Starting phenix.real_space_refine
on Mon Jul 28 05:00:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x68_22073/07_2025/6x68_22073.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x68_22073/07_2025/6x68_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x68_22073/07_2025/6x68_22073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x68_22073/07_2025/6x68_22073.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x68_22073/07_2025/6x68_22073.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x68_22073/07_2025/6x68_22073.cif"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.33, per 1000 atoms: 0.62
  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: 2.96
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  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: 3.57
  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: 3.87

  Time building geometry restraints manager: 3.23 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 594 or resid 601 or resid 603))
  selection = (chain 'D' and (resid 117 through 594 or resid 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:             0.330
  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:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     30.510
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.570
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (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
 TRP   0.040   0.009   TRP C 465 
 HIS   0.009   0.003   HIS C 585 
 PHE   0.031   0.006   PHE D 349 
 TYR   0.061   0.010   TYR D 507 
 ARG   0.006   0.001   ARG C 526 

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

*********************** 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  : 1.026 
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: 0.7625 (t70)
REVERT: C  413 MET cc_start: 0.6567 (mpp) cc_final: 0.6333 (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: 0.2748
  time to fit residues: 130.6763
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  : 0.979 
-------------------------------------------------------------------------------
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 89 optimal weight:   20.0000
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0670
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    1.3522

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

Flipped N/Q/H residues before XYZ refinement:
C 357 ASN
C 384 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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.146785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.111883 restraints weight = 18006.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.115703 restraints weight = 8225.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.117989 restraints weight = 5199.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  10718  Z= 0.201
  Angle     :  0.812   9.072  14988  Z= 0.447
  Chirality :  0.045   0.158   1658
  Planarity :  0.005   0.052   1472
  Dihedral  : 24.392 163.576   2456
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.31 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.76 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.27), residues: 952
  helix:  0.49 (0.27), residues: 361
  sheet:  1.28 (0.49), residues: 110
  loop : -0.04 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 150 
 HIS   0.004   0.001   HIS D 264 
 PHE   0.037   0.002   PHE C 241 
 TYR   0.016   0.002   TYR D 439 
 ARG   0.007   0.001   ARG D 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06726 (  459)
  hydrogen bonds       : angle       4.63864 ( 1164)
  metal coordination   : bond        0.01850 (   16)
  metal coordination   : angle       4.21439 (   18)
  covalent geometry    : bond        0.00464 (10702)
  covalent geometry    : angle       0.79877 (14970)

*********************** 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
  275 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 242
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8799 (m-80) cc_final: 0.8398 (m-80)
REVERT: C  182 ILE cc_start: 0.9191 (mm) cc_final: 0.8990 (mm)
REVERT: C  257 GLN cc_start: 0.8399 (mm110) cc_final: 0.8101 (tm-30)
REVERT: C  356 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8487 (mtmm)
REVERT: C  413 MET cc_start: 0.5809 (mpp) cc_final: 0.5300 (mpp)
REVERT: C  430 THR cc_start: 0.8773 (t) cc_final: 0.8545 (p)
REVERT: C  440 ASN cc_start: 0.8413 (m-40) cc_final: 0.8158 (m110)
REVERT: C  452 MET cc_start: 0.9112 (mtt) cc_final: 0.8869 (mtp)
REVERT: C  565 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8071 (mmtp)
REVERT: D  146 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7670 (mt-10)
REVERT: D  169 ARG cc_start: 0.7317 (mtm110) cc_final: 0.7034 (mtm110)
REVERT: D  208 TYR cc_start: 0.8891 (m-80) cc_final: 0.8680 (m-10)
REVERT: D  214 ARG cc_start: 0.7713 (ttm110) cc_final: 0.7330 (ttp-170)
REVERT: D  331 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8190 (tm-30)
REVERT: D  332 LEU cc_start: 0.8588 (mm) cc_final: 0.8100 (mm)
REVERT: D  372 ARG cc_start: 0.7675 (mtt90) cc_final: 0.7474 (mtm-85)
REVERT: D  394 MET cc_start: 0.6798 (mtp) cc_final: 0.6575 (ttm)
REVERT: D  536 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8046 (tp)
REVERT: D  569 LYS cc_start: 0.6646 (mttt) cc_final: 0.5429 (tmtt)
  outliers start: 33
  outliers final: 21
  residues processed: 262
  average time/residue: 0.2313
  time to fit residues: 84.1153
Evaluate side-chains
  239 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 216
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
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  356 LYS
Chi-restraints excluded: chain C residue  384 ASN
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 40 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 87 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.1786

