Starting phenix.real_space_refine
on Wed Mar  4 05:28:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7syf_25524/03_2026/7syf_25524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7syf_25524/03_2026/7syf_25524.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7syf_25524/03_2026/7syf_25524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7syf_25524/03_2026/7syf_25524.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7syf_25524/03_2026/7syf_25524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7syf_25524/03_2026/7syf_25524.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.016 sd=   0.092
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    7024      2.51       5
     N    1942      2.21       5
     O    2070      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11108
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1391, 11108
          Classifications: {'peptide': 1391}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 47, 'TRANS': 1340}
          Chain breaks: 7
  Time building chain proxies: 2.63, per 1000 atoms: 0.24
  Number of scatterers: 11108
  At special positions: 0
  Unit cell: (111.688, 123.799, 139.947, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    2070      8.00
     N    1942      7.00
     C    7024      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 513.8 milliseconds
  

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2636

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 7 sheets defined
      58.6% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 82
      removed outlier: 3.715A  pdb=" N   HIS A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ARG A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ASN A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 121
      removed outlier: 3.511A  pdb=" N   SER A 101 " --> pdb=" O   LYS A  97 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   ASN A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLU A 104 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   VAL A 109 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 143
      removed outlier: 4.282A  pdb=" N   ASP A 140 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LYS A 141 " --> pdb=" O   LYS A 137 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   CYS A 143 " --> pdb=" O   LYS A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 165
      removed outlier: 3.780A  pdb=" N   TYR A 148 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   GLU A 153 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   LYS A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLU A 161 " --> pdb=" O   ARG A 157 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE A 165 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 180
      removed outlier: 3.673A  pdb=" N   MET A 176 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 193 through 213
      Proline residue:  A 203  - end of helix
      removed outlier: 3.667A  pdb=" N   ARG A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 237
      removed outlier: 4.610A  pdb=" N   ALA A 222 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE A 237 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 256
      removed outlier: 3.709A  pdb=" N   LEU A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 269
      removed outlier: 3.646A  pdb=" N   ILE A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 421
    Processing helix  chain 'A' and resid 444 through 454
    Processing helix  chain 'A' and resid 459 through 473
      removed outlier: 3.539A  pdb=" N   GLY A 463 " --> pdb=" O   LYS A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 523
      removed outlier: 3.512A  pdb=" N   ASP A 509 " --> pdb=" O   SER A 505 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ILE A 510 " --> pdb=" O   GLU A 506 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   MET A 511 " --> pdb=" O   LEU A 507 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   SER A 512 " --> pdb=" O   GLU A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 555
    Processing helix  chain 'A' and resid 560 through 574
    Processing helix  chain 'A' and resid 596 through 603
      removed outlier: 3.906A  pdb=" N   MET A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 610
    Processing helix  chain 'A' and resid 655 through 661
    Processing helix  chain 'A' and resid 675 through 679
    Processing helix  chain 'A' and resid 680 through 694
      removed outlier: 3.515A  pdb=" N   SER A 686 " --> pdb=" O   SER A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 744
    Processing helix  chain 'A' and resid 763 through 769
    Processing helix  chain 'A' and resid 771 through 778
    Processing helix  chain 'A' and resid 779 through 782
      removed outlier: 4.135A  pdb=" N   LEU A 782 " --> pdb=" O   GLU A 779 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 779 through 782'
    Processing helix  chain 'A' and resid 791 through 806
    Processing helix  chain 'A' and resid 878 through 908
    Processing helix  chain 'A' and resid 913 through 946
    Processing helix  chain 'A' and resid 963 through 968
    Processing helix  chain 'A' and resid 1064 through 1068
    Processing helix  chain 'A' and resid 1069 through 1108
      removed outlier: 3.622A  pdb=" N   ARG A1073 " --> pdb=" O   LYS A1069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1237
      removed outlier: 4.925A  pdb=" N   LEU A1235 " --> pdb=" O   SER A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1238 through 1248
    Processing helix  chain 'A' and resid 1256 through 1263
    Processing helix  chain 'A' and resid 1263 through 1281
    Processing helix  chain 'A' and resid 1284 through 1315
    Processing helix  chain 'A' and resid 1316 through 1346
    Processing helix  chain 'A' and resid 1353 through 1357
      removed outlier: 3.565A  pdb=" N   GLU A1357 " --> pdb=" O   GLY A1354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1359 through 1375
    Processing helix  chain 'A' and resid 1389 through 1407
      removed outlier: 4.241A  pdb=" N   VAL A1401 " --> pdb=" O   GLU A1397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1444 through 1450
    Processing helix  chain 'A' and resid 1452 through 1457
    Processing helix  chain 'A' and resid 1480 through 1517
    Processing helix  chain 'A' and resid 1521 through 1551
      removed outlier: 4.216A  pdb=" N   ARG A1534 " --> pdb=" O   ASP A1530 " (cutoff:3.500A)
      Proline residue:  A1535  - end of helix
    Processing helix  chain 'A' and resid 1563 through 1576
    Processing helix  chain 'A' and resid 1588 through 1606
    Processing helix  chain 'A' and resid 1609 through 1611
      No H-bonds generated for 'chain 'A' and resid 1609 through 1611'
    Processing helix  chain 'A' and resid 1612 through 1624
    Processing helix  chain 'A' and resid 1626 through 1631
      removed outlier: 4.133A  pdb=" N   LEU A1630 " --> pdb=" O   ARG A1626 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 258
      removed outlier: 3.559A  pdb=" N   PHE A 327 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   PHE A 327 " --> pdb=" O   LYS A 302 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   LYS A 302 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   GLN A 287 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   LEU A 279 " --> pdb=" O   GLN A 287 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ARG A 289 " --> pdb=" O   THR A 277 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   THR A 277 " --> pdb=" O   ARG A 289 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   PHE A 291 " --> pdb=" O   GLN A 275 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   GLN A 275 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LEU A 293 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 431
      removed outlier: 5.299A  pdb=" N   LYS A 429 " --> pdb=" O   LYS A 440 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS A 440 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
      removed outlier: 8.715A  pdb=" N   LYS A 440 " --> pdb=" O   PHE A 494 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   PHE A 494 " --> pdb=" O   LYS A 440 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 530 through 533
      removed outlier: 5.048A  pdb=" N   ARG A 532 " --> pdb=" O   LYS A 540 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   LYS A 540 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   SER A 541 " --> pdb=" O   PHE A 595 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   PHE A 595 " --> pdb=" O   SER A 541 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 668 through 671
      removed outlier: 6.337A  pdb=" N   LEU A 701 " --> pdb=" O   TYR A 669 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ILE A 671 " --> pdb=" O   ARG A 699 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ARG A 699 " --> pdb=" O   ILE A 671 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   PHE A 615 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   VAL A 860 " --> pdb=" O   PHE A 615 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   LEU A 617 " --> pdb=" O   GLU A 858 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   GLU A 858 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLU A 619 " --> pdb=" O   VAL A 856 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   HIS A 868 " --> pdb=" O   SER A 980 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLN A1579 " --> pdb=" O   CYS A1021 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   CYS A1583 " --> pdb=" O   MET A1025 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL A1376 " --> pdb=" O   HIS A1464 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   ALA A1466 " --> pdb=" O   VAL A1376 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU A1378 " --> pdb=" O   ALA A1466 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   PHE A1468 " --> pdb=" O   LEU A1378 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   CYS A1380 " --> pdb=" O   PHE A1468 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   THR A1410 " --> pdb=" O   VAL A1439 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   PHE A1441 " --> pdb=" O   THR A1410 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   SER A1412 " --> pdb=" O   PHE A1441 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   LEU A1443 " --> pdb=" O   SER A1412 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   LYS A1414 " --> pdb=" O   LEU A1443 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 637 through 642
      removed outlier: 6.651A  pdb=" N   ASP A 638 " --> pdb=" O   LYS A 649 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 713
      removed outlier: 6.485A  pdb=" N   THR A 843 " --> pdb=" O   VAL A 754 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   VAL A 754 " --> pdb=" O   THR A 843 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   THR A 845 " --> pdb=" O   LEU A 752 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 721 through 724
      removed outlier: 6.672A  pdb=" N   GLN A 722 " --> pdb=" O   TYR A 732 " (cutoff:3.500A)

    691 hydrogen bonds defined for protein.
