cc_start: 0.9251 (mtp) cc_final: 0.8958 (mtm)
REVERT: D  536 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8270 (tp)
REVERT: D  569 LYS cc_start: 0.6414 (mttt) cc_final: 0.5449 (tttm)
  outliers start: 37
  outliers final: 21
  residues processed: 233
  average time/residue: 0.0865
  time to fit residues: 29.0187
Evaluate side-chains
  226 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 202
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  255 CYS
Chi-restraints excluded: chain C residue  282 MET
Chi-restraints excluded: chain C residue  343 ILE
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  580 VAL
Chi-restraints excluded: chain D residue  155 ILE
Chi-restraints excluded: chain D residue  171 THR
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  211 VAL
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  267 ILE
Chi-restraints excluded: chain D residue  271 LEU
Chi-restraints excluded: chain D residue  280 PHE
Chi-restraints excluded: chain D residue  414 VAL
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  453 CYS
Chi-restraints excluded: chain D residue  527 TYR
Chi-restraints excluded: chain D residue  536 LEU
Chi-restraints excluded: chain D residue  557 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 23 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   chunk 85 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0020
   chunk 88 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
D 254 GLN
D 480 ASN
D 531 ASN
D 538 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.146990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.112514 restraints weight = 19072.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.116241 restraints weight = 8677.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.118524 restraints weight = 5493.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.119928 restraints weight = 4252.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.120573 restraints weight = 3673.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.5256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10718  Z= 0.143
  Angle     :  0.658   9.739  14988  Z= 0.355
  Chirality :  0.039   0.140   1658
  Planarity :  0.005   0.050   1472
  Dihedral  : 24.188 159.136   2454
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 22.51 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.32 (0.28), residues: 952
  helix:  1.55 (0.29), residues: 354
  sheet:  0.40 (0.49), residues: 115
  loop : -0.86 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 214 
 TYR   0.012   0.001   TYR D 439 
 PHE   0.026   0.001   PHE C 241 
 TRP   0.006   0.001   TRP C 348 
 HIS   0.003   0.001   HIS D 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10702)
  covalent geometry    : angle       0.65041 (14970)
  hydrogen bonds       : bond        0.04062 (  459)
  hydrogen bonds       : angle       3.83959 ( 1164)
  metal coordination   : bond        0.00517 (   16)
  metal coordination   : angle       3.01541 (   18)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 226
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  356 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8518 (mtmm)
REVERT: C  388 ARG cc_start: 0.8823 (mtp85) cc_final: 0.8473 (ttm-80)
REVERT: C  413 MET cc_start: 0.5611 (mpp) cc_final: 0.4818 (mpp)
REVERT: C  437 MET cc_start: 0.8792 (mmm) cc_final: 0.8328 (mmt)
REVERT: C  440 ASN cc_start: 0.9044 (m-40) cc_final: 0.8538 (m110)
REVERT: C  467 MET cc_start: 0.7339 (mmm) cc_final: 0.6802 (mmm)
REVERT: C  487 HIS cc_start: 0.7740 (t-90) cc_final: 0.7461 (t-90)
REVERT: C  565 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8236 (mmtp)
REVERT: D  218 ASP cc_start: 0.8668 (m-30) cc_final: 0.8338 (m-30)
REVERT: D  264 HIS cc_start: 0.8401 (m-70) cc_final: 0.8145 (m90)
REVERT: D  286 ASN cc_start: 0.7993 (m-40) cc_final: 0.7773 (p0)
REVERT: D  372 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7510 (mmt180)
REVERT: D  456 MET cc_start: 0.8653 (mmt) cc_final: 0.8390 (mmt)
REVERT: D  467 MET cc_start: 0.7302 (mmm) cc_final: 0.6705 (mmm)
REVERT: D  515 MET cc_start: 0.9228 (mtp) cc_final: 0.8879 (mtm)
  outliers start: 20
  outliers final: 13
  residues processed: 236
  average time/residue: 0.0915
  time to fit residues: 31.1199
Evaluate side-chains
  224 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 210
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  139 PHE
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  255 CYS
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  397 PHE
