Starting phenix.real_space_refine
on Tue Jan 13 18:11:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7op5_13013/01_2026/7op5_13013.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7op5_13013/01_2026/7op5_13013.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7op5_13013/01_2026/7op5_13013.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7op5_13013/01_2026/7op5_13013.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7op5_13013/01_2026/7op5_13013.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7op5_13013/01_2026/7op5_13013.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      53      5.16       5
     Be      1      3.05       5
     C    5544      2.51       5
     N    1426      2.21       5
     O    1526      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8554
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1076, 8549
          Classifications: {'peptide': 1076}
          Link IDs: {'PTRANS': 50, 'TRANS': 1025}
          Chain breaks: 9
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' MG': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.91, per 1000 atoms: 0.22
  Number of scatterers: 8554
  At special positions: 0
  Unit cell: (79.8136, 91.7585, 144.425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      53     16.00
     Mg      1     11.99
     F       3      9.00
     O    1526      8.00
     N    1426      7.00
     C    5544      6.00
     Be      1      4.00
    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: 0.75
  Conformation dependent library (CDL) restraints added in 292.5 milliseconds
  

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2038

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 10 sheets defined
      46.2% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 241 through 251
      removed outlier: 4.111A  pdb=" N   TRP A 245 " --> pdb=" O   GLY A 241 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   TRP A 250 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   TYR A 251 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 260
    Processing helix  chain 'A' and resid 264 through 268
      removed outlier: 3.574A  pdb=" N   CYS A 268 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 373
      removed outlier: 3.538A  pdb=" N   PHE A 372 " --> pdb=" O   ARG A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 392
      removed outlier: 3.945A  pdb=" N   LEU A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 410
    Processing helix  chain 'A' and resid 412 through 444
      removed outlier: 3.900A  pdb=" N   ALA A 416 " --> pdb=" O   TYR A 412 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA A 417 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   MET A 444 " --> pdb=" O   ARG A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 503
    Processing helix  chain 'A' and resid 529 through 535
    Processing helix  chain 'A' and resid 565 through 568
      removed outlier: 4.132A  pdb=" N   ASN A 568 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 565 through 568'
    Processing helix  chain 'A' and resid 569 through 580
      removed outlier: 3.852A  pdb=" N   LEU A 574 " --> pdb=" O   THR A 570 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL A 575 " --> pdb=" O   ARG A 571 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 579 " --> pdb=" O   VAL A 575 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 580 " --> pdb=" O   ARG A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 618
      removed outlier: 3.553A  pdb=" N   LEU A 605 " --> pdb=" O   CYS A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 625
      removed outlier: 3.508A  pdb=" N   LEU A 625 " --> pdb=" O   THR A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 636
      removed outlier: 3.836A  pdb=" N   THR A 633 " --> pdb=" O   LEU A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 657
      removed outlier: 3.652A  pdb=" N   THR A 643 " --> pdb=" O   ALA A 639 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA A 651 " --> pdb=" O   GLY A 647 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   ARG A 654 " --> pdb=" O   PHE A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 674
      removed outlier: 3.502A  pdb=" N   VAL A 668 " --> pdb=" O   PRO A 665 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN A 669 " --> pdb=" O   GLN A 666 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ILE A 674 " --> pdb=" O   GLY A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 718
      removed outlier: 4.048A  pdb=" N   TRP A 717 " --> pdb=" O   ASP A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 759
      removed outlier: 3.866A  pdb=" N   VAL A 756 " --> pdb=" O   ALA A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 784
      removed outlier: 3.651A  pdb=" N   VAL A 777 " --> pdb=" O   ASP A 773 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   LYS A 778 " --> pdb=" O   PRO A 774 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   MET A 779 " --> pdb=" O   LEU A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 871
      removed outlier: 3.580A  pdb=" N   GLU A 870 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 890
    Processing helix  chain 'A' and resid 909 through 914
    Processing helix  chain 'A' and resid 915 through 920