    2007 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2166
        1.32 -     1.45: 2626
        1.45 -     1.57: 6413
        1.57 -     1.70: 0
        1.70 -     1.83: 105
  Bond restraints: 11310
  Sorted by residual:
  bond pdb=" C   PHE A1260 "
       pdb=" N   LYS A1261 "
    ideal  model  delta    sigma   weight residual
    1.335  1.571 -0.237 1.25e-02 6.40e+03 3.59e+02
  bond pdb=" C   ARG A 181 "
       pdb=" N   LYS A 182 "
    ideal  model  delta    sigma   weight residual
    1.331  1.490 -0.159 1.42e-02 4.96e+03 1.25e+02
  bond pdb=" C   GLU A 619 "
       pdb=" N   ASN A 620 "
    ideal  model  delta    sigma   weight residual
    1.330  1.253  0.077 1.38e-02 5.25e+03 3.14e+01
  bond pdb=" C   VAL A 618 "
       pdb=" N   GLU A 619 "
    ideal  model  delta    sigma   weight residual
    1.332  1.260  0.072 1.40e-02 5.10e+03 2.66e+01
  bond pdb=" C   LEU A 227 "
       pdb=" N   GLN A 228 "
    ideal  model  delta    sigma   weight residual
    1.335  1.387 -0.053 1.31e-02 5.83e+03 1.61e+01
  ... (remaining 11305 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 11715
        2.17 -     4.33: 3173
        4.33 -     6.50: 338
        6.50 -     8.67: 28
        8.67 -    10.83: 8
  Bond angle restraints: 15262
  Sorted by residual:
  angle pdb=" C   PHE A1260 "
        pdb=" N   LYS A1261 "
        pdb=" CA  LYS A1261 "
      ideal   model   delta    sigma   weight residual
     120.54  109.71   10.83 1.35e+00 5.49e-01 6.44e+01
  angle pdb=" N   TYR A 539 "
        pdb=" CA  TYR A 539 "
        pdb=" C   TYR A 539 "
      ideal   model   delta    sigma   weight residual
     109.95   99.43   10.52 1.59e+00 3.96e-01 4.38e+01
  angle pdb=" CA  PHE A  70 "
        pdb=" CB  PHE A  70 "
        pdb=" CG  PHE A  70 "
      ideal   model   delta    sigma   weight residual
     113.80  120.01   -6.21 1.00e+00 1.00e+00 3.86e+01
  angle pdb=" N   ILE A 103 "
        pdb=" CA  ILE A 103 "
        pdb=" CB  ILE A 103 "
      ideal   model   delta    sigma   weight residual
     110.51  117.25   -6.74 1.11e+00 8.12e-01 3.69e+01
  angle pdb=" O   PHE A1260 "
        pdb=" C   PHE A1260 "
        pdb=" N   LYS A1261 "
      ideal   model   delta    sigma   weight residual
     122.12  128.45   -6.33 1.06e+00 8.90e-01 3.57e+01
  ... (remaining 15257 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 6298
       17.72 -    35.44: 481
       35.44 -    53.15: 99
       53.15 -    70.87: 35
       70.87 -    88.59: 11
  Dihedral angle restraints: 6924
    sinusoidal: 2859
      harmonic: 4065
  Sorted by residual:
  dihedral pdb=" CA  LEU A1068 "
           pdb=" C   LEU A1068 "
           pdb=" N   LYS A1069 "
           pdb=" CA  LYS A1069 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.57   29.43     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  LEU A 700 "
           pdb=" C   LEU A 700 "
           pdb=" N   LEU A 701 "
           pdb=" CA  LEU A 701 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.98   29.02     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  ALA A 283 "
           pdb=" C   ALA A 283 "
           pdb=" N   GLY A 284 "
           pdb=" CA  GLY A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.65  -28.35     0      5.00e+00 4.00e-02 3.21e+01
  ... (remaining 6921 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1210
       0.098 -    0.196: 426
       0.196 -    0.294: 56
       0.294 -    0.392: 11
       0.392 -    0.490: 6
  Chirality restraints: 1709
  Sorted by residual:
  chirality pdb=" CA  ILE A 103 "
            pdb=" N   ILE A 103 "
            pdb=" C   ILE A 103 "
            pdb=" CB  ILE A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.94    0.49 2.00e-01 2.50e+01 6.00e+00
  chirality pdb=" CA  ARG A 303 "
            pdb=" N   ARG A 303 "
            pdb=" C   ARG A 303 "
            pdb=" CB  ARG A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.73e+00
  chirality pdb=" CA  ARG A 198 "
            pdb=" N   ARG A 198 "
            pdb=" C   ARG A 198 "
            pdb=" CB  ARG A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.26e+00
  ... (remaining 1706 not shown)

  Planarity restraints: 1973
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 260 "   -0.134 2.00e-02 2.50e+03   7.38e-02 1.36e+02
        pdb=" CG  TRP A 260 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 260 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 260 "    0.108 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 260 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 260 "    0.038 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 260 "    0.102 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 260 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 260 "   -0.020 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 260 "   -0.101 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 787 "   -0.093 2.00e-02 2.50e+03   5.11e-02 6.52e+01
        pdb=" CG  TRP A 787 "    0.002 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 787 "    0.051 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 787 "    0.020 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 787 "    0.039 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 787 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 787 "    0.074 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 787 "   -0.064 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 787 "    0.031 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 787 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A1020 "    0.084 2.00e-02 2.50e+03   6.25e-02 5.85e+01
        pdb=" CG  HIS A1020 "   -0.095 2.00e-02 2.50e+03
        pdb=" ND1 HIS A1020 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 HIS A1020 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE1 HIS A1020 "    0.034 2.00e-02 2.50e+03
        pdb=" NE2 HIS A1020 "    0.055 2.00e-02 2.50e+03
  ... (remaining 1970 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.95: 4664
        2.95 -     3.44: 11727
        3.44 -     3.92: 18891
        3.92 -     4.41: 21061
        4.41 -     4.90: 34498
  Nonbonded interactions: 90841
  Sorted by model distance:
  nonbonded pdb=" N   TYR A 539 "
            pdb=" O   TYR A 539 "
     model   vdw
     2.460 2.496
  nonbonded pdb=" OG  SER A 458 "
            pdb=" OE2 GLU A 462 "
     model   vdw
     2.478 3.040
  nonbonded pdb=" OG  SER A1569 "
            pdb=" OE2 GLU A1597 "
     model   vdw
     2.512 3.040
  nonbonded pdb=" ND1 HIS A  77 "
            pdb=" NH2 ARG A  80 "
     model   vdw
     2.520 3.200
  nonbonded pdb=" OG1 THR A 354 "
            pdb=" OE1 GLU A1092 "
     model   vdw
     2.564 3.040
  ... (remaining 90836 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.300
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.680
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6223
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      :  0.013   0.237  11310  Z= 0.818
  Angle     :  1.861  10.834  15262  Z= 1.269
  Chirality :  0.098   0.490   1709
  Planarity :  0.015   0.128   1973
  Dihedral  : 14.320  88.585   4288
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  3.60 %
    Favored  : 95.09 %
  Cbeta Deviations :  0.61 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.20), residues: 1375
  helix: -1.07 (0.15), residues: 766
  sheet: -0.80 (0.39), residues: 153
  loop : -0.65 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 212 
 TYR   0.097   0.016   TYR A 191 
 PHE   0.067   0.014   PHE A 593 
 TRP   0.134   0.032   TRP A 260 
 HIS   0.019   0.005   HIS A 579 

Details of bonding type rmsd
  covalent geometry    : bond        0.01269 (11310)
  covalent geometry    : angle       1.86146 (15262)
  hydrogen bonds       : bond        0.16062 (  691)
  hydrogen bonds       : angle       7.53870 ( 2007)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  425 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 409
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8207 (pp30)
REVERT: A  104 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8567 (pt0)
REVERT: A  112 ASP cc_start: 0.8719 (m-30) cc_final: 0.8499 (t0)
REVERT: A  144 VAL cc_start: 0.8328 (m) cc_final: 0.7642 (p)
REVERT: A  169 ARG cc_start: 0.6643 (ttp-110) cc_final: 0.5641 (ttp80)
REVERT: A  176 MET cc_start: 0.6393 (mtm) cc_final: 0.5856 (ttt)
REVERT: A  177 LEU cc_start: 0.2601 (OUTLIER) cc_final: 0.0965 (mm)
REVERT: A  230 MET cc_start: 0.7197 (mmp) cc_final: 0.6594 (mmp)
REVERT: A  292 PHE cc_start: 0.6897 (m-80) cc_final: 0.6464 (m-80)
REVERT: A  359 TRP cc_start: 0.6886 (p90) cc_final: 0.6223 (p90)
REVERT: A  370 PHE cc_start: 0.7952 (p90) cc_final: 0.7623 (p90)
REVERT: A  510 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5512 (tt)