Chi-restraints excluded: chain D residue  267 ILE
Chi-restraints excluded: chain D residue  271 LEU
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  453 CYS
Chi-restraints excluded: chain D residue  454 SER
Chi-restraints excluded: chain D residue  557 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 98 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 56 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
C 585 HIS
D 538 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.144108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.109623 restraints weight = 18931.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.113248 restraints weight = 8620.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.115469 restraints weight = 5482.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.116764 restraints weight = 4257.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.117373 restraints weight = 3712.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.5354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.022   2.191  10718  Z= 0.416
  Angle     :  0.690  13.217  14988  Z= 0.367
  Chirality :  0.041   0.171   1658
  Planarity :  0.005   0.049   1472
  Dihedral  : 24.161 159.410   2454
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 23.42 %
    Favored  : 74.21 %
  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 (0.28), residues: 952
  helix:  1.41 (0.29), residues: 361
  sheet:  0.45 (0.49), residues: 114
  loop : -0.96 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 169 
 TYR   0.012   0.001   TYR D 561 
 PHE   0.026   0.002   PHE C 241 
 TRP   0.006   0.001   TRP D 465 
 HIS   0.003   0.001   HIS D 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (10702)
  covalent geometry    : angle       0.68300 (14970)
  hydrogen bonds       : bond        0.04601 (  459)
  hydrogen bonds       : angle       3.95739 ( 1164)
  metal coordination   : bond        0.54786 (   16)
  metal coordination   : angle       2.99252 (   18)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 214
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8129 (t80)
REVERT: C  312 TYR cc_start: 0.8848 (t80) cc_final: 0.8460 (t80)
REVERT: C  356 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8538 (mtmm)
REVERT: C  413 MET cc_start: 0.5489 (mpp) cc_final: 0.4692 (mpp)
REVERT: C  437 MET cc_start: 0.8808 (mmm) cc_final: 0.8319 (mmt)
REVERT: C  440 ASN cc_start: 0.9117 (m-40) cc_final: 0.8656 (m110)
REVERT: C  467 MET cc_start: 0.7684 (mmm) cc_final: 0.7426 (mmm)
REVERT: C  487 HIS cc_start: 0.7814 (t-90) cc_final: 0.7537 (t-90)
REVERT: C  565 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8247 (mmtp)
REVERT: C  584 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8427 (tm-30)
REVERT: D  286 ASN cc_start: 0.8080 (m-40) cc_final: 0.7836 (p0)
REVERT: D  351 SER cc_start: 0.8961 (m) cc_final: 0.8688 (m)
REVERT: D  372 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7556 (mmt180)
REVERT: D  456 MET cc_start: 0.8669 (mmt) cc_final: 0.8320 (mmt)
REVERT: D  515 MET cc_start: 0.9229 (mtp) cc_final: 0.8890 (mtm)
REVERT: D  569 LYS cc_start: 0.6205 (mttt) cc_final: 0.5283 (tttm)
  outliers start: 21
  outliers final: 17
  residues processed: 221
  average time/residue: 0.0900
  time to fit residues: 28.5058
Evaluate side-chains
  229 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 210
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  139 PHE
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  255 CYS
Chi-restraints excluded: chain C residue  343 ILE
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  267 ILE
Chi-restraints excluded: chain D residue  269 GLU
Chi-restraints excluded: chain D residue  271 LEU
Chi-restraints excluded: chain D residue  280 PHE
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  453 CYS
Chi-restraints excluded: chain D residue  524 LEU
Chi-restraints excluded: chain D residue  557 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   chunk 2 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 66 optimal weight:    0.2980
   chunk 78 optimal weight:    6.9990
   chunk 102 optimal weight:    8.9990
   chunk 13 optimal weight:    0.2980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 538 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.147701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.113731 restraints weight = 18825.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.117417 restraints weight = 8490.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.119651 restraints weight = 5337.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.120983 restraints weight = 4130.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.121565 restraints weight = 3578.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.5579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.508  10718  Z= 0.170