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.146133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.111230 restraints weight = 18646.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.115021 restraints weight = 8537.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.117359 restraints weight = 5400.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10718  Z= 0.163
  Angle     :  0.709   7.030  14988  Z= 0.391
  Chirality :  0.041   0.161   1658
  Planarity :  0.005   0.043   1472
  Dihedral  : 24.530 159.368   2456
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.94 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.28), residues: 952
  helix:  1.01 (0.28), residues: 358
  sheet:  1.09 (0.51), residues: 112
  loop : -0.40 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 465 
 HIS   0.002   0.001   HIS D 585 
 PHE   0.050   0.002   PHE C 241 
 TYR   0.011   0.001   TYR D 177 
 ARG   0.006   0.000   ARG C 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05209 (  459)
  hydrogen bonds       : angle       4.24638 ( 1164)
  metal coordination   : bond        0.00697 (   16)
  metal coordination   : angle       3.08307 (   18)
  covalent geometry    : bond        0.00380 (10702)
  covalent geometry    : angle       0.70096 (14970)

*********************** 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: 29
    poor density    : 239
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  182 ILE cc_start: 0.9179 (mm) cc_final: 0.8880 (mm)
REVERT: C  185 MET cc_start: 0.8807 (tpp) cc_final: 0.8373 (tpp)
REVERT: C  310 MET cc_start: 0.7582 (ptp) cc_final: 0.7341 (ptp)
REVERT: C  388 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8160 (ttm-80)
REVERT: C  413 MET cc_start: 0.5785 (mpp) cc_final: 0.5342 (mpp)
REVERT: C  440 ASN cc_start: 0.8710 (m-40) cc_final: 0.8272 (m110)
REVERT: C  534 ASN cc_start: 0.8528 (m-40) cc_final: 0.8318 (t0)
REVERT: C  565 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8193 (mmtp)
REVERT: D  146 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7609 (mt-10)
REVERT: D  229 LYS cc_start: 0.9048 (pttm) cc_final: 0.8695 (mmtm)
REVERT: D  264 HIS cc_start: 0.8625 (m-70) cc_final: 0.8146 (m90)
REVERT: D  286 ASN cc_start: 0.8181 (m-40) cc_final: 0.7877 (p0)
REVERT: D  372 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7629 (mtm-85)
REVERT: D  515 MET cc_start: 0.9096 (mtp) cc_final: 0.8860 (mtm)
REVERT: D  536 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7996 (tp)
REVERT: D  569 LYS cc_start: 0.6709 (mttt) cc_final: 0.5390 (tmtt)
REVERT: D  589 MET cc_start: 0.8140 (mtp) cc_final: 0.7890 (mtt)
  outliers start: 29
  outliers final: 19
  residues processed: 254
  average time/residue: 0.2140
  time to fit residues: 76.9446
Evaluate side-chains
  221 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 201
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
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  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 C residue  580 VAL
Chi-restraints excluded: chain D residue  171 THR
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  453 CYS
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 54 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 92 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
C 475 ASN
C 571 ASN
D 254 GLN
D 347 ASN
** 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 = 0.3787 r_free = 0.3787 target = 0.141345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.106138 restraints weight = 18819.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.109688 restraints weight = 8769.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.111883 restraints weight = 5660.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10718  Z= 0.200
  Angle     :  0.726   6.491  14988  Z= 0.398
  Chirality :  0.042   0.155   1658
  Planarity :  0.005   0.047   1472
  Dihedral  : 24.527 163.661   2454
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.68 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 20.14 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.28), residues: 952
  helix:  1.07 (0.28), residues: 354
  sheet:  0.91 (0.51), residues: 110
  loop : -0.63 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 465 
 HIS   0.002   0.001   HIS D 253 
 PHE   0.042   0.002   PHE C 241 
 TYR   0.012   0.002   TYR C 283 
 ARG   0.006   0.001   ARG C 499 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05487 (  459)
  hydrogen bonds       : angle       4.26651 ( 1164)
  metal coordination   : bond        0.00777 (   16)
  metal coordination   : angle       3.39066 (   18)
  covalent geometry    : bond        0.00469 (10702)
  covalent geometry    : angle       0.71665 (14970)