REVERT: A  511 MET cc_start: 0.5830 (mpp) cc_final: 0.4851 (mpp)
REVERT: A  539 TYR cc_start: 0.7354 (m-80) cc_final: 0.6964 (m-80)
REVERT: A  591 GLN cc_start: 0.7824 (mt0) cc_final: 0.6739 (tt0)
REVERT: A  598 ASP cc_start: 0.8273 (m-30) cc_final: 0.7587 (m-30)
REVERT: A  622 LEU cc_start: 0.7602 (tp) cc_final: 0.7054 (tp)
REVERT: A  631 GLN cc_start: 0.7013 (mt0) cc_final: 0.6460 (mt0)
REVERT: A  691 SER cc_start: 0.6742 (m) cc_final: 0.6482 (p)
REVERT: A  701 LEU cc_start: 0.7785 (mt) cc_final: 0.7479 (mm)
REVERT: A  741 MET cc_start: 0.7502 (ttm) cc_final: 0.6183 (ttm)
REVERT: A  768 LEU cc_start: 0.8776 (mt) cc_final: 0.8527 (mt)
REVERT: A  770 HIS cc_start: 0.8372 (m-70) cc_final: 0.7837 (m-70)
REVERT: A  900 ASN cc_start: 0.8730 (m-40) cc_final: 0.8322 (t0)
REVERT: A  915 PRO cc_start: 0.6507 (Cg_exo) cc_final: 0.5514 (Cg_endo)
REVERT: A  919 PHE cc_start: 0.7522 (t80) cc_final: 0.7110 (t80)
REVERT: A  922 ILE cc_start: 0.8722 (mt) cc_final: 0.8077 (mt)
REVERT: A  923 CYS cc_start: 0.7634 (m) cc_final: 0.6912 (m)
REVERT: A  924 ASP cc_start: 0.8929 (m-30) cc_final: 0.8714 (m-30)
REVERT: A  925 THR cc_start: 0.8956 (m) cc_final: 0.8753 (p)
REVERT: A  926 LYS cc_start: 0.8618 (mttt) cc_final: 0.8281 (mttt)
REVERT: A  928 GLU cc_start: 0.8744 (tt0) cc_final: 0.8491 (tt0)
REVERT: A  929 SER cc_start: 0.9131 (t) cc_final: 0.8916 (p)
REVERT: A  932 GLN cc_start: 0.8093 (mt0) cc_final: 0.7499 (tp-100)
REVERT: A  936 CYS cc_start: 0.8731 (m) cc_final: 0.7418 (m)
REVERT: A  939 GLU cc_start: 0.7806 (tp30) cc_final: 0.6878 (tp30)
REVERT: A  940 PHE cc_start: 0.8560 (m-10) cc_final: 0.7663 (m-10)
REVERT: A  943 GLN cc_start: 0.7534 (mt0) cc_final: 0.6305 (mt0)
REVERT: A  977 MET cc_start: 0.8000 (ttp) cc_final: 0.6705 (ttp)
REVERT: A 1079 TYR cc_start: 0.6817 (m-10) cc_final: 0.6305 (m-10)
REVERT: A 1104 LEU cc_start: 0.6206 (mt) cc_final: 0.5569 (tt)
REVERT: A 1214 LYS cc_start: 0.8444 (mttt) cc_final: 0.7991 (mtmm)
REVERT: A 1324 ASP cc_start: 0.8176 (m-30) cc_final: 0.7699 (m-30)
REVERT: A 1328 CYS cc_start: 0.6946 (t) cc_final: 0.6195 (t)
REVERT: A 1332 VAL cc_start: 0.9021 (t) cc_final: 0.8337 (t)
REVERT: A 1339 SER cc_start: 0.9047 (t) cc_final: 0.8672 (p)
REVERT: A 1343 LEU cc_start: 0.8889 (mt) cc_final: 0.8674 (mm)
REVERT: A 1353 ASN cc_start: 0.6419 (m-40) cc_final: 0.5992 (m-40)
REVERT: A 1366 LYS cc_start: 0.8935 (mttt) cc_final: 0.8545 (mttt)
REVERT: A 1369 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8222 (mt-10)
REVERT: A 1378 LEU cc_start: 0.7679 (tp) cc_final: 0.7396 (tp)
REVERT: A 1384 LEU cc_start: 0.8469 (mt) cc_final: 0.7938 (mp)
REVERT: A 1414 LYS cc_start: 0.7917 (mttt) cc_final: 0.7283 (mmmm)
REVERT: A 1428 TYR cc_start: 0.7256 (m-80) cc_final: 0.6756 (m-80)
REVERT: A 1438 LYS cc_start: 0.8282 (ttpt) cc_final: 0.8068 (ttpp)
REVERT: A 1441 PHE cc_start: 0.8074 (m-80) cc_final: 0.6520 (m-80)
REVERT: A 1504 TYR cc_start: 0.8498 (t80) cc_final: 0.8226 (t80)
REVERT: A 1507 LYS cc_start: 0.8570 (mttt) cc_final: 0.8237 (tptt)
REVERT: A 1508 LEU cc_start: 0.8727 (tp) cc_final: 0.7533 (tp)
REVERT: A 1512 TYR cc_start: 0.7252 (m-80) cc_final: 0.6734 (m-80)
REVERT: A 1530 ASP cc_start: 0.6688 (m-30) cc_final: 0.6473 (m-30)
REVERT: A 1531 GLN cc_start: 0.8564 (mt0) cc_final: 0.7793 (mm110)
REVERT: A 1536 ILE cc_start: 0.8915 (mt) cc_final: 0.8444 (tp)
REVERT: A 1542 LEU cc_start: 0.9254 (mt) cc_final: 0.9026 (mt)
REVERT: A 1546 MET cc_start: 0.8415 (tpp) cc_final: 0.8077 (mmm)
REVERT: A 1593 SER cc_start: 0.7864 (t) cc_final: 0.7644 (p)
REVERT: A 1598 GLN cc_start: 0.8134 (mt0) cc_final: 0.7634 (mt0)
REVERT: A 1605 SER cc_start: 0.8432 (m) cc_final: 0.7972 (p)
REVERT: A 1620 MET cc_start: 0.6815 (mtt) cc_final: 0.6518 (mtp)
REVERT: A 1633 ASN cc_start: 0.8377 (m-40) cc_final: 0.7301 (m-40)
  outliers start: 16
  outliers final: 3
  residues processed: 418
  average time/residue: 0.1359
  time to fit residues: 75.4412
Evaluate side-chains
  300 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 295
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
A 110 HIS
A 228 GLN
A 256 HIS
A 393 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 HIS
A 522 HIS
A 578 HIS
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 ASN
A 722 GLN
A 790 HIS
A1370 GLN
A1379 HIS
A1502 GLN
A1503 GLN
A1615 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.141078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.122608 restraints weight = 32842.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.125899 restraints weight = 21141.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.128223 restraints weight = 14801.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.129900 restraints weight = 11036.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.131162 restraints weight = 8659.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6228
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11310  Z= 0.169
  Angle     :  0.679   9.560  15262  Z= 0.366
  Chirality :  0.044   0.200   1709
  Planarity :  0.005   0.085   1973
  Dihedral  :  6.082  75.654   1510
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.11 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.35 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.22), residues: 1375
  helix:  0.89 (0.18), residues: 767
  sheet: -0.65 (0.36), residues: 173
  loop :  0.00 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 777 
 TYR   0.030   0.002   TYR A1096 
 PHE   0.027   0.002   PHE A  70 
 TRP   0.023   0.003   TRP A 369 
 HIS   0.007   0.001   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (11310)
  covalent geometry    : angle       0.67911 (15262)
  hydrogen bonds       : bond        0.05398 (  691)
  hydrogen bonds       : angle       5.17947 ( 2007)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 322
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LEU cc_start: 0.6976 (mp) cc_final: 0.6616 (pp)
REVERT: A   72 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8099 (tm-30)
REVERT: A  104 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8398 (mp0)
REVERT: A  108 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8074 (pm20)
REVERT: A  176 MET cc_start: 0.6888 (mtm) cc_final: 0.6398 (ttt)
REVERT: A  353 TYR cc_start: 0.8313 (m-80) cc_final: 0.8067 (m-10)
REVERT: A  359 TRP cc_start: 0.6317 (p90) cc_final: 0.5334 (p90)
REVERT: A  360 LYS cc_start: 0.7187 (tmtt) cc_final: 0.6847 (tmmt)
REVERT: A  372 CYS cc_start: 0.8194 (m) cc_final: 0.7683 (t)
REVERT: A  373 MET cc_start: 0.6585 (mpp) cc_final: 0.5926 (mpp)
REVERT: A  419 MET cc_start: 0.8079 (mmp) cc_final: 0.7554 (tmm)
REVERT: A  447 PHE cc_start: 0.8281 (t80) cc_final: 0.8053 (t80)
REVERT: A  468 GLN cc_start: 0.6989 (tp40) cc_final: 0.6084 (pp30)
REVERT: A  532 ARG cc_start: 0.2874 (tpt170) cc_final: 0.2329 (tpm170)
REVERT: A  539 TYR cc_start: 0.7434 (m-80) cc_final: 0.7061 (m-80)
REVERT: A  547 LYS cc_start: 0.7059 (mmtt) cc_final: 0.6750 (tppt)
REVERT: A  591 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7264 (mt0)
REVERT: A  598 ASP cc_start: 0.8129 (m-30) cc_final: 0.7421 (m-30)
REVERT: A  691 SER cc_start: 0.6864 (m) cc_final: 0.6476 (p)
REVERT: A  711 LYS cc_start: 0.7485 (mppt) cc_final: 0.7219 (mppt)
REVERT: A  754 VAL cc_start: 0.8527 (m) cc_final: 0.8323 (t)
REVERT: A  770 HIS cc_start: 0.8580 (m-70) cc_final: 0.7966 (m90)
REVERT: A  922 ILE cc_start: 0.8726 (mt) cc_final: 0.8051 (mt)
REVERT: A  926 LYS cc_start: 0.8477 (mttt) cc_final: 0.8069 (mttt)
REVERT: A  928 GLU cc_start: 0.8538 (tt0) cc_final: 0.8210 (tt0)
REVERT: A  932 GLN cc_start: 0.7938 (mt0) cc_final: 0.7672 (tp40)
REVERT: A  936 CYS cc_start: 0.8616 (m) cc_final: 0.7945 (m)
REVERT: A  939 GLU cc_start: 0.7610 (tp30) cc_final: 0.6508 (tp30)
REVERT: A  940 PHE cc_start: 0.8499 (m-10) cc_final: 0.7428 (m-10)
REVERT: A  943 GLN cc_start: 0.7213 (mt0) cc_final: 0.5898 (mt0)
REVERT: A 1021 CYS cc_start: 0.7997 (t) cc_final: 0.7794 (t)
REVERT: A 1022 ILE cc_start: 0.7684 (mp) cc_final: 0.7460 (mp)
REVERT: A 1023 THR cc_start: 0.7430 (m) cc_final: 0.7194 (p)
REVERT: A 1079 TYR cc_start: 0.6916 (m-10) cc_final: 0.6580 (m-10)
REVERT: A 1104 LEU cc_start: 0.6134 (mt) cc_final: 0.5847 (tp)
REVERT: A 1214 LYS cc_start: 0.8334 (mttt) cc_final: 0.7703 (pttm)
REVERT: A 1233 ASN cc_start: 0.7566 (m110) cc_final: 0.7131 (m110)
REVERT: A 1271 ARG cc_start: 0.8530 (mtm-85) cc_final: 0.8177 (mtm110)
REVERT: A 1296 ILE cc_start: 0.9172 (mt) cc_final: 0.8918 (pt)
REVERT: A 1320 GLN cc_start: 0.8457 (tp40) cc_final: 0.8057 (tp40)
REVERT: A 1324 ASP cc_start: 0.7915 (m-30) cc_final: 0.7689 (m-30)
REVERT: A 1332 VAL cc_start: 0.8939 (t) cc_final: 0.8569 (t)
REVERT: A 1338 PHE cc_start: 0.8436 (t80) cc_final: 0.8180 (t80)
REVERT: A 1339 SER cc_start: 0.8931 (t) cc_final: 0.8356 (p)
REVERT: A 1343 LEU cc_start: 0.8783 (mt) cc_final: 0.8269 (pp)