      removed outlier: 3.881A  pdb=" N   VAL A 919 " --> pdb=" O   THR A 915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 938 through 949
      removed outlier: 3.674A  pdb=" N   VAL A 942 " --> pdb=" O   THR A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 972
    Processing helix  chain 'A' and resid 1044 through 1052
    Processing helix  chain 'A' and resid 1056 through 1065
    Processing helix  chain 'A' and resid 1072 through 1086
    Processing helix  chain 'A' and resid 1096 through 1098
      No H-bonds generated for 'chain 'A' and resid 1096 through 1098'
    Processing helix  chain 'A' and resid 1099 through 1106
    Processing helix  chain 'A' and resid 1117 through 1121
      removed outlier: 3.986A  pdb=" N   ALA A1120 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ALA A1121 " --> pdb=" O   SER A1118 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1117 through 1121'
    Processing helix  chain 'A' and resid 1132 through 1167
      removed outlier: 3.579A  pdb=" N   VAL A1136 " --> pdb=" O   CYS A1132 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   SER A1158 " --> pdb=" O   MET A1154 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   PHE A1159 " --> pdb=" O   SER A1155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1186
    Processing helix  chain 'A' and resid 1187 through 1195
      removed outlier: 3.901A  pdb=" N   ILE A1191 " --> pdb=" O   LEU A1187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1219 through 1243
      removed outlier: 4.053A  pdb=" N   MET A1231 " --> pdb=" O   PHE A1227 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLN A1242 " --> pdb=" O   VAL A1238 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLN A1243 " --> pdb=" O   ALA A1239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.752A  pdb=" N   SER A1270 " --> pdb=" O   LEU A1266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1314
      removed outlier: 4.476A  pdb=" N   LEU A1298 " --> pdb=" O   THR A1294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1316 through 1323
    Processing helix  chain 'A' and resid 1329 through 1353
      removed outlier: 3.626A  pdb=" N   ILE A1337 " --> pdb=" O   LYS A1333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1353 through 1368
      removed outlier: 3.505A  pdb=" N   TRP A1357 " --> pdb=" O   TYR A1353 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ARG A1368 " --> pdb=" O   ARG A1364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1378 through 1383
    Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 208
    Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 325
      removed outlier: 3.778A  pdb=" N   LYS A 338 " --> pdb=" O   HIS A 333 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 450 through 455
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.500A  pdb=" N   VAL A 563 " --> pdb=" O   ASP A 486 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   ASP A 486 " --> pdb=" O   VAL A 563 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU A 537 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510
      removed outlier: 3.753A  pdb=" N   CYS A 494 " --> pdb=" O   LYS A 510 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASN A 497 " --> pdb=" O   LEU A 543 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   LEU A 543 " --> pdb=" O   ASN A 497 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 660 through 662
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1067 through 1068
      removed outlier: 8.991A  pdb=" N   TYR A1068 " --> pdb=" O   THR A 953 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   MET A 955 " --> pdb=" O   TYR A1068 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A 954 " --> pdb=" O   MET A 677 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 691 through 697
      removed outlier: 7.191A  pdb=" N   ILE A 930 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   ILE A 695 " --> pdb=" O   PHE A 928 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   PHE A 928 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   VAL A 697 " --> pdb=" O   VAL A 926 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   VAL A 926 " --> pdb=" O   VAL A 697 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   PHE A 925 " --> pdb=" O   THR A 900 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   THR A 900 " --> pdb=" O   PHE A 925 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLY A 927 " --> pdb=" O   CYS A 898 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ARG A 834 " --> pdb=" O   ILE A 848 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ARG A 850 " --> pdb=" O   VAL A 832 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   VAL A 832 " --> pdb=" O   ARG A 850 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 830 " --> pdb=" O   ALA A 793 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 764 through 765
      removed outlier: 3.581A  pdb=" N   ARG A 764 " --> pdb=" O   VAL A 771 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL A 771 " --> pdb=" O   ARG A 764 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 996 through 1001
      removed outlier: 7.104A  pdb=" N   LYS A 996 " --> pdb=" O   ILE A 986 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1050 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: 1.36