*********************** 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
  258 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 220
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8036 (t80)
REVERT: C  182 ILE cc_start: 0.9302 (mm) cc_final: 0.9039 (mm)
REVERT: C  257 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8196 (tm-30)
REVERT: C  318 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7941 (tp-100)
REVERT: C  356 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8427 (mtmm)
REVERT: C  413 MET cc_start: 0.5659 (mpp) cc_final: 0.5200 (mpp)
REVERT: C  440 ASN cc_start: 0.8945 (m-40) cc_final: 0.8517 (m110)
REVERT: C  534 ASN cc_start: 0.8618 (m-40) cc_final: 0.8370 (t0)
REVERT: C  565 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8350 (mmtp)
REVERT: D  146 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7385 (mm-30)
REVERT: D  169 ARG cc_start: 0.7541 (mtm110) cc_final: 0.7163 (ptp90)
REVERT: D  206 MET cc_start: 0.8561 (mmt) cc_final: 0.8191 (tpp)
REVERT: D  214 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7131 (ttp-170)
REVERT: D  218 ASP cc_start: 0.8623 (m-30) cc_final: 0.8325 (m-30)
REVERT: D  297 MET cc_start: 0.8992 (ttm) cc_final: 0.8720 (mtp)
REVERT: D  372 ARG cc_start: 0.8128 (mtt90) cc_final: 0.7863 (mtm-85)
REVERT: D  515 MET cc_start: 0.9170 (mtp) cc_final: 0.8904 (mtm)
REVERT: D  536 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8190 (tp)
REVERT: D  569 LYS cc_start: 0.6523 (mttt) cc_final: 0.5341 (tmtt)
REVERT: D  581 ILE cc_start: 0.5286 (pt) cc_final: 0.5062 (pt)
REVERT: D  589 MET cc_start: 0.8113 (mtp) cc_final: 0.7842 (mtm)
  outliers start: 38
  outliers final: 27
  residues processed: 239
  average time/residue: 0.2593
  time to fit residues: 88.2318
Evaluate side-chains
  229 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
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  207 VAL
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  256 ILE
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  299 CYS
Chi-restraints excluded: chain C residue  317 THR
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 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  188 VAL
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  324 LEU
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  436 VAL
Chi-restraints excluded: chain D residue  453 CYS
Chi-restraints excluded: chain D residue  454 SER
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 65 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 100 optimal weight:    8.9990
   overall best weight:    1.1382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.144253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.109531 restraints weight = 18672.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.113178 restraints weight = 8538.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.115444 restraints weight = 5455.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.4721