REVERT: A 1352 ASN cc_start: 0.7243 (p0) cc_final: 0.6451 (p0)
REVERT: A 1353 ASN cc_start: 0.5664 (m-40) cc_final: 0.5335 (m-40)
REVERT: A 1366 LYS cc_start: 0.9176 (mttt) cc_final: 0.8907 (mttt)
REVERT: A 1378 LEU cc_start: 0.7726 (tp) cc_final: 0.7386 (tp)
REVERT: A 1403 LEU cc_start: 0.8049 (mt) cc_final: 0.7713 (mp)
REVERT: A 1428 TYR cc_start: 0.7114 (m-80) cc_final: 0.6719 (m-80)
REVERT: A 1438 LYS cc_start: 0.8280 (ttpt) cc_final: 0.7797 (ttpp)
REVERT: A 1441 PHE cc_start: 0.8012 (m-80) cc_final: 0.7178 (m-10)
REVERT: A 1467 LEU cc_start: 0.6579 (tp) cc_final: 0.6349 (tp)
REVERT: A 1488 ASP cc_start: 0.7149 (m-30) cc_final: 0.6949 (m-30)
REVERT: A 1490 GLN cc_start: 0.8134 (tt0) cc_final: 0.7711 (mt0)
REVERT: A 1508 LEU cc_start: 0.8860 (tp) cc_final: 0.6899 (tp)
REVERT: A 1530 ASP cc_start: 0.6479 (m-30) cc_final: 0.6259 (m-30)
REVERT: A 1531 GLN cc_start: 0.8490 (mt0) cc_final: 0.7688 (mm-40)
REVERT: A 1546 MET cc_start: 0.8290 (tpp) cc_final: 0.8019 (mmm)
REVERT: A 1580 MET cc_start: 0.6606 (mtp) cc_final: 0.6181 (mtp)
REVERT: A 1640 MET cc_start: 0.6745 (tpp) cc_final: 0.5893 (mmm)
REVERT: A 1647 LEU cc_start: 0.7327 (tp) cc_final: 0.6739 (tp)
  outliers start: 5
  outliers final: 2
  residues processed: 326
  average time/residue: 0.1179
  time to fit residues: 52.8149
Evaluate side-chains
  275 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 272
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0470
   chunk 30 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0980
   chunk 92 optimal weight:    0.7980
   chunk 135 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A 243 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 631 GLN
** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1095 GLN
A1227 ASN
A1502 GLN
A1537 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.139686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.121400 restraints weight = 33447.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.124650 restraints weight = 21734.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.127008 restraints weight = 15312.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.128706 restraints weight = 11419.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.129878 restraints weight = 8926.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6238
moved from start:          0.4615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11310  Z= 0.140
  Angle     :  0.622   9.637  15262  Z= 0.329
  Chirality :  0.042   0.210   1709
  Planarity :  0.004   0.055   1973
  Dihedral  :  5.538  74.495   1510
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.04 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.22), residues: 1375
  helix:  1.36 (0.18), residues: 768
  sheet: -0.58 (0.37), residues: 153
  loop :  0.12 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1454 
 TYR   0.024   0.002   TYR A1096 
 PHE   0.020   0.002   PHE A 370 
 TRP   0.017   0.002   TRP A 369 
 HIS   0.003   0.001   HIS A 770 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (11310)
  covalent geometry    : angle       0.62214 (15262)
  hydrogen bonds       : bond        0.04664 (  691)
  hydrogen bonds       : angle       4.81475 ( 2007)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 309
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LEU cc_start: 0.7023 (mp) cc_final: 0.6631 (pp)
REVERT: A   72 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7891 (pp30)
REVERT: A  104 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8107 (mp0)
REVERT: A  108 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7912 (pt0)
REVERT: A  176 MET cc_start: 0.6852 (mtm) cc_final: 0.6451 (ttt)
REVERT: A  278 LEU cc_start: 0.8103 (mt) cc_final: 0.7807 (pp)
REVERT: A  353 TYR cc_start: 0.8289 (m-80) cc_final: 0.8057 (m-10)
REVERT: A  373 MET cc_start: 0.6602 (mpp) cc_final: 0.6164 (mpp)
REVERT: A  419 MET cc_start: 0.7964 (mmp) cc_final: 0.7747 (tmm)
REVERT: A  468 GLN cc_start: 0.6889 (tp40) cc_final: 0.6000 (pp30)
REVERT: A  539 TYR cc_start: 0.7379 (m-80) cc_final: 0.6963 (m-80)
REVERT: A  591 GLN cc_start: 0.6043 (pt0) cc_final: 0.5596 (pm20)
REVERT: A  598 ASP cc_start: 0.8036 (m-30) cc_final: 0.7491 (m-30)
REVERT: A  674 ASP cc_start: 0.7197 (t0) cc_final: 0.6459 (p0)
REVERT: A  691 SER cc_start: 0.6987 (m) cc_final: 0.6572 (p)
REVERT: A  695 ARG cc_start: 0.7718 (mmp80) cc_final: 0.7442 (mmp-170)
REVERT: A  721 PHE cc_start: 0.8556 (p90) cc_final: 0.8338 (p90)
REVERT: A  741 MET cc_start: 0.7673 (mtt) cc_final: 0.7024 (mtt)
REVERT: A  770 HIS cc_start: 0.8500 (m-70) cc_final: 0.7948 (m90)
REVERT: A  922 ILE cc_start: 0.8510 (mt) cc_final: 0.8265 (pt)
REVERT: A  928 GLU cc_start: 0.8461 (tt0) cc_final: 0.8182 (tt0)
REVERT: A  932 GLN cc_start: 0.7968 (mt0) cc_final: 0.7696 (tp40)
REVERT: A  936 CYS cc_start: 0.8672 (m) cc_final: 0.8048 (m)
REVERT: A  939 GLU cc_start: 0.7578 (tp30) cc_final: 0.6493 (tp30)
REVERT: A  940 PHE cc_start: 0.8614 (m-10) cc_final: 0.7587 (m-10)
REVERT: A  943 GLN cc_start: 0.7486 (mt0) cc_final: 0.6497 (mt0)
REVERT: A 1015 MET cc_start: 0.5310 (mpp) cc_final: 0.4158 (mpp)
REVERT: A 1022 ILE cc_start: 0.7533 (mp) cc_final: 0.7325 (mp)
REVERT: A 1079 TYR cc_start: 0.6809 (m-10) cc_final: 0.6409 (m-10)
REVERT: A 1104 LEU cc_start: 0.6011 (mt) cc_final: 0.5720 (tp)
REVERT: A 1214 LYS cc_start: 0.8296 (mttt) cc_final: 0.7737 (pttm)
REVERT: A 1236 LEU cc_start: 0.8393 (mt) cc_final: 0.8161 (mm)
REVERT: A 1250 HIS cc_start: 0.6318 (m90) cc_final: 0.5698 (m90)
REVERT: A 1271 ARG cc_start: 0.8530 (mtm-85) cc_final: 0.8185 (mtm110)
REVERT: A 1319 LEU cc_start: 0.7667 (mt) cc_final: 0.7442 (tt)
REVERT: A 1320 GLN cc_start: 0.8433 (tp40) cc_final: 0.8118 (tp-100)
REVERT: A 1324 ASP cc_start: 0.8230 (m-30) cc_final: 0.7468 (m-30)
REVERT: A 1339 SER cc_start: 0.8827 (t) cc_final: 0.8363 (p)
REVERT: A 1343 LEU cc_start: 0.8639 (mt) cc_final: 0.8300 (pp)
REVERT: A 1351 ASN cc_start: 0.7563 (t0) cc_final: 0.7205 (t0)
REVERT: A 1352 ASN cc_start: 0.7108 (p0) cc_final: 0.6670 (p0)
REVERT: A 1366 LYS cc_start: 0.9109 (mttt) cc_final: 0.8808 (mttt)
REVERT: A 1369 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7519 (mt-10)
REVERT: A 1376 VAL cc_start: 0.7845 (t) cc_final: 0.7590 (t)
REVERT: A 1378 LEU cc_start: 0.7626 (tp) cc_final: 0.7264 (tp)
REVERT: A 1382 SER cc_start: 0.8136 (t) cc_final: 0.7638 (t)
REVERT: A 1384 LEU cc_start: 0.8337 (mt) cc_final: 0.7455 (mp)
REVERT: A 1392 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6638 (mm-30)
REVERT: A 1403 LEU cc_start: 0.7912 (mt) cc_final: 0.7446 (mt)
REVERT: A 1456 GLU cc_start: 0.7326 (pp20) cc_final: 0.7058 (pp20)
REVERT: A 1463 LEU cc_start: 0.7914 (tp) cc_final: 0.7469 (mm)
REVERT: A 1467 LEU cc_start: 0.6608 (tp) cc_final: 0.6373 (tp)
REVERT: A 1474 ASN cc_start: 0.8045 (p0) cc_final: 0.7788 (p0)
REVERT: A 1488 ASP cc_start: 0.7372 (m-30) cc_final: 0.7137 (m-30)
REVERT: A 1502 GLN cc_start: 0.7914 (tm130) cc_final: 0.7529 (tm-30)
REVERT: A 1530 ASP cc_start: 0.6531 (m-30) cc_final: 0.6312 (m-30)
REVERT: A 1531 GLN cc_start: 0.8527 (mt0) cc_final: 0.7759 (mm110)
REVERT: A 1536 ILE cc_start: 0.8505 (pt) cc_final: 0.8266 (mt)
REVERT: A 1542 LEU cc_start: 0.9258 (mt) cc_final: 0.9041 (mt)
REVERT: A 1546 MET cc_start: 0.8346 (tpp) cc_final: 0.8028 (mmm)
REVERT: A 1583 CYS cc_start: 0.7902 (p) cc_final: 0.7367 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 309
  average time/residue: 0.1154
  time to fit residues: 49.1606
Evaluate side-chains
  267 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 138 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 89 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    8.9990
   chunk 115 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN
A 133 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
A 574 ASN
A 591 GLN
A 722 GLN
A1070 GLN
A1502 GLN
A1551 HIS
A1633 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.133183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.115336 restraints weight = 34430.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.118446 restraints weight = 22439.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.120661 restraints weight = 15869.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.122326 restraints weight = 11925.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.123440 restraints weight = 9385.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6431
moved from start:          0.5342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11310  Z= 0.206
  Angle     :  0.676   9.772  15262  Z= 0.359
  Chirality :  0.044   0.231   1709
  Planarity :  0.005   0.051   1973
  Dihedral  :  5.649  73.601   1510
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.25 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.23), residues: 1375