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2683
        1.34 -     1.46: 1647
        1.46 -     1.58: 4348
        1.58 -     1.69: 0
        1.69 -     1.81: 77
  Bond restraints: 8755
  Sorted by residual:
  bond pdb=" F2  BEF A1401 "
       pdb="BE   BEF A1401 "
    ideal  model  delta    sigma   weight residual
    1.476  1.561 -0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" F3  BEF A1401 "
       pdb="BE   BEF A1401 "
    ideal  model  delta    sigma   weight residual
    1.476  1.545 -0.069 2.00e-02 2.50e+03 1.18e+01
  bond pdb=" F1  BEF A1401 "
       pdb="BE   BEF A1401 "
    ideal  model  delta    sigma   weight residual
    1.476  1.533 -0.057 2.00e-02 2.50e+03 7.99e+00
  bond pdb=" N   LYS A 582 "
       pdb=" CA  LYS A 582 "
    ideal  model  delta    sigma   weight residual
    1.458  1.504 -0.046 1.90e-02 2.77e+03 5.91e+00
  bond pdb=" N   GLN A 382 "
       pdb=" CA  GLN A 382 "
    ideal  model  delta    sigma   weight residual
    1.457  1.479 -0.021 1.29e-02 6.01e+03 2.73e+00
  ... (remaining 8750 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 11730
        2.54 -     5.08: 140
        5.08 -     7.62: 12
        7.62 -    10.16: 1
       10.16 -    12.70: 3
  Bond angle restraints: 11886
  Sorted by residual:
  angle pdb=" C   ASP A 378 "
        pdb=" N   VAL A 379 "
        pdb=" CA  VAL A 379 "
      ideal   model   delta    sigma   weight residual
     121.97  126.35   -4.38 1.00e+00 1.00e+00 1.92e+01
  angle pdb=" F2  BEF A1401 "
        pdb="BE   BEF A1401 "
        pdb=" F3  BEF A1401 "
      ideal   model   delta    sigma   weight residual
     119.96  107.39   12.57 3.00e+00 1.11e-01 1.75e+01
  angle pdb=" N   SER A 487 "
        pdb=" CA  SER A 487 "
        pdb=" C   SER A 487 "
      ideal   model   delta    sigma   weight residual
     108.34  113.44   -5.10 1.31e+00 5.83e-01 1.51e+01
  angle pdb=" C   GLY A 863 "
        pdb=" N   SER A 864 "
        pdb=" CA  SER A 864 "
      ideal   model   delta    sigma   weight residual
     121.27  133.97  -12.70 3.40e+00 8.65e-02 1.39e+01
  angle pdb=" F1  BEF A1401 "
        pdb="BE   BEF A1401 "
        pdb=" F3  BEF A1401 "
      ideal   model   delta    sigma   weight residual
     120.12  109.69   10.43 3.00e+00 1.11e-01 1.21e+01
  ... (remaining 11881 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.26: 4586
       16.26 -    32.52: 504
       32.52 -    48.78: 91
       48.78 -    65.04: 12
       65.04 -    81.30: 3
  Dihedral angle restraints: 5196
    sinusoidal: 2051
      harmonic: 3145
  Sorted by residual:
  dihedral pdb=" CA  GLU A 381 "
           pdb=" C   GLU A 381 "
           pdb=" N   GLN A 382 "
           pdb=" CA  GLN A 382 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.57  -27.43     0      5.00e+00 4.00e-02 3.01e+01
  dihedral pdb=" CA  PRO A 581 "
           pdb=" C   PRO A 581 "
           pdb=" N   LYS A 582 "
           pdb=" CA  LYS A 582 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.80   22.20     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  LEU A1354 "
           pdb=" C   LEU A1354 "
           pdb=" N   PHE A1355 "
           pdb=" CA  PHE A1355 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.49  -19.51     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 5193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 825
       0.034 -    0.068: 355
       0.068 -    0.102: 124
       0.102 -    0.136: 47
       0.136 -    0.171: 9
  Chirality restraints: 1360
  Sorted by residual:
  chirality pdb=" CB  ILE A 282 "
            pdb=" CA  ILE A 282 "
            pdb=" CG1 ILE A 282 "
            pdb=" CG2 ILE A 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.27e-01
  chirality pdb=" CB  ILE A1232 "
            pdb=" CA  ILE A1232 "
            pdb=" CG1 ILE A1232 "
            pdb=" CG2 ILE A1232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.19e-01
  chirality pdb=" CA  GLU A 781 "
            pdb=" N   GLU A 781 "
            pdb=" C   GLU A 781 "
            pdb=" CB  GLU A 781 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.49e-01
  ... (remaining 1357 not shown)