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= 0.153
  Angle     :  0.673   9.878  14988  Z= 0.366
  Chirality :  0.040   0.146   1658
  Planarity :  0.005   0.047   1472
  Dihedral  : 24.438 159.903   2454
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 21.72 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.28), residues: 952
  helix:  1.30 (0.28), residues: 352
  sheet:  0.67 (0.50), residues: 115
  loop : -0.57 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 348 
 HIS   0.003   0.001   HIS D 487 
 PHE   0.047   0.002   PHE C 241 
 TYR   0.009   0.001   TYR D 438 
 ARG   0.004   0.000   ARG C 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04532 (  459)
  hydrogen bonds       : angle       4.02433 ( 1164)
  metal coordination   : bond        0.00533 (   16)
  metal coordination   : angle       2.88580 (   18)
  covalent geometry    : bond        0.00359 (10702)
  covalent geometry    : angle       0.66551 (14970)

*********************** 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
  247 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 219
  time to evaluate  : 1.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8018 (t80)
REVERT: C  257 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: C  356 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8563 (mtmm)
REVERT: C  413 MET cc_start: 0.5563 (mpp) cc_final: 0.5147 (mpp)
REVERT: C  440 ASN cc_start: 0.8984 (m-40) cc_final: 0.8508 (m110)
REVERT: C  467 MET cc_start: 0.7297 (mmm) cc_final: 0.7001 (mmm)
REVERT: C  565 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8248 (mmtp)
REVERT: C  579 LYS cc_start: 0.8077 (mmmm) cc_final: 0.7854 (mmmm)
REVERT: D  146 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7571 (mt-10)
REVERT: D  191 ASP cc_start: 0.8915 (p0) cc_final: 0.8665 (p0)
REVERT: D  206 MET cc_start: 0.8460 (mmt) cc_final: 0.8224 (mmt)
REVERT: D  214 ARG cc_start: 0.7327 (ttm-80) cc_final: 0.6982 (ttp-170)
REVERT: D  218 ASP cc_start: 0.8624 (m-30) cc_final: 0.8269 (m-30)
REVERT: D  286 ASN cc_start: 0.8116 (m-40) cc_final: 0.7863 (p0)
REVERT: D  297 MET cc_start: 0.8932 (ttm) cc_final: 0.8583 (mtp)
REVERT: D  332 LEU cc_start: 0.8757 (mm) cc_final: 0.8311 (mm)
REVERT: D  372 ARG cc_start: 0.8054 (mtt90) cc_final: 0.7770 (mtm-85)
REVERT: D  394 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6769 (ptt)
REVERT: D  456 MET cc_start: 0.8668 (mmt) cc_final: 0.8320 (mmt)
REVERT: D  515 MET cc_start: 0.9192 (mtp) cc_final: 0.8905 (mtm)
REVERT: D  569 LYS cc_start: 0.6441 (mttt) cc_final: 0.5332 (tmtt)
REVERT: D  589 MET cc_start: 0.8063 (mtp) cc_final: 0.7818 (mtm)
  outliers start: 28
  outliers final: 18
  residues processed: 235
  average time/residue: 0.2756
  time to fit residues: 93.1234
Evaluate side-chains
  229 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 208
  time to evaluate  : 1.325 
-------------------------------------------------------------------------------
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  317 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 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  280 PHE
Chi-restraints excluded: chain D residue  351 SER
Chi-restraints excluded: chain D residue  394 MET
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  527 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 36 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 497 GLN
** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.138444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.104238 restraints weight = 19129.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.107722 restraints weight = 8657.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.109852 restraints weight = 5525.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.4932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  10718  Z= 0.260
  Angle     :  0.765   8.379  14988  Z= 0.413
  Chirality :  0.044   0.166   1658
  Planarity :  0.005   0.049   1472
  Dihedral  : 24.598 162.553   2454
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 21.04 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.28), residues: 952
  helix:  1.20 (0.28), residues: 356
  sheet:  0.50 (0.49), residues: 115
  loop : -0.88 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 465 
 HIS   0.006   0.001   HIS C 193 
 PHE   0.038   0.002   PHE C 241 
 TYR   0.015   0.002   TYR C 527 
 ARG   0.006   0.000   ARG D 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06139 (  459)
  hydrogen bonds       : angle       4.38696 ( 1164)
  metal coordination   : bond        0.01090 (   16)
  metal coordination   : angle       3.76170 (   18)
  covalent geometry    : bond        0.00606 (10702)
  covalent geometry    : angle       0.75387 (14970)