  Angle     :  0.719  21.132  14988  Z= 0.365
  Chirality :  0.040   0.170   1658
  Planarity :  0.005   0.055   1472
  Dihedral  : 24.029 157.792   2454
  Min Nonbonded Distance : 1.762

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 24.55 %
    Favored  : 73.53 %
  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:  0.17 (0.28), residues: 952
  helix:  1.42 (0.29), residues: 362
  sheet:  0.35 (0.49), residues: 112
  loop : -0.98 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 169 
 TYR   0.013   0.001   TYR D 561 
 PHE   0.023   0.001   PHE C 241 
 TRP   0.006   0.001   TRP C 348 
 HIS   0.056   0.004   HIS C 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (10702)
  covalent geometry    : angle       0.67087 (14970)
  hydrogen bonds       : bond        0.03953 (  459)
  hydrogen bonds       : angle       3.90281 ( 1164)
  metal coordination   : bond        0.12756 (   16)
  metal coordination   : angle       7.45462 (   18)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 230
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8106 (t80)
REVERT: C  312 TYR cc_start: 0.8833 (t80) cc_final: 0.8461 (t80)
REVERT: C  356 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8459 (mtmm)
REVERT: C  388 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7705 (ttt-90)
REVERT: C  413 MET cc_start: 0.5495 (mpp) cc_final: 0.4673 (mpp)
REVERT: C  437 MET cc_start: 0.8820 (mmm) cc_final: 0.8326 (mmt)
REVERT: C  440 ASN cc_start: 0.9156 (m-40) cc_final: 0.8680 (m110)
REVERT: C  467 MET cc_start: 0.7461 (mmm) cc_final: 0.7218 (mmm)
REVERT: C  487 HIS cc_start: 0.7746 (t-90) cc_final: 0.7528 (t-90)
REVERT: C  565 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8209 (mmtp)
REVERT: D  169 ARG cc_start: 0.7603 (ptp90) cc_final: 0.7305 (ptp-110)
REVERT: D  189 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7493 (ttt90)
REVERT: D  264 HIS cc_start: 0.8448 (m-70) cc_final: 0.8222 (m90)
REVERT: D  286 ASN cc_start: 0.8032 (m-40) cc_final: 0.7806 (p0)
REVERT: D  320 ASN cc_start: 0.7972 (m-40) cc_final: 0.7734 (p0)
REVERT: D  351 SER cc_start: 0.8875 (m) cc_final: 0.8616 (m)
REVERT: D  372 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7487 (mmt180)
REVERT: D  456 MET cc_start: 0.8625 (mmt) cc_final: 0.8279 (mmt)
REVERT: D  467 MET cc_start: 0.7243 (mmm) cc_final: 0.6825 (mmm)
REVERT: D  508 MET cc_start: 0.8274 (mmm) cc_final: 0.8059 (mmm)
REVERT: D  515 MET cc_start: 0.9209 (mtp) cc_final: 0.8864 (mtm)
  outliers start: 17
  outliers final: 14
  residues processed: 237
  average time/residue: 0.0955
  time to fit residues: 32.2480
Evaluate side-chains
  235 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 219
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  134 CYS
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  139 PHE
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  256 ILE
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  267 ILE
Chi-restraints excluded: chain D residue  269 GLU
Chi-restraints excluded: chain D residue  271 LEU
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  453 CYS
Chi-restraints excluded: chain D residue  454 SER
Chi-restraints excluded: chain D residue  557 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 81 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 93 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 538 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.141595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.106901 restraints weight = 18782.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.110527 restraints weight = 8401.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.112753 restraints weight = 5294.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.113879 restraints weight = 4089.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.114731 restraints weight = 3596.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.5551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.442  10718  Z= 0.220
  Angle     :  0.762  19.333  14988  Z= 0.393
  Chirality :  0.042   0.183   1658
  Planarity :  0.005   0.051   1472
  Dihedral  : 24.115 159.432   2454
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 24.21 %
    Favored  : 73.30 %