  Planarity restraints: 1485
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 581 "   -0.020 2.00e-02 2.50e+03   4.06e-02 1.65e+01
        pdb=" C   PRO A 581 "    0.070 2.00e-02 2.50e+03
        pdb=" O   PRO A 581 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   LYS A 582 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 785 "    0.022 2.00e-02 2.50e+03   1.65e-02 6.77e+00
        pdb=" CG  TRP A 785 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 785 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 785 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 785 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 785 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 785 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 785 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 785 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 785 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 233 "   -0.017 2.00e-02 2.50e+03   1.55e-02 4.78e+00
        pdb=" CG  TYR A 233 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 233 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 233 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 233 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 233 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 233 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 233 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1482 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 54
        2.53 -     3.12: 6637
        3.12 -     3.72: 12538
        3.72 -     4.31: 16327
        4.31 -     4.90: 27711
  Nonbonded interactions: 63267
  Sorted by model distance:
  nonbonded pdb=" F2  BEF A1401 "
            pdb="MG    MG A1402 "
     model   vdw
     1.940 2.120
  nonbonded pdb=" O   ASP A 680 "
            pdb=" OG1 THR A 684 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" F1  BEF A1401 "
            pdb="MG    MG A1402 "
     model   vdw
     2.232 2.120
  nonbonded pdb=" OG1 THR A1253 "
            pdb=" O   LYS A1255 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OH  TYR A 332 "
            pdb=" OD1 ASP A 337 "
     model   vdw
     2.255 3.040
  ... (remaining 63262 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:             19.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.150
  Find NCS groups from input model:        0.030
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   8755  Z= 0.176
  Angle     :  0.716  12.696  11886  Z= 0.391
  Chirality :  0.046   0.171   1360
  Planarity :  0.005   0.047   1485
  Dihedral  : 13.583  81.295   3158
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.25), residues: 1056
  helix:  0.30 (0.25), residues: 434
  sheet: -1.87 (0.41), residues: 171
  loop : -2.22 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 266 
 TYR   0.038   0.002   TYR A 233 
 PHE   0.020   0.001   PHE A1167 
 TRP   0.044   0.002   TRP A 785 
 HIS   0.014   0.001   HIS A1201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8755)
  covalent geometry    : angle       0.71616 (11886)
  hydrogen bonds       : bond        0.14338 (  368)
  hydrogen bonds       : angle       6.02879 ( 1050)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  329 LYS cc_start: 0.8278 (tttm) cc_final: 0.7989 (tttp)
REVERT: A  578 MET cc_start: 0.8317 (tmm) cc_final: 0.7805 (ttp)
REVERT: A 1366 ARG cc_start: 0.8328 (tmt170) cc_final: 0.8017 (ttt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1099
  time to fit residues: 20.1421
Evaluate side-chains
  104 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.5980
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0770
   overall best weight:    0.6340

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.167010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.135897 restraints weight = 12831.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.139206 restraints weight = 8247.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.141540 restraints weight = 6212.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.142775 restraints weight = 5159.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.143906 restraints weight = 4586.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8755  Z= 0.132
  Angle     :  0.586   7.530  11886  Z= 0.309
  Chirality :  0.044   0.154   1360
  Planarity :  0.004   0.047   1485
  Dihedral  :  5.033  24.814   1171
  Min Nonbonded Distance : 1.732