*********************** 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
  250 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 210
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8166 (t80)
REVERT: C  312 TYR cc_start: 0.8826 (t80) cc_final: 0.8448 (t80)
REVERT: C  356 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8539 (mtmm)
REVERT: C  437 MET cc_start: 0.8739 (mmm) cc_final: 0.8502 (mmm)
REVERT: C  440 ASN cc_start: 0.9176 (m-40) cc_final: 0.8757 (m110)
REVERT: C  467 MET cc_start: 0.7997 (mmm) cc_final: 0.7736 (mmm)
REVERT: C  565 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8296 (mmtp)
REVERT: D  169 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7455 (ptp90)
REVERT: D  206 MET cc_start: 0.8581 (mmt) cc_final: 0.8366 (mmt)
REVERT: D  214 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7638 (ttp-170)
REVERT: D  372 ARG cc_start: 0.8339 (mtt90) cc_final: 0.7829 (mtm-85)
REVERT: D  456 MET cc_start: 0.8696 (mmt) cc_final: 0.8286 (mmt)
REVERT: D  536 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8284 (tp)
REVERT: D  589 MET cc_start: 0.8015 (mtp) cc_final: 0.7709 (mtm)
  outliers start: 40
  outliers final: 30
  residues processed: 232
  average time/residue: 0.2676
  time to fit residues: 88.8294
Evaluate side-chains
  234 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 201
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
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  186 THR
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  317 THR
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  456 MET
Chi-restraints excluded: chain C residue  463 ASN
Chi-restraints excluded: chain C residue  580 VAL
Chi-restraints excluded: chain D residue  151 THR
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  280 PHE
Chi-restraints excluded: chain D residue  351 SER
Chi-restraints excluded: chain D residue  418 SER
Chi-restraints excluded: chain D residue  420 CYS
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  527 TYR
Chi-restraints excluded: chain D residue  536 LEU
Chi-restraints excluded: chain D residue  557 THR
Chi-restraints excluded: chain D residue  565 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 64 optimal weight:    0.4980
   chunk 82 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   chunk 47 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 497 GLN
C 585 HIS
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 = 0.3805 r_free = 0.3805 target = 0.142731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.108307 restraints weight = 19018.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.111995 restraints weight = 8317.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.114262 restraints weight = 5189.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.5211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.021   2.183  10718  Z= 0.407
  Angle     :  0.687  11.898  14988  Z= 0.371
  Chirality :  0.040   0.166   1658
  Planarity :  0.005   0.050   1472
  Dihedral  : 24.395 159.434   2454
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 22.85 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.28), residues: 952
  helix:  1.39 (0.29), residues: 356
  sheet:  0.41 (0.49), residues: 115
  loop : -0.89 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 348 
 HIS   0.005   0.001   HIS D 264 
 PHE   0.028   0.002   PHE C 241 
 TYR   0.009   0.001   TYR C 259 
 ARG   0.003   0.000   ARG D 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04568 (  459)
  hydrogen bonds       : angle       4.04992 ( 1164)
  metal coordination   : bond        0.54576 (   16)
  metal coordination   : angle       2.80859 (   18)
  covalent geometry    : bond        0.00360 (10702)
  covalent geometry    : angle       0.68075 (14970)