  helix:  1.19 (0.18), residues: 773
  sheet: -0.67 (0.38), residues: 154
  loop : -0.10 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 587 
 TYR   0.026   0.002   TYR A1428 
 PHE   0.028   0.002   PHE A1226 
 TRP   0.037   0.003   TRP A 369 
 HIS   0.008   0.002   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (11310)
  covalent geometry    : angle       0.67574 (15262)
  hydrogen bonds       : bond        0.04823 (  691)
  hydrogen bonds       : angle       5.00153 ( 2007)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 301
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8265 (tm-30)
REVERT: A  104 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8505 (pt0)
REVERT: A  111 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8109 (mmmm)
REVERT: A  202 TYR cc_start: 0.6517 (m-10) cc_final: 0.5974 (m-80)
REVERT: A  257 ILE cc_start: 0.6936 (mt) cc_final: 0.6544 (mm)
REVERT: A  343 ASP cc_start: 0.8264 (m-30) cc_final: 0.8053 (t0)
REVERT: A  353 TYR cc_start: 0.8315 (m-80) cc_final: 0.8085 (m-10)
REVERT: A  355 VAL cc_start: 0.7989 (t) cc_final: 0.7632 (m)
REVERT: A  359 TRP cc_start: 0.6577 (p90) cc_final: 0.5919 (p90)
REVERT: A  372 CYS cc_start: 0.7904 (m) cc_final: 0.7643 (t)
REVERT: A  421 MET cc_start: 0.1715 (mmm) cc_final: 0.1514 (mmm)
REVERT: A  519 CYS cc_start: 0.9020 (m) cc_final: 0.8816 (m)
REVERT: A  539 TYR cc_start: 0.7472 (m-80) cc_final: 0.6741 (m-80)
REVERT: A  563 GLU cc_start: 0.7648 (mp0) cc_final: 0.6922 (mp0)
REVERT: A  598 ASP cc_start: 0.8135 (m-30) cc_final: 0.7424 (m-30)
REVERT: A  691 SER cc_start: 0.7032 (m) cc_final: 0.6609 (p)
REVERT: A  721 PHE cc_start: 0.8553 (p90) cc_final: 0.8344 (p90)
REVERT: A  741 MET cc_start: 0.7794 (mtt) cc_final: 0.7106 (mtt)
REVERT: A  760 MET cc_start: 0.8214 (ttp) cc_final: 0.7666 (tpp)
REVERT: A  770 HIS cc_start: 0.8444 (m-70) cc_final: 0.8084 (m90)
REVERT: A  841 MET cc_start: 0.6675 (mmm) cc_final: 0.6218 (mmm)
REVERT: A  844 LEU cc_start: 0.7743 (mp) cc_final: 0.7532 (mp)
REVERT: A  928 GLU cc_start: 0.8481 (tt0) cc_final: 0.8159 (tt0)
REVERT: A  932 GLN cc_start: 0.7983 (mt0) cc_final: 0.7615 (tp40)
REVERT: A  936 CYS cc_start: 0.8639 (m) cc_final: 0.8025 (m)
REVERT: A  939 GLU cc_start: 0.7796 (tp30) cc_final: 0.7022 (tp30)
REVERT: A  977 MET cc_start: 0.7767 (ttp) cc_final: 0.7464 (ttp)
REVERT: A 1015 MET cc_start: 0.5252 (mpp) cc_final: 0.4608 (mpp)
REVERT: A 1021 CYS cc_start: 0.8123 (t) cc_final: 0.7551 (t)
REVERT: A 1022 ILE cc_start: 0.7521 (mp) cc_final: 0.6831 (tt)
REVERT: A 1079 TYR cc_start: 0.6819 (m-10) cc_final: 0.6355 (m-10)
REVERT: A 1214 LYS cc_start: 0.8397 (mttt) cc_final: 0.7891 (pttm)
REVERT: A 1250 HIS cc_start: 0.6426 (m90) cc_final: 0.5741 (m90)
REVERT: A 1296 ILE cc_start: 0.9153 (mt) cc_final: 0.8860 (pt)
REVERT: A 1320 GLN cc_start: 0.8389 (tp40) cc_final: 0.7962 (tp40)
REVERT: A 1324 ASP cc_start: 0.8234 (m-30) cc_final: 0.7436 (m-30)
REVERT: A 1332 VAL cc_start: 0.9185 (t) cc_final: 0.8787 (t)
REVERT: A 1339 SER cc_start: 0.9043 (t) cc_final: 0.8744 (p)
REVERT: A 1342 LEU cc_start: 0.8508 (tp) cc_final: 0.8004 (tt)
REVERT: A 1343 LEU cc_start: 0.8663 (mt) cc_final: 0.8385 (pp)
REVERT: A 1346 LEU cc_start: 0.9029 (mt) cc_final: 0.8685 (mp)
REVERT: A 1357 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6521 (tm-30)
REVERT: A 1366 LYS cc_start: 0.9134 (mttt) cc_final: 0.8682 (mttt)
REVERT: A 1369 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7572 (mt-10)
REVERT: A 1378 LEU cc_start: 0.7418 (tp) cc_final: 0.7061 (tp)
REVERT: A 1384 LEU cc_start: 0.8531 (mt) cc_final: 0.8278 (mt)
REVERT: A 1392 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6382 (mm-30)
REVERT: A 1403 LEU cc_start: 0.8091 (mt) cc_final: 0.7726 (mp)
REVERT: A 1453 SER cc_start: 0.8577 (p) cc_final: 0.7799 (m)
REVERT: A 1456 GLU cc_start: 0.7478 (pp20) cc_final: 0.7260 (pp20)
REVERT: A 1474 ASN cc_start: 0.7846 (p0) cc_final: 0.7509 (p0)
REVERT: A 1499 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6903 (mp0)
REVERT: A 1502 GLN cc_start: 0.8026 (tm130) cc_final: 0.7626 (tm-30)
REVERT: A 1514 GLU cc_start: 0.7792 (mp0) cc_final: 0.7082 (mp0)
REVERT: A 1531 GLN cc_start: 0.8558 (mt0) cc_final: 0.8179 (mt0)
REVERT: A 1542 LEU cc_start: 0.9298 (mt) cc_final: 0.9083 (mt)
REVERT: A 1546 MET cc_start: 0.8439 (tpp) cc_final: 0.8090 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 301
  average time/residue: 0.1101
  time to fit residues: 46.6154
Evaluate side-chains
  265 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 264
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   chunk 105 optimal weight:    9.9990
   chunk 72 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 122 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 ASN
A1370 GLN
A1579 GLN
A1633 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.134551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.115618 restraints weight = 33759.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.118682 restraints weight = 22182.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.120883 restraints weight = 15867.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.122472 restraints weight = 12098.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.123649 restraints weight = 9694.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6453
moved from start:          0.5730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11310  Z= 0.181
  Angle     :  0.649   9.668  15262  Z= 0.342
  Chirality :  0.042   0.227   1709
  Planarity :  0.005   0.054   1973
  Dihedral  :  5.556  72.763   1510
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.88 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.23), residues: 1375
  helix:  1.27 (0.18), residues: 777
  sheet: -0.58 (0.38), residues: 152
  loop : -0.03 (0.33), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1454 
 TYR   0.015   0.002   TYR A1428 
 PHE   0.023   0.002   PHE A1226 
 TRP   0.022   0.002   TRP A 369 
 HIS   0.006   0.001   HIS A1020 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (11310)
  covalent geometry    : angle       0.64916 (15262)
  hydrogen bonds       : bond        0.04596 (  691)
  hydrogen bonds       : angle       4.83297 ( 2007)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 300
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 ARG cc_start: 0.6589 (tmm160) cc_final: 0.6381 (ptm-80)
REVERT: A  202 TYR cc_start: 0.6519 (m-10) cc_final: 0.5967 (m-80)
REVERT: A  257 ILE cc_start: 0.7446 (mt) cc_final: 0.7196 (mt)
REVERT: A  264 ASN cc_start: 0.7707 (t0) cc_final: 0.7507 (m-40)
REVERT: A  343 ASP cc_start: 0.8310 (m-30) cc_final: 0.8052 (t0)
REVERT: A  353 TYR cc_start: 0.7967 (m-80) cc_final: 0.7643 (m-10)
REVERT: A  539 TYR cc_start: 0.7509 (m-80) cc_final: 0.6843 (m-80)
REVERT: A  598 ASP cc_start: 0.7944 (m-30) cc_final: 0.7206 (m-30)
REVERT: A  691 SER cc_start: 0.6917 (m) cc_final: 0.6535 (p)
REVERT: A  711 LYS cc_start: 0.7365 (mppt) cc_final: 0.6919 (mppt)
REVERT: A  721 PHE cc_start: 0.8530 (p90) cc_final: 0.8159 (p90)
REVERT: A  741 MET cc_start: 0.7721 (mtt) cc_final: 0.7055 (mtt)
REVERT: A  760 MET cc_start: 0.8130 (ttp) cc_final: 0.7742 (tpp)
REVERT: A  841 MET cc_start: 0.6805 (mmm) cc_final: 0.6155 (mmm)
REVERT: A  928 GLU cc_start: 0.8600 (tt0) cc_final: 0.8337 (tt0)
REVERT: A  932 GLN cc_start: 0.8139 (mt0) cc_final: 0.7731 (tp40)
REVERT: A  936 CYS cc_start: 0.8706 (m) cc_final: 0.8193 (m)
REVERT: A  939 GLU cc_start: 0.7827 (tp30) cc_final: 0.7050 (tp30)
REVERT: A  953 LYS cc_start: 0.8112 (tttt) cc_final: 0.7907 (tttt)
REVERT: A  977 MET cc_start: 0.7770 (ttp) cc_final: 0.7480 (ttp)
REVERT: A 1021 CYS cc_start: 0.8074 (t) cc_final: 0.7461 (t)
REVERT: A 1022 ILE cc_start: 0.7474 (mp) cc_final: 0.6830 (tt)
REVERT: A 1079 TYR cc_start: 0.6711 (m-10) cc_final: 0.6334 (m-10)
REVERT: A 1214 LYS cc_start: 0.8397 (mttt) cc_final: 0.7863 (pttm)
REVERT: A 1250 HIS cc_start: 0.6310 (m90) cc_final: 0.5785 (m90)
REVERT: A 1283 TRP cc_start: 0.6577 (m100) cc_final: 0.5963 (m-90)
REVERT: A 1320 GLN cc_start: 0.8418 (tp40) cc_final: 0.7991 (tp40)
REVERT: A 1324 ASP cc_start: 0.8223 (m-30) cc_final: 0.7572 (m-30)
REVERT: A 1332 VAL cc_start: 0.9167 (t) cc_final: 0.8850 (t)
REVERT: A 1339 SER cc_start: 0.9085 (t) cc_final: 0.8794 (p)
REVERT: A 1342 LEU cc_start: 0.8436 (tp) cc_final: 0.8191 (tp)
REVERT: A 1343 LEU cc_start: 0.8565 (mt) cc_final: 0.8269 (pp)
REVERT: A 1346 LEU cc_start: 0.9049 (mt) cc_final: 0.8702 (mt)
REVERT: A 1357 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6516 (tm-30)
REVERT: A 1378 LEU cc_start: 0.7520 (tp) cc_final: 0.6837 (tp)
REVERT: A 1403 LEU cc_start: 0.8007 (mt) cc_final: 0.7773 (mp)
REVERT: A 1407 ASP cc_start: 0.7649 (m-30) cc_final: 0.7410 (m-30)
REVERT: A 1427 PHE cc_start: 0.5672 (m-80) cc_final: 0.5457 (m-10)