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  8.09 %
    Favored  : 90.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.26), residues: 1056
  helix:  0.82 (0.25), residues: 423
  sheet: -1.55 (0.42), residues: 162
  loop : -2.17 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 442 
 TYR   0.014   0.001   TYR A 251 
 PHE   0.011   0.001   PHE A 928 
 TRP   0.022   0.001   TRP A 459 
 HIS   0.003   0.001   HIS A 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8755)
  covalent geometry    : angle       0.58550 (11886)
  hydrogen bonds       : bond        0.04348 (  368)
  hydrogen bonds       : angle       4.64649 ( 1050)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7551 (mmmt)
REVERT: A  379 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.7524 (t)
REVERT: A  578 MET cc_start: 0.8289 (tmm) cc_final: 0.7689 (ttp)
REVERT: A  718 SER cc_start: 0.9054 (m) cc_final: 0.8797 (t)
REVERT: A 1366 ARG cc_start: 0.8311 (tmt170) cc_final: 0.8090 (ttt-90)
  outliers start: 11
  outliers final: 8
  residues processed: 130
  average time/residue: 0.1038
  time to fit residues: 18.4548
Evaluate side-chains
  114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  436 GLU
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1298 LEU
Chi-restraints excluded: chain A residue 1354 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0370
   chunk 9 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0040
   chunk 4 optimal weight:    0.9980
   chunk 102 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0870
   overall best weight:    0.3848

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.169444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.138272 restraints weight = 12551.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.141656 restraints weight = 8041.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.144008 restraints weight = 6083.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.145564 restraints weight = 5050.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.146371 restraints weight = 4460.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8755  Z= 0.108
  Angle     :  0.536   6.750  11886  Z= 0.281
  Chirality :  0.042   0.146   1360
  Planarity :  0.004   0.042   1485
  Dihedral  :  4.667  19.499   1171
  Min Nonbonded Distance : 1.788

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.78 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.26), residues: 1056
  helix:  1.12 (0.25), residues: 425
  sheet: -1.20 (0.43), residues: 156
  loop : -2.09 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 916 
 TYR   0.022   0.001   TYR A 233 
 PHE   0.012   0.001   PHE A1083 
 TRP   0.018   0.001   TRP A 459 
 HIS   0.004   0.000   HIS A 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8755)
  covalent geometry    : angle       0.53621 (11886)
  hydrogen bonds       : bond        0.03764 (  368)
  hydrogen bonds       : angle       4.32513 ( 1050)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  277 PHE cc_start: 0.7391 (m-10) cc_final: 0.7114 (m-10)
REVERT: A  329 LYS cc_start: 0.8390 (tttm) cc_final: 0.7832 (tttp)
REVERT: A  718 SER cc_start: 0.9032 (m) cc_final: 0.8767 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 125
  average time/residue: 0.0968
  time to fit residues: 16.7598
Evaluate side-chains
  114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  436 GLU
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  757 MET
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1298 LEU
Chi-restraints excluded: chain A residue 1354 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0670
   chunk 11 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    0.4980
   chunk 90 optimal weight:    3.9990
   overall best weight:    0.6120

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.165246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.135339 restraints weight = 12899.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.138315 restraints weight = 9414.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.140359 restraints weight = 6545.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.140032 restraints weight = 5546.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.140338 restraints weight = 5472.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8755  Z= 0.118
  Angle     :  0.536   6.980  11886  Z= 0.280
  Chirality :  0.042   0.156   1360
  Planarity :  0.004   0.045   1485
  Dihedral  :  4.569  20.212   1171
  Min Nonbonded Distance : 1.756