*********************** 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
  256 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 225
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8289 (t80)
REVERT: C  312 TYR cc_start: 0.8854 (t80) cc_final: 0.8483 (t80)
REVERT: C  356 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8565 (mtmm)
REVERT: C  413 MET cc_start: 0.5380 (mpp) cc_final: 0.4525 (mpp)
REVERT: C  437 MET cc_start: 0.8767 (mmm) cc_final: 0.8502 (mmm)
REVERT: C  440 ASN cc_start: 0.9104 (m-40) cc_final: 0.8666 (m110)
REVERT: C  565 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8249 (mmtp)
REVERT: D  169 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7506 (ptp90)
REVERT: D  214 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7318 (ttp-170)
REVERT: D  264 HIS cc_start: 0.8668 (m-70) cc_final: 0.8378 (m90)
REVERT: D  286 ASN cc_start: 0.8000 (m-40) cc_final: 0.7796 (p0)
REVERT: D  372 ARG cc_start: 0.8004 (mtt90) cc_final: 0.7729 (mtm-85)
REVERT: D  456 MET cc_start: 0.8658 (mmt) cc_final: 0.8446 (mmt)
REVERT: D  536 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8284 (tp)
  outliers start: 31
  outliers final: 22
  residues processed: 239
  average time/residue: 0.1957
  time to fit residues: 67.9109
Evaluate side-chains
  233 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 208
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
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  186 THR
Chi-restraints excluded: chain C residue  207 VAL
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 C residue  456 MET
Chi-restraints excluded: chain C residue  580 VAL
Chi-restraints excluded: chain D residue  195 SER
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  280 PHE
Chi-restraints excluded: chain D residue  404 VAL
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  532 ILE
Chi-restraints excluded: chain D residue  536 LEU
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 45 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 26 optimal weight:    0.2980
   chunk 63 optimal weight:    0.0070
   chunk 44 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 531 ASN
D 538 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.145902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.112053 restraints weight = 19057.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.115739 restraints weight = 8552.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.118004 restraints weight = 5404.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.5490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.341  10718  Z= 0.162
  Angle     :  0.728  19.871  14988  Z= 0.379
  Chirality :  0.039   0.154   1658
  Planarity :  0.005   0.055   1472
  Dihedral  : 24.243 159.428   2454
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 24.32 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.28), residues: 952
  helix:  1.48 (0.29), residues: 355
  sheet:  0.27 (0.50), residues: 113
  loop : -0.89 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 348 
 HIS   0.058   0.005   HIS C 585 
 PHE   0.024   0.001   PHE C 241 
 TYR   0.010   0.001   TYR C 439 
 ARG   0.005   0.000   ARG D 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04115 (  459)
  hydrogen bonds       : angle       3.87655 ( 1164)
  metal coordination   : bond        0.08604 (   16)
  metal coordination   : angle       6.69531 (   18)
  covalent geometry    : bond        0.00350 (10702)
  covalent geometry    : angle       0.69089 (14970)