REVERT: A 1453 SER cc_start: 0.8622 (p) cc_final: 0.8195 (p)
REVERT: A 1488 ASP cc_start: 0.7511 (m-30) cc_final: 0.7298 (m-30)
REVERT: A 1502 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7515 (tm-30)
REVERT: A 1512 TYR cc_start: 0.7161 (m-80) cc_final: 0.6887 (m-80)
REVERT: A 1531 GLN cc_start: 0.8560 (mt0) cc_final: 0.7784 (mt0)
REVERT: A 1536 ILE cc_start: 0.8465 (pt) cc_final: 0.8072 (tp)
REVERT: A 1537 ASN cc_start: 0.8508 (m110) cc_final: 0.8257 (m110)
REVERT: A 1546 MET cc_start: 0.8465 (tpp) cc_final: 0.7877 (tpt)
REVERT: A 1580 MET cc_start: 0.6462 (mtp) cc_final: 0.5869 (mtp)
REVERT: A 1597 GLU cc_start: 0.7903 (tt0) cc_final: 0.7657 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 300
  average time/residue: 0.1101
  time to fit residues: 46.4558
Evaluate side-chains
  255 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 123 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1633 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.136530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.117796 restraints weight = 33467.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.120865 restraints weight = 21997.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.123052 restraints weight = 15695.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.124661 restraints weight = 11912.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.125845 restraints weight = 9491.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6402
moved from start:          0.5962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11310  Z= 0.143
  Angle     :  0.622  10.344  15262  Z= 0.325
  Chirality :  0.041   0.197   1709
  Planarity :  0.004   0.061   1973
  Dihedral  :  5.300  70.400   1510
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.23), residues: 1375
  helix:  1.37 (0.18), residues: 775
  sheet: -0.49 (0.38), residues: 152
  loop :  0.01 (0.33), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1393 
 TYR   0.009   0.002   TYR A1504 
 PHE   0.014   0.002   PHE A 327 
 TRP   0.047   0.003   TRP A 369 
 HIS   0.006   0.001   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (11310)
  covalent geometry    : angle       0.62154 (15262)
  hydrogen bonds       : bond        0.04324 (  691)
  hydrogen bonds       : angle       4.74621 ( 2007)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.6528 (mmm) cc_final: 0.5958 (mmm)
REVERT: A  257 ILE cc_start: 0.7410 (mt) cc_final: 0.7205 (mt)
REVERT: A  353 TYR cc_start: 0.8004 (m-80) cc_final: 0.7690 (m-10)
REVERT: A  359 TRP cc_start: 0.6182 (p90) cc_final: 0.5463 (p90)
REVERT: A  539 TYR cc_start: 0.7409 (m-80) cc_final: 0.6824 (m-80)
REVERT: A  562 GLU cc_start: 0.8206 (pm20) cc_final: 0.7977 (pm20)
REVERT: A  598 ASP cc_start: 0.7883 (m-30) cc_final: 0.7397 (m-30)
REVERT: A  691 SER cc_start: 0.6969 (m) cc_final: 0.6594 (p)
REVERT: A  741 MET cc_start: 0.7695 (mtt) cc_final: 0.7006 (mtt)
REVERT: A  760 MET cc_start: 0.7979 (ttp) cc_final: 0.7749 (tpp)
REVERT: A  841 MET cc_start: 0.6697 (mmm) cc_final: 0.6038 (mmm)
REVERT: A  926 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8182 (mttt)
REVERT: A  928 GLU cc_start: 0.8546 (tt0) cc_final: 0.8286 (tt0)
REVERT: A  932 GLN cc_start: 0.8042 (mt0) cc_final: 0.7629 (tp40)
REVERT: A  936 CYS cc_start: 0.8650 (m) cc_final: 0.8092 (m)
REVERT: A  939 GLU cc_start: 0.7727 (tp30) cc_final: 0.7362 (tp30)
REVERT: A  977 MET cc_start: 0.7745 (ttp) cc_final: 0.7202 (ttt)
REVERT: A 1021 CYS cc_start: 0.7989 (t) cc_final: 0.7510 (t)
REVERT: A 1079 TYR cc_start: 0.6754 (m-10) cc_final: 0.6279 (m-10)
REVERT: A 1214 LYS cc_start: 0.8348 (mttt) cc_final: 0.7821 (pttm)
REVERT: A 1250 HIS cc_start: 0.6105 (m90) cc_final: 0.5214 (m90)
REVERT: A 1283 TRP cc_start: 0.6602 (m100) cc_final: 0.5990 (m-90)
REVERT: A 1320 GLN cc_start: 0.8334 (tp40) cc_final: 0.7904 (tp40)
REVERT: A 1324 ASP cc_start: 0.8324 (m-30) cc_final: 0.7554 (m-30)
REVERT: A 1339 SER cc_start: 0.9131 (t) cc_final: 0.8838 (p)
REVERT: A 1343 LEU cc_start: 0.8558 (mt) cc_final: 0.8279 (pp)
REVERT: A 1357 GLU cc_start: 0.6671 (tm-30) cc_final: 0.6376 (tm-30)
REVERT: A 1366 LYS cc_start: 0.9098 (mttt) cc_final: 0.8790 (mttt)
REVERT: A 1378 LEU cc_start: 0.7527 (tp) cc_final: 0.6723 (tp)
REVERT: A 1382 SER cc_start: 0.7925 (t) cc_final: 0.7725 (t)
REVERT: A 1384 LEU cc_start: 0.8417 (mt) cc_final: 0.8044 (mt)
REVERT: A 1392 GLU cc_start: 0.6279 (mm-30) cc_final: 0.5786 (mm-30)
REVERT: A 1403 LEU cc_start: 0.7955 (mt) cc_final: 0.7689 (mp)
REVERT: A 1453 SER cc_start: 0.8543 (p) cc_final: 0.8097 (p)
REVERT: A 1488 ASP cc_start: 0.7614 (m-30) cc_final: 0.7397 (m-30)
REVERT: A 1502 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7501 (tm-30)
REVERT: A 1514 GLU cc_start: 0.7879 (mp0) cc_final: 0.7503 (mp0)
REVERT: A 1530 ASP cc_start: 0.6522 (p0) cc_final: 0.5621 (p0)
REVERT: A 1531 GLN cc_start: 0.8170 (mt0) cc_final: 0.7500 (mm110)
REVERT: A 1536 ILE cc_start: 0.8434 (pt) cc_final: 0.8021 (tp)
REVERT: A 1537 ASN cc_start: 0.8485 (m110) cc_final: 0.8212 (m110)
REVERT: A 1546 MET cc_start: 0.8442 (tpp) cc_final: 0.7842 (tpt)
REVERT: A 1565 ILE cc_start: 0.8452 (mt) cc_final: 0.8002 (mt)
REVERT: A 1580 MET cc_start: 0.6332 (mtp) cc_final: 0.5714 (mtp)
REVERT: A 1597 GLU cc_start: 0.8036 (tt0) cc_final: 0.7550 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 282
  average time/residue: 0.1188
  time to fit residues: 46.6895
Evaluate side-chains
  250 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0030
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 131 optimal weight:    0.9990
   overall best weight:    1.1596

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 HIS
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.137016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.118281 restraints weight = 33396.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.121382 restraints weight = 22015.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.123608 restraints weight = 15689.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.125227 restraints weight = 11897.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.126419 restraints weight = 9492.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6398
moved from start:          0.6243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11310  Z= 0.144
  Angle     :  0.630  10.041  15262  Z= 0.325
  Chirality :  0.042   0.289   1709
  Planarity :  0.004   0.051   1973
  Dihedral  :  5.194  67.445   1510
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.23), residues: 1375
  helix:  1.40 (0.18), residues: 779
  sheet: -0.57 (0.38), residues: 155
  loop : -0.00 (0.33), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1454 
 TYR   0.028   0.002   TYR A 937 
 PHE   0.016   0.002   PHE A 370 
 TRP   0.048   0.003   TRP A 369 
 HIS   0.005   0.001   HIS A 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (11310)
  covalent geometry    : angle       0.63021 (15262)
  hydrogen bonds       : bond        0.04213 (  691)
  hydrogen bonds       : angle       4.63724 ( 2007)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7910 (pt0)
REVERT: A  202 TYR cc_start: 0.6616 (m-10) cc_final: 0.6173 (m-80)
REVERT: A  257 ILE cc_start: 0.7526 (mt) cc_final: 0.7322 (mt)
REVERT: A  353 TYR cc_start: 0.8009 (m-80) cc_final: 0.7682 (m-10)
REVERT: A  359 TRP cc_start: 0.6152 (p90) cc_final: 0.5886 (p90)
REVERT: A  539 TYR cc_start: 0.7349 (m-80) cc_final: 0.6844 (m-80)
REVERT: A  540 LYS cc_start: 0.8395 (mttp) cc_final: 0.7885 (ptpt)
REVERT: A  598 ASP cc_start: 0.8064 (m-30) cc_final: 0.7334 (m-30)
REVERT: A  691 SER cc_start: 0.7168 (m) cc_final: 0.6817 (p)
REVERT: A  741 MET cc_start: 0.7587 (mtt) cc_final: 0.6937 (mtt)
REVERT: A  760 MET cc_start: 0.7960 (ttp) cc_final: 0.7758 (tpp)
REVERT: A  792 HIS cc_start: 0.7697 (t-170) cc_final: 0.7416 (t70)
REVERT: A  841 MET cc_start: 0.6685 (mmm) cc_final: 0.6051 (mmm)
REVERT: A  928 GLU cc_start: 0.8438 (tt0) cc_final: 0.8201 (tt0)
REVERT: A  932 GLN cc_start: 0.8101 (mt0) cc_final: 0.7855 (tp40)
REVERT: A  936 CYS cc_start: 0.8529 (m) cc_final: 0.7870 (m)
REVERT: A  937 TYR cc_start: 0.8359 (m-80) cc_final: 0.8061 (m-80)
REVERT: A  939 GLU cc_start: 0.7717 (tp30) cc_final: 0.7001 (tp30)
REVERT: A  977 MET cc_start: 0.7814 (ttp) cc_final: 0.6663 (ttp)
REVERT: A 1017 TYR cc_start: 0.7112 (m-80) cc_final: 0.6695 (m-10)
REVERT: A 1079 TYR cc_start: 0.6760 (m-10) cc_final: 0.6171 (m-10)
REVERT: A 1214 LYS cc_start: 0.8333 (mttt) cc_final: 0.7807 (pttm)
REVERT: A 1250 HIS cc_start: 0.5822 (m90) cc_final: 0.5401 (m90)
REVERT: A 1283 TRP cc_start: 0.6630 (m100) cc_final: 0.5985 (m-90)
REVERT: A 1320 GLN cc_start: 0.8291 (tp40) cc_final: 0.7660 (tp40)
REVERT: A 1324 ASP cc_start: 0.8271 (m-30) cc_final: 0.7269 (m-30)
REVERT: A 1328 CYS cc_start: 0.7964 (m) cc_final: 0.7681 (m)