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.21 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.26), residues: 1056
  helix:  1.21 (0.25), residues: 435
  sheet: -1.17 (0.43), residues: 158
  loop : -2.01 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1366 
 TYR   0.021   0.001   TYR A 233 
 PHE   0.014   0.001   PHE A1083 
 TRP   0.020   0.001   TRP A 345 
 HIS   0.005   0.001   HIS A 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8755)
  covalent geometry    : angle       0.53572 (11886)
  hydrogen bonds       : bond        0.03784 (  368)
  hydrogen bonds       : angle       4.21624 ( 1050)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.8617 (mt) cc_final: 0.8262 (tp)
REVERT: A  718 SER cc_start: 0.9043 (m) cc_final: 0.8802 (t)
REVERT: A  999 TRP cc_start: 0.8081 (m100) cc_final: 0.7080 (m-90)
  outliers start: 19
  outliers final: 13
  residues processed: 130
  average time/residue: 0.0870
  time to fit residues: 16.0222
Evaluate side-chains
  122 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  757 MET
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1164 SER
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1298 LEU
Chi-restraints excluded: chain A residue 1354 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 80 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:   10.0000
   chunk 73 optimal weight:    0.6980
   chunk 93 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A1263 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.162966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.133874 restraints weight = 12910.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.135458 restraints weight = 9885.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.137142 restraints weight = 7803.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.137464 restraints weight = 6435.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.137626 restraints weight = 6061.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8755  Z= 0.185
  Angle     :  0.593   6.477  11886  Z= 0.311
  Chirality :  0.045   0.161   1360
  Planarity :  0.004   0.047   1485
  Dihedral  :  4.850  20.465   1171
  Min Nonbonded Distance : 1.681

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.23 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.26), residues: 1056
  helix:  0.95 (0.25), residues: 441
  sheet: -1.17 (0.43), residues: 158
  loop : -2.15 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1366 
 TYR   0.022   0.002   TYR A 233 
 PHE   0.019   0.001   PHE A1355 
 TRP   0.017   0.001   TRP A 785 
 HIS   0.003   0.001   HIS A 761 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 8755)
  covalent geometry    : angle       0.59337 (11886)
  hydrogen bonds       : bond        0.04560 (  368)
  hydrogen bonds       : angle       4.44316 ( 1050)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.8685 (mt) cc_final: 0.8404 (tp)
REVERT: A  718 SER cc_start: 0.9104 (m) cc_final: 0.8805 (t)
  outliers start: 23
  outliers final: 20
  residues processed: 129
  average time/residue: 0.0826
  time to fit residues: 15.3024
Evaluate side-chains
  126 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  436 GLU
Chi-restraints excluded: chain A residue  500 MET
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  757 MET
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1164 SER
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1298 LEU
Chi-restraints excluded: chain A residue 1354 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.1786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.163154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.132336 restraints weight = 12842.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.136849 restraints weight = 9280.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.137728 restraints weight = 6738.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.137867 restraints weight = 5446.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.138270 restraints weight = 5215.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8755  Z= 0.168
  Angle     :  0.580   7.346  11886  Z= 0.305
  Chirality :  0.044   0.162   1360
  Planarity :  0.004   0.046   1485
  Dihedral  :  4.843  19.353   1171
  Min Nonbonded Distance : 1.626

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.40 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.26), residues: 1056
  helix:  0.96 (0.25), residues: 441
  sheet: -1.18 (0.43), residues: 160
  loop : -2.17 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1366 
 TYR   0.023   0.002   TYR A 332 
 PHE   0.014   0.001   PHE A1083 
 TRP   0.013   0.001   TRP A 785 
 HIS   0.003   0.001   HIS A 761 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8755)
  covalent geometry    : angle       0.58026 (11886)
  hydrogen bonds       : bond        0.04459 (  368)
  hydrogen bonds       : angle       4.39546 ( 1050)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  254 TYR cc_start: 0.7500 (m-80) cc_final: 0.6981 (m-80)
REVERT: A  277 PHE cc_start: 0.7565 (m-10) cc_final: 0.7278 (t80)
REVERT: A  320 LEU cc_start: 0.8649 (mt) cc_final: 0.8265 (tp)
REVERT: A  718 SER cc_start: 0.9112 (m) cc_final: 0.8818 (t)
REVERT: A  781 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7728 (mt-10)
REVERT: A 1324 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7131 (mt0)
  outliers start: 27
  outliers final: 20
  residues processed: 128
  average time/residue: 0.0877
  time to fit residues: 15.8584
Evaluate side-chains
  126 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  436 GLU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  757 MET
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1164 SER
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1298 LEU
Chi-restraints excluded: chain A residue 1324 GLN
Chi-restraints excluded: chain A residue 1354 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 47 optimal weight:    0.0970
   chunk 1 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.164204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.134496 restraints weight = 12819.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.138048 restraints weight = 9681.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.138963 restraints weight = 7619.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.139051 restraints weight = 6185.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.139573 restraints weight = 5870.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8755  Z= 0.148
  Angle     :  0.582  10.954  11886  Z= 0.302
  Chirality :  0.044   0.152   1360
  Planarity :  0.004   0.046   1485
  Dihedral  :  4.752  18.678   1171
  Min Nonbonded Distance : 1.590