*********************** 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
  246 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 223
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8332 (t80)
REVERT: C  254 GLN cc_start: 0.8684 (tp40) cc_final: 0.8481 (tp40)
REVERT: C  312 TYR cc_start: 0.8810 (t80) cc_final: 0.8456 (t80)
REVERT: C  356 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8566 (mtmm)
REVERT: C  413 MET cc_start: 0.5471 (mpp) cc_final: 0.4671 (mpp)
REVERT: C  437 MET cc_start: 0.8791 (mmm) cc_final: 0.8532 (mmm)
REVERT: C  440 ASN cc_start: 0.9067 (m-40) cc_final: 0.8606 (m110)
REVERT: C  487 HIS cc_start: 0.7775 (t-90) cc_final: 0.7498 (t-90)
REVERT: C  565 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8206 (mmtp)
REVERT: D  169 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7565 (ptp-110)
REVERT: D  286 ASN cc_start: 0.8062 (m-40) cc_final: 0.7826 (p0)
REVERT: D  320 ASN cc_start: 0.8149 (m-40) cc_final: 0.7853 (p0)
REVERT: D  372 ARG cc_start: 0.7943 (mtt90) cc_final: 0.7664 (mtm-85)
REVERT: D  394 MET cc_start: 0.7168 (ptp) cc_final: 0.6966 (ptt)
REVERT: D  456 MET cc_start: 0.8645 (mmt) cc_final: 0.8425 (mmt)
REVERT: D  536 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8290 (tp)
  outliers start: 23
  outliers final: 16
  residues processed: 235
  average time/residue: 0.2208
  time to fit residues: 74.6719
Evaluate side-chains
  226 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 207
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
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  207 VAL
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  358 LEU
Chi-restraints excluded: chain C residue  456 MET
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  267 ILE
Chi-restraints excluded: chain D residue  280 PHE
Chi-restraints excluded: chain D residue  404 VAL
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  532 ILE
Chi-restraints excluded: chain D residue  536 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 13 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 94 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 286 ASN
C 475 ASN
** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.141143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.106715 restraints weight = 19106.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.110372 restraints weight = 8404.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.112587 restraints weight = 5260.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.5542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.368  10718  Z= 0.212
  Angle     :  0.769  17.219  14988  Z= 0.398
  Chirality :  0.042   0.155   1658
  Planarity :  0.005   0.051   1472
  Dihedral  : 24.264 160.262   2454
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 24.89 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.27), residues: 952
  helix:  1.31 (0.29), residues: 357
  sheet:  0.34 (0.48), residues: 115
  loop : -1.04 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 465 
 HIS   0.050   0.004   HIS C 585 
 PHE   0.023   0.002   PHE C 241 
 TYR   0.012   0.001   TYR C 527 
 ARG   0.006   0.000   ARG D 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05066 (  459)
  hydrogen bonds       : angle       4.07208 ( 1164)
  metal coordination   : bond        0.09273 (   16)
  metal coordination   : angle       6.46150 (   18)
  covalent geometry    : bond        0.00479 (10702)
  covalent geometry    : angle       0.73568 (14970)

*********************** 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
  233 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 204
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8395 (t80)
REVERT: C  356 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8581 (mtmm)
REVERT: C  437 MET cc_start: 0.8821 (mmm) cc_final: 0.8544 (mmm)
REVERT: C  440 ASN cc_start: 0.9256 (m-40) cc_final: 0.8876 (m110)
REVERT: C  487 HIS cc_start: 0.7895 (t-90) cc_final: 0.7624 (t-90)
REVERT: C  565 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8232 (mmtp)
REVERT: D  264 HIS cc_start: 0.8768 (m-70) cc_final: 0.8420 (m90)
REVERT: D  320 ASN cc_start: 0.8244 (m-40) cc_final: 0.7929 (p0)
REVERT: D  372 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7738 (mtm-85)
REVERT: D  456 MET cc_start: 0.8642 (mmt) cc_final: 0.8302 (mmm)
REVERT: D  515 MET cc_start: 0.8767 (mtm) cc_final: 0.8523 (mtm)
REVERT: D  536 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8346 (tp)
  outliers start: 29
  outliers final: 23
  residues processed: 215
  average time/residue: 0.2016
  time to fit residues: 62.3212
Evaluate side-chains
  229 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 203
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
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  186 THR
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  267 ILE
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  358 LEU
Chi-restraints excluded: chain C residue  456 MET
Chi-restraints excluded: chain C residue  532 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  224 LEU
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  267 ILE
Chi-restraints excluded: chain D residue  280 PHE
Chi-restraints excluded: chain D residue  404 VAL
Chi-restraints excluded: chain D residue  416 LEU
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  527 TYR
Chi-restraints excluded: chain D residue  532 ILE
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 29 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0770
   chunk 42 optimal weight:    0.0670
   chunk 97 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 71 optimal weight:    8.9990
   chunk 89 optimal weight:    0.0570
   chunk 47 optimal weight:   10.0000
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.145956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.112729 restraints weight = 19184.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.116403 restraints weight = 8591.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.118679 restraints weight = 5389.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.5745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.300  10718  Z= 0.157
  Angle     :  0.713  15.387  14988  Z= 0.372
  Chirality :  0.040   0.148   1658
  Planarity :  0.005   0.066   1472
  Dihedral  : 24.122 158.030   2454
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 26.13 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.28), residues: 952
  helix:  1.33 (0.29), residues: 356
  sheet:  0.36 (0.50), residues: 113
  loop : -1.02 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 348 
 HIS   0.040   0.003   HIS C 585 
 PHE   0.022   0.001   PHE C 241 
 TYR   0.011   0.001   TYR C 259 
 ARG   0.008   0.000   ARG D 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 (  459)
  hydrogen bonds       : angle       3.90682 ( 1164)
  metal coordination   : bond        0.07569 (   16)
  metal coordination   : angle       5.66788 (   18)
  covalent geometry    : bond        0.00341 (10702)
  covalent geometry    : angle       0.68627 (14970)