REVERT: A 1332 VAL cc_start: 0.9169 (t) cc_final: 0.8841 (t)
REVERT: A 1339 SER cc_start: 0.9069 (t) cc_final: 0.8852 (p)
REVERT: A 1343 LEU cc_start: 0.8537 (mt) cc_final: 0.8218 (pp)
REVERT: A 1357 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6347 (tm-30)
REVERT: A 1366 LYS cc_start: 0.9080 (mttt) cc_final: 0.8870 (mttt)
REVERT: A 1378 LEU cc_start: 0.7537 (tp) cc_final: 0.6948 (tp)
REVERT: A 1403 LEU cc_start: 0.7911 (mt) cc_final: 0.7646 (mp)
REVERT: A 1488 ASP cc_start: 0.7635 (m-30) cc_final: 0.7388 (m-30)
REVERT: A 1502 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: A 1530 ASP cc_start: 0.6485 (p0) cc_final: 0.5553 (p0)
REVERT: A 1531 GLN cc_start: 0.8073 (mt0) cc_final: 0.7396 (mm110)
REVERT: A 1536 ILE cc_start: 0.8425 (pt) cc_final: 0.8024 (tp)
REVERT: A 1537 ASN cc_start: 0.8406 (m110) cc_final: 0.8122 (m110)
REVERT: A 1546 MET cc_start: 0.8456 (tpp) cc_final: 0.7797 (tpt)
REVERT: A 1580 MET cc_start: 0.6353 (mtp) cc_final: 0.5857 (mtp)
REVERT: A 1583 CYS cc_start: 0.8086 (p) cc_final: 0.7879 (p)
REVERT: A 1598 GLN cc_start: 0.8242 (mt0) cc_final: 0.8017 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 283
  average time/residue: 0.1159
  time to fit residues: 45.7562
Evaluate side-chains
  247 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 112 optimal weight:    0.6980
   chunk 101 optimal weight:    9.9990
   chunk 133 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 122 optimal weight:   10.0000
   chunk 136 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 88 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 137 optimal weight:    0.0670
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 522 HIS
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1070 GLN
A1101 ASN
A1297 GLN
** A1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1381 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.137095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.118507 restraints weight = 33442.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.121608 restraints weight = 22040.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.123841 restraints weight = 15699.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.125431 restraints weight = 11872.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.126652 restraints weight = 9446.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6362
moved from start:          0.6487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11310  Z= 0.131
  Angle     :  0.638  10.900  15262  Z= 0.326
  Chirality :  0.042   0.197   1709
  Planarity :  0.004   0.042   1973
  Dihedral  :  5.056  62.719   1510
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.23), residues: 1375
  helix:  1.47 (0.18), residues: 775
  sheet: -0.44 (0.38), residues: 158
  loop : -0.06 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 695 
 TYR   0.018   0.001   TYR A 937 
 PHE   0.015   0.002   PHE A 370 
 TRP   0.045   0.003   TRP A 369 
 HIS   0.003   0.001   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (11310)
  covalent geometry    : angle       0.63821 (15262)
  hydrogen bonds       : bond        0.04101 (  691)
  hydrogen bonds       : angle       4.62481 ( 2007)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7991 (pt0)
REVERT: A  202 TYR cc_start: 0.6462 (m-10) cc_final: 0.5860 (m-80)
REVERT: A  353 TYR cc_start: 0.7987 (m-80) cc_final: 0.7710 (m-10)
REVERT: A  359 TRP cc_start: 0.6115 (p90) cc_final: 0.5857 (p90)
REVERT: A  539 TYR cc_start: 0.7378 (m-80) cc_final: 0.6856 (m-80)
REVERT: A  563 GLU cc_start: 0.7152 (pm20) cc_final: 0.6928 (pm20)
REVERT: A  598 ASP cc_start: 0.7995 (m-30) cc_final: 0.7361 (m-30)
REVERT: A  691 SER cc_start: 0.7166 (m) cc_final: 0.6871 (p)
REVERT: A  741 MET cc_start: 0.7565 (mtt) cc_final: 0.6921 (mtt)
REVERT: A  841 MET cc_start: 0.6604 (mmm) cc_final: 0.5985 (mmm)
REVERT: A  926 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8147 (mttt)
REVERT: A  928 GLU cc_start: 0.8415 (tt0) cc_final: 0.8107 (tt0)
REVERT: A  932 GLN cc_start: 0.8107 (mt0) cc_final: 0.7871 (tp40)
REVERT: A  936 CYS cc_start: 0.8599 (m) cc_final: 0.7877 (m)
REVERT: A  937 TYR cc_start: 0.8386 (m-80) cc_final: 0.8162 (m-80)
REVERT: A  939 GLU cc_start: 0.7559 (tp30) cc_final: 0.6812 (tp30)
REVERT: A  953 LYS cc_start: 0.7804 (ttpp) cc_final: 0.7595 (ttpp)
REVERT: A 1079 TYR cc_start: 0.6787 (m-10) cc_final: 0.6188 (m-10)
REVERT: A 1214 LYS cc_start: 0.8319 (mttt) cc_final: 0.7799 (pttm)
REVERT: A 1250 HIS cc_start: 0.5648 (m90) cc_final: 0.5331 (m90)
REVERT: A 1283 TRP cc_start: 0.6627 (m100) cc_final: 0.5977 (m-90)
REVERT: A 1320 GLN cc_start: 0.8236 (tp40) cc_final: 0.7650 (tp40)
REVERT: A 1324 ASP cc_start: 0.8295 (m-30) cc_final: 0.7336 (m-30)
REVERT: A 1328 CYS cc_start: 0.7981 (m) cc_final: 0.7750 (m)
REVERT: A 1357 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6250 (tm-30)
REVERT: A 1366 LYS cc_start: 0.9156 (mttt) cc_final: 0.8356 (mttt)
REVERT: A 1369 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7672 (mp0)
REVERT: A 1403 LEU cc_start: 0.7704 (mt) cc_final: 0.7486 (mp)
REVERT: A 1453 SER cc_start: 0.8715 (p) cc_final: 0.8342 (p)
REVERT: A 1488 ASP cc_start: 0.7689 (m-30) cc_final: 0.7461 (m-30)
REVERT: A 1502 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7330 (tm-30)
REVERT: A 1530 ASP cc_start: 0.6449 (p0) cc_final: 0.5472 (p0)
REVERT: A 1531 GLN cc_start: 0.8055 (mt0) cc_final: 0.7342 (mm110)
REVERT: A 1536 ILE cc_start: 0.8395 (pt) cc_final: 0.8020 (tp)
REVERT: A 1537 ASN cc_start: 0.8349 (m110) cc_final: 0.8080 (m110)
REVERT: A 1546 MET cc_start: 0.8470 (tpp) cc_final: 0.7758 (tpt)
REVERT: A 1565 ILE cc_start: 0.7694 (mt) cc_final: 0.7474 (mt)
REVERT: A 1580 MET cc_start: 0.6373 (mtp) cc_final: 0.6012 (mtp)
REVERT: A 1583 CYS cc_start: 0.8059 (p) cc_final: 0.7805 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.1187
  time to fit residues: 48.1431
Evaluate side-chains
  253 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 124 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1070 GLN
** A1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1415 GLN
** A1502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1633 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.135291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.116827 restraints weight = 33167.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.119784 restraints weight = 21923.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.121885 restraints weight = 15759.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.123406 restraints weight = 12079.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.124573 restraints weight = 9737.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6497
moved from start:          0.6748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11310  Z= 0.204
  Angle     :  0.701  10.930  15262  Z= 0.367
  Chirality :  0.045   0.334   1709
  Planarity :  0.005   0.061   1973
  Dihedral  :  5.276  58.074   1510
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.23), residues: 1375
  helix:  1.22 (0.18), residues: 776
  sheet: -0.55 (0.39), residues: 156
  loop : -0.12 (0.33), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1393 
 TYR   0.019   0.002   TYR A  64 
 PHE   0.016   0.002   PHE A 370 
 TRP   0.041   0.003   TRP A 369 
 HIS   0.008   0.001   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (11310)
  covalent geometry    : angle       0.70071 (15262)
  hydrogen bonds       : bond        0.04441 (  691)
  hydrogen bonds       : angle       4.84345 ( 2007)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7976 (pt0)
REVERT: A  192 LEU cc_start: 0.8618 (mt) cc_final: 0.8400 (tp)
REVERT: A  202 TYR cc_start: 0.6520 (m-10) cc_final: 0.5734 (m-80)
REVERT: A  257 ILE cc_start: 0.6751 (mp) cc_final: 0.6459 (mp)
REVERT: A  539 TYR cc_start: 0.7623 (m-80) cc_final: 0.7098 (m-80)
REVERT: A  540 LYS cc_start: 0.8394 (mttt) cc_final: 0.7927 (ptpt)
REVERT: A  563 GLU cc_start: 0.7464 (pm20) cc_final: 0.6994 (pm20)
REVERT: A  576 PHE cc_start: 0.8049 (m-80) cc_final: 0.7822 (m-10)
REVERT: A  598 ASP cc_start: 0.8003 (m-30) cc_final: 0.7518 (m-30)
REVERT: A  691 SER cc_start: 0.7058 (m) cc_final: 0.6674 (p)
REVERT: A  721 PHE cc_start: 0.8478 (p90) cc_final: 0.8174 (p90)
REVERT: A  741 MET cc_start: 0.7843 (mtt) cc_final: 0.7322 (mtt)
REVERT: A  760 MET cc_start: 0.7849 (tpp) cc_final: 0.7615 (tpp)
REVERT: A  841 MET cc_start: 0.6863 (mmm) cc_final: 0.6283 (mmm)
REVERT: A  928 GLU cc_start: 0.8569 (tt0) cc_final: 0.8309 (tt0)
REVERT: A  932 GLN cc_start: 0.8218 (mt0) cc_final: 0.7983 (tp40)
REVERT: A  936 CYS cc_start: 0.8669 (m) cc_final: 0.7967 (m)
REVERT: A  953 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7723 (ttpp)
REVERT: A  977 MET cc_start: 0.7284 (ttm) cc_final: 0.6371 (mtm)