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.36 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.26), residues: 1056
  helix:  1.05 (0.25), residues: 440
  sheet: -1.21 (0.42), residues: 162
  loop : -2.15 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1366 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.012   0.001   PHE A1083 
 TRP   0.013   0.001   TRP A 345 
 HIS   0.002   0.001   HIS A 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8755)
  covalent geometry    : angle       0.58219 (11886)
  hydrogen bonds       : bond        0.04236 (  368)
  hydrogen bonds       : angle       4.32376 ( 1050)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  277 PHE cc_start: 0.7427 (m-10) cc_final: 0.7027 (t80)
REVERT: A  279 LYS cc_start: 0.7602 (mmtt) cc_final: 0.7245 (mmmt)
REVERT: A  320 LEU cc_start: 0.8563 (mt) cc_final: 0.8232 (tp)
REVERT: A  718 SER cc_start: 0.9066 (m) cc_final: 0.8802 (t)
REVERT: A  781 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7587 (mt-10)
REVERT: A 1324 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7051 (mt0)
  outliers start: 27
  outliers final: 22
  residues processed: 126
  average time/residue: 0.0906
  time to fit residues: 16.0726
Evaluate side-chains
  128 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  436 GLU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  757 MET
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1164 SER
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1298 LEU
Chi-restraints excluded: chain A residue 1324 GLN
Chi-restraints excluded: chain A residue 1354 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0000
   chunk 4 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.159681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.129409 restraints weight = 12854.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.131391 restraints weight = 9267.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.132478 restraints weight = 7143.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.132680 restraints weight = 6412.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.132907 restraints weight = 5998.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   8755  Z= 0.236
  Angle     :  0.669  10.088  11886  Z= 0.347
  Chirality :  0.047   0.173   1360
  Planarity :  0.004   0.049   1485
  Dihedral  :  5.213  21.911   1171
  Min Nonbonded Distance : 1.382

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.68 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.26), residues: 1056
  helix:  0.57 (0.25), residues: 446
  sheet: -1.46 (0.41), residues: 169
  loop : -2.26 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1366 
 TYR   0.025   0.002   TYR A 332 
 PHE   0.016   0.002   PHE A1180 
 TRP   0.014   0.001   TRP A 785 
 HIS   0.003   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 8755)
  covalent geometry    : angle       0.66912 (11886)
  hydrogen bonds       : bond        0.05233 (  368)
  hydrogen bonds       : angle       4.66446 ( 1050)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A  277 PHE cc_start: 0.7504 (m-10) cc_final: 0.6876 (t80)
REVERT: A  279 LYS cc_start: 0.7568 (mmtt) cc_final: 0.7131 (mmmt)
REVERT: A  280 MET cc_start: 0.7700 (mmt) cc_final: 0.7245 (mmt)
REVERT: A  320 LEU cc_start: 0.8654 (mt) cc_final: 0.8242 (tp)
REVERT: A  578 MET cc_start: 0.8079 (tmm) cc_final: 0.7347 (ttt)
REVERT: A  718 SER cc_start: 0.9106 (m) cc_final: 0.8841 (t)
REVERT: A  781 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7718 (mt-10)
REVERT: A 1324 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7337 (mt0)
REVERT: A 1328 MET cc_start: 0.6626 (mtt) cc_final: 0.6259 (mtt)
  outliers start: 28
  outliers final: 24
  residues processed: 124
  average time/residue: 0.0826
  time to fit residues: 14.8453
Evaluate side-chains
  127 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  397 TYR
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  500 MET
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  757 MET
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1164 SER
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1258 ILE
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1298 LEU
Chi-restraints excluded: chain A residue 1324 GLN
Chi-restraints excluded: chain A residue 1354 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 5 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.164717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.133849 restraints weight = 12657.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.136962 restraints weight = 8430.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.139027 restraints weight = 6502.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.140387 restraints weight = 5469.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.141223 restraints weight = 4904.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8755  Z= 0.127
  Angle     :  0.573   9.496  11886  Z= 0.295
  Chirality :  0.043   0.156   1360
  Planarity :  0.004   0.045   1485
  Dihedral  :  4.743  18.027   1171
  Min Nonbonded Distance : 1.493