********************** 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
  238 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 217
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
REVERT: C  138 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8388 (t80)
REVERT: C  312 TYR cc_start: 0.8809 (t80) cc_final: 0.8499 (t80)
REVERT: C  356 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8540 (mtmm)
REVERT: C  437 MET cc_start: 0.8781 (mmm) cc_final: 0.8520 (mmm)
REVERT: C  440 ASN cc_start: 0.9236 (m-40) cc_final: 0.8823 (m110)
REVERT: C  487 HIS cc_start: 0.7804 (t-90) cc_final: 0.7578 (t-90)
REVERT: C  565 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8146 (mmtp)
REVERT: D  169 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7563 (ptp90)
REVERT: D  264 HIS cc_start: 0.8670 (m-70) cc_final: 0.8024 (m-70)
REVERT: D  286 ASN cc_start: 0.8048 (m-40) cc_final: 0.7819 (p0)
REVERT: D  310 MET cc_start: 0.7221 (mtp) cc_final: 0.6853 (ptp)
REVERT: D  320 ASN cc_start: 0.8149 (m-40) cc_final: 0.7882 (p0)
REVERT: D  372 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7813 (mtm-85)
REVERT: D  394 MET cc_start: 0.7228 (ptp) cc_final: 0.6900 (ptt)
REVERT: D  456 MET cc_start: 0.8639 (mmt) cc_final: 0.8264 (mmt)
REVERT: D  467 MET cc_start: 0.7365 (mmm) cc_final: 0.6820 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 226
  average time/residue: 0.2052
  time to fit residues: 65.8471
Evaluate side-chains
  225 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 206
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
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  267 ILE
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  358 LEU
Chi-restraints excluded: chain C residue  456 MET
Chi-restraints excluded: chain C residue  532 ILE
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  267 ILE
Chi-restraints excluded: chain D residue  280 PHE
Chi-restraints excluded: chain D residue  404 VAL
Chi-restraints excluded: chain D residue  426 ILE
Chi-restraints excluded: chain D residue  453 CYS
Chi-restraints excluded: chain D residue  532 ILE
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 10 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.142992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.109165 restraints weight = 18808.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.112740 restraints weight = 8344.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.114947 restraints weight = 5246.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.5754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.300  10718  Z= 0.192
  Angle     :  0.746  15.375  14988  Z= 0.387
  Chirality :  0.041   0.157   1658
  Planarity :  0.006   0.051   1472
  Dihedral  : 24.146 159.169   2454
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 24.89 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.27), residues: 952
  helix:  1.27 (0.28), residues: 360
  sheet:  0.32 (0.49), residues: 113
  loop : -1.06 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 248 
 HIS   0.041   0.004   HIS C 585 
 PHE   0.024   0.002   PHE C 241 
 TYR   0.011   0.001   TYR C 527 
 ARG   0.010   0.001   ARG D 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04744 (  459)
  hydrogen bonds       : angle       4.00017 ( 1164)
  metal coordination   : bond        0.07564 (   16)
  metal coordination   : angle       5.80992 (   18)
  covalent geometry    : bond        0.00436 (10702)
  covalent geometry    : angle       0.71896 (14970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3816.82 seconds
wall clock time: 69 minutes 49.00 seconds (4189.00 seconds total)