  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 (0.27), residues: 952
  helix:  1.36 (0.28), residues: 371
  sheet:  0.40 (0.49), residues: 114
  loop : -1.17 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 169 
 TYR   0.021   0.002   TYR D 305 
 PHE   0.023   0.002   PHE C 241 
 TRP   0.013   0.001   TRP C 465 
 HIS   0.053   0.004   HIS C 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (10702)
  covalent geometry    : angle       0.72234 (14970)
  hydrogen bonds       : bond        0.05145 (  459)
  hydrogen bonds       : angle       4.05808 ( 1164)
  metal coordination   : bond        0.11130 (   16)
  metal coordination   : angle       7.07865 (   18)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8117 (t80)
REVERT: C  356 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8528 (mtmm)
REVERT: C  437 MET cc_start: 0.8828 (mmm) cc_final: 0.8319 (mmt)
REVERT: C  440 ASN cc_start: 0.9290 (m-40) cc_final: 0.8927 (m110)
REVERT: C  467 MET cc_start: 0.7931 (mmm) cc_final: 0.7611 (mmm)
REVERT: C  487 HIS cc_start: 0.7950 (t-90) cc_final: 0.7615 (t-90)
REVERT: C  565 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8206 (mmtp)
REVERT: D  124 MET cc_start: 0.7707 (mmp) cc_final: 0.7165 (mmt)
REVERT: D  169 ARG cc_start: 0.7846 (ptp90) cc_final: 0.7482 (ptp-110)
REVERT: D  210 SER cc_start: 0.9041 (p) cc_final: 0.8573 (t)
REVERT: D  257 GLN cc_start: 0.8902 (tp40) cc_final: 0.8673 (tt0)
REVERT: D  297 MET cc_start: 0.8861 (tpp) cc_final: 0.8603 (tpp)
REVERT: D  320 ASN cc_start: 0.8073 (m-40) cc_final: 0.7792 (p0)
REVERT: D  351 SER cc_start: 0.8958 (m) cc_final: 0.8697 (m)
REVERT: D  372 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7533 (mmt180)
REVERT: D  438 TYR cc_start: 0.8908 (t80) cc_final: 0.8686 (t80)
REVERT: D  536 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8284 (tp)
  outliers start: 22
  outliers final: 15
  residues processed: 220
  average time/residue: 0.0915
  time to fit residues: 29.1844
Evaluate side-chains
  233 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 215
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  134 CYS
Chi-restraints excluded: chain C residue  138 PHE
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  269 GLU
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  267 ILE
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  453 CYS
Chi-restraints excluded: chain D residue  454 SER
Chi-restraints excluded: chain D residue  524 LEU
Chi-restraints excluded: chain D residue  527 TYR
Chi-restraints excluded: chain D residue  536 LEU
Chi-restraints excluded: chain D residue  557 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    0.0050
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 95 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.1598

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

Flipped N/Q/H residues before XYZ refinement:
D 538 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.144894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.111383 restraints weight = 19029.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.115041 restraints weight = 8584.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.117283 restraints weight = 5405.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.118382 restraints weight = 4171.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.119308 restraints weight = 3659.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.5712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.363  10718  Z= 0.167
  Angle     :  0.720  17.380  14988  Z= 0.373
  Chirality :  0.040   0.171   1658
  Planarity :  0.005   0.052   1472
  Dihedral  : 24.049 157.687   2454
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 25.34 %
    Favored  : 72.62 %
  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:  0.10 (0.27), residues: 952
  helix:  1.47 (0.29), residues: 363
  sheet:  0.30 (0.51), residues: 107
  loop : -1.12 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 169 
 TYR   0.012   0.001   TYR D 561 
 PHE   0.022   0.001   PHE C 241 
 TRP   0.006   0.001   TRP C 348 
 HIS   0.048   0.004   HIS C 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (10702)
  covalent geometry    : angle       0.68664 (14970)
  hydrogen bonds       : bond        0.04335 (  459)
  hydrogen bonds       : angle       3.92656 ( 1164)
  metal coordination   : bond        0.09144 (   16)
  metal coordination   : angle       6.29104 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1834.58 seconds
wall clock time: 32 minutes 15.24 seconds (1935.24 seconds total)