REVERT: A 1025 MET cc_start: 0.7161 (ppp) cc_final: 0.6890 (ppp)
REVERT: A 1079 TYR cc_start: 0.6846 (m-10) cc_final: 0.6528 (m-10)
REVERT: A 1095 GLN cc_start: 0.5557 (tt0) cc_final: 0.5270 (tm-30)
REVERT: A 1214 LYS cc_start: 0.8408 (mttt) cc_final: 0.8011 (pttm)
REVERT: A 1250 HIS cc_start: 0.5691 (m90) cc_final: 0.5172 (m90)
REVERT: A 1283 TRP cc_start: 0.6856 (m100) cc_final: 0.6181 (m-90)
REVERT: A 1320 GLN cc_start: 0.8354 (tp40) cc_final: 0.7663 (tp40)
REVERT: A 1323 ARG cc_start: 0.7591 (ttt180) cc_final: 0.7065 (ttt90)
REVERT: A 1324 ASP cc_start: 0.8417 (m-30) cc_final: 0.7353 (m-30)
REVERT: A 1328 CYS cc_start: 0.8192 (m) cc_final: 0.7978 (m)
REVERT: A 1343 LEU cc_start: 0.8560 (mm) cc_final: 0.8029 (pp)
REVERT: A 1357 GLU cc_start: 0.6714 (tm-30) cc_final: 0.6359 (tm-30)
REVERT: A 1366 LYS cc_start: 0.9145 (mttt) cc_final: 0.8340 (mttt)
REVERT: A 1369 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7655 (mp0)
REVERT: A 1403 LEU cc_start: 0.7757 (mt) cc_final: 0.7525 (mp)
REVERT: A 1470 LYS cc_start: 0.8239 (pttp) cc_final: 0.7996 (ptmm)
REVERT: A 1488 ASP cc_start: 0.7618 (m-30) cc_final: 0.7404 (m-30)
REVERT: A 1502 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7343 (tm-30)
REVERT: A 1530 ASP cc_start: 0.6492 (p0) cc_final: 0.5348 (p0)
REVERT: A 1531 GLN cc_start: 0.8051 (mt0) cc_final: 0.7364 (mm-40)
REVERT: A 1536 ILE cc_start: 0.8455 (pt) cc_final: 0.8066 (tp)
REVERT: A 1537 ASN cc_start: 0.8425 (m110) cc_final: 0.8157 (m110)
REVERT: A 1541 GLU cc_start: 0.8205 (tp30) cc_final: 0.7885 (tp30)
REVERT: A 1580 MET cc_start: 0.6494 (mtp) cc_final: 0.6287 (mtp)
REVERT: A 1585 THR cc_start: 0.8789 (p) cc_final: 0.8578 (p)
REVERT: A 1598 GLN cc_start: 0.7942 (mt0) cc_final: 0.7243 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.1145
  time to fit residues: 46.5179
Evaluate side-chains
  258 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 135 optimal weight:    0.9990
   chunk 122 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 93 optimal weight:    4.9990
   chunk 116 optimal weight:    0.2980
   chunk 83 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1227 ASN
** A1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1435 GLN
** A1606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.136092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.117628 restraints weight = 33190.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.120717 restraints weight = 21865.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.122953 restraints weight = 15582.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.124590 restraints weight = 11784.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.125745 restraints weight = 9347.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6410
moved from start:          0.6927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11310  Z= 0.142
  Angle     :  0.670  11.160  15262  Z= 0.344
  Chirality :  0.043   0.300   1709
  Planarity :  0.005   0.114   1973
  Dihedral  :  5.102  53.702   1510
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.23), residues: 1375
  helix:  1.24 (0.18), residues: 777
  sheet: -0.45 (0.39), residues: 155
  loop : -0.02 (0.33), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A1393 
 TYR   0.015   0.001   TYR A 937 
 PHE   0.015   0.002   PHE A 370 
 TRP   0.041   0.003   TRP A 369 
 HIS   0.006   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (11310)
  covalent geometry    : angle       0.66960 (15262)
  hydrogen bonds       : bond        0.04155 (  691)
  hydrogen bonds       : angle       4.76848 ( 2007)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8043 (pt0)
REVERT: A  202 TYR cc_start: 0.6338 (m-10) cc_final: 0.5633 (m-80)
REVERT: A  247 LEU cc_start: 0.7047 (mt) cc_final: 0.6821 (mt)
REVERT: A  257 ILE cc_start: 0.6321 (mp) cc_final: 0.6051 (mp)
REVERT: A  264 ASN cc_start: 0.7800 (t0) cc_final: 0.7580 (t0)
REVERT: A  539 TYR cc_start: 0.7374 (m-80) cc_final: 0.6941 (m-80)
REVERT: A  562 GLU cc_start: 0.8218 (pm20) cc_final: 0.7995 (pm20)
REVERT: A  563 GLU cc_start: 0.7339 (pm20) cc_final: 0.6737 (pm20)
REVERT: A  586 PHE cc_start: 0.7586 (t80) cc_final: 0.7144 (t80)
REVERT: A  598 ASP cc_start: 0.7858 (m-30) cc_final: 0.7253 (m-30)
REVERT: A  691 SER cc_start: 0.7049 (m) cc_final: 0.6743 (p)
REVERT: A  721 PHE cc_start: 0.8391 (p90) cc_final: 0.8122 (p90)
REVERT: A  741 MET cc_start: 0.7650 (mtt) cc_final: 0.7059 (mtt)
REVERT: A  760 MET cc_start: 0.7962 (tpp) cc_final: 0.7737 (tpp)
REVERT: A  841 MET cc_start: 0.6655 (mmm) cc_final: 0.6080 (mmm)
REVERT: A  928 GLU cc_start: 0.8395 (tt0) cc_final: 0.8146 (tt0)
REVERT: A  932 GLN cc_start: 0.8142 (mt0) cc_final: 0.7939 (tp40)
REVERT: A  936 CYS cc_start: 0.8709 (m) cc_final: 0.8157 (m)
REVERT: A  953 LYS cc_start: 0.7874 (ttpp) cc_final: 0.7660 (ttpp)
REVERT: A  977 MET cc_start: 0.7051 (ttm) cc_final: 0.6503 (mtm)
REVERT: A 1017 TYR cc_start: 0.7017 (m-80) cc_final: 0.6728 (m-10)
REVERT: A 1025 MET cc_start: 0.7389 (ppp) cc_final: 0.7181 (ppp)
REVERT: A 1079 TYR cc_start: 0.6764 (m-10) cc_final: 0.6165 (m-10)
REVERT: A 1095 GLN cc_start: 0.5543 (tt0) cc_final: 0.5257 (tm-30)
REVERT: A 1214 LYS cc_start: 0.8323 (mttt) cc_final: 0.7843 (pttm)
REVERT: A 1250 HIS cc_start: 0.5582 (m90) cc_final: 0.5253 (m90)
REVERT: A 1283 TRP cc_start: 0.6803 (m100) cc_final: 0.6095 (m-90)
REVERT: A 1320 GLN cc_start: 0.8221 (tp40) cc_final: 0.7522 (tp40)
REVERT: A 1323 ARG cc_start: 0.7638 (ttt180) cc_final: 0.7079 (ttt90)
REVERT: A 1324 ASP cc_start: 0.8352 (m-30) cc_final: 0.7332 (m-30)
REVERT: A 1343 LEU cc_start: 0.8552 (mm) cc_final: 0.8071 (pp)
REVERT: A 1357 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6006 (tm-30)
REVERT: A 1366 LYS cc_start: 0.9130 (mttt) cc_final: 0.8197 (mttt)
REVERT: A 1369 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7547 (mp0)
REVERT: A 1370 GLN cc_start: 0.8799 (pt0) cc_final: 0.8588 (pt0)
REVERT: A 1376 VAL cc_start: 0.7829 (t) cc_final: 0.7568 (t)
REVERT: A 1403 LEU cc_start: 0.7749 (mt) cc_final: 0.7479 (mp)
REVERT: A 1407 ASP cc_start: 0.7425 (m-30) cc_final: 0.7204 (m-30)
REVERT: A 1502 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7403 (tm-30)
REVERT: A 1530 ASP cc_start: 0.6468 (p0) cc_final: 0.5383 (p0)
REVERT: A 1531 GLN cc_start: 0.8062 (mt0) cc_final: 0.7365 (mm110)
REVERT: A 1536 ILE cc_start: 0.8386 (pt) cc_final: 0.8002 (tp)
REVERT: A 1537 ASN cc_start: 0.8335 (m110) cc_final: 0.8059 (m110)
REVERT: A 1541 GLU cc_start: 0.8084 (tp30) cc_final: 0.7803 (tp30)
REVERT: A 1546 MET cc_start: 0.8573 (mtt) cc_final: 0.8303 (mtt)
REVERT: A 1570 GLU cc_start: 0.6818 (mp0) cc_final: 0.6268 (mp0)
REVERT: A 1580 MET cc_start: 0.6299 (mtp) cc_final: 0.6088 (mtp)
REVERT: A 1598 GLN cc_start: 0.8031 (mt0) cc_final: 0.7442 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1100
  time to fit residues: 44.1030
Evaluate side-chains
  252 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0060
   chunk 92 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 20 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 89 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9980
   chunk 100 optimal weight:    0.7980
   chunk 115 optimal weight:    4.9990
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1633 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.137569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.118649 restraints weight = 33422.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.121726 restraints weight = 22139.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.123948 restraints weight = 15819.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.125578 restraints weight = 12053.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.126687 restraints weight = 9630.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6410
moved from start:          0.7029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11310  Z= 0.135
  Angle     :  0.681  20.755  15262  Z= 0.341
  Chirality :  0.042   0.289   1709
  Planarity :  0.004   0.056   1973
  Dihedral  :  4.947  48.800   1510
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.23), residues: 1375
  helix:  1.27 (0.18), residues: 778
  sheet: -0.35 (0.40), residues: 156
  loop : -0.05 (0.33), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1454 
 TYR   0.017   0.001   TYR A 937 
 PHE   0.015   0.002   PHE A  75 
 TRP   0.038   0.002   TRP A 369 
 HIS   0.006   0.001   HIS A1020 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11310)
  covalent geometry    : angle       0.68092 (15262)
  hydrogen bonds       : bond        0.04059 (  691)
  hydrogen bonds       : angle       4.69990 ( 2007)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1894.01 seconds
wall clock time: 33 minutes 39.43 seconds (2019.43 seconds total)