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.42 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.26), residues: 1056
  helix:  1.06 (0.25), residues: 435
  sheet: -1.29 (0.42), residues: 164
  loop : -2.12 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1366 
 TYR   0.034   0.001   TYR A 233 
 PHE   0.013   0.001   PHE A1355 
 TRP   0.020   0.001   TRP A1237 
 HIS   0.003   0.001   HIS A 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8755)
  covalent geometry    : angle       0.57306 (11886)
  hydrogen bonds       : bond        0.04018 (  368)
  hydrogen bonds       : angle       4.27887 ( 1050)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  320 LEU cc_start: 0.8555 (mt) cc_final: 0.8181 (tp)
REVERT: A  578 MET cc_start: 0.8034 (tmm) cc_final: 0.7279 (ttt)
REVERT: A  718 SER cc_start: 0.9060 (m) cc_final: 0.8777 (t)
REVERT: A  781 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7624 (mt-10)
REVERT: A 1061 MET cc_start: 0.7347 (ttm) cc_final: 0.7049 (ttp)
REVERT: A 1324 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7008 (mt0)
REVERT: A 1328 MET cc_start: 0.6475 (mtt) cc_final: 0.6084 (mtt)
  outliers start: 24
  outliers final: 20
  residues processed: 124
  average time/residue: 0.0810
  time to fit residues: 14.4044
Evaluate side-chains
  125 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  397 TYR
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1164 SER
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1298 LEU
Chi-restraints excluded: chain A residue 1324 GLN
Chi-restraints excluded: chain A residue 1354 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.0870
   chunk 56 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.0160

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.165326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.134401 restraints weight = 12666.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.137440 restraints weight = 8443.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.139441 restraints weight = 6512.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.140807 restraints weight = 5515.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.141558 restraints weight = 4934.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8755  Z= 0.153
  Angle     :  0.591   8.935  11886  Z= 0.304
  Chirality :  0.044   0.150   1360
  Planarity :  0.004   0.046   1485
  Dihedral  :  4.778  19.653   1171
  Min Nonbonded Distance : 1.408

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.21 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.26), residues: 1056
  helix:  1.03 (0.25), residues: 435
  sheet: -1.26 (0.42), residues: 163
  loop : -2.12 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1366 
 TYR   0.032   0.002   TYR A 233 
 PHE   0.015   0.001   PHE A1083 
 TRP   0.014   0.001   TRP A1237 
 HIS   0.002   0.001   HIS A 761 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8755)
  covalent geometry    : angle       0.59099 (11886)
  hydrogen bonds       : bond        0.04255 (  368)
  hydrogen bonds       : angle       4.33977 ( 1050)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  280 MET cc_start: 0.7733 (mmt) cc_final: 0.7235 (mmt)
REVERT: A  320 LEU cc_start: 0.8584 (mt) cc_final: 0.8205 (tp)
REVERT: A  718 SER cc_start: 0.9056 (m) cc_final: 0.8800 (t)
REVERT: A  781 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7626 (mt-10)
REVERT: A 1324 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7089 (mt0)
  outliers start: 25
  outliers final: 22
  residues processed: 124
  average time/residue: 0.0812
  time to fit residues: 14.6198
Evaluate side-chains
  127 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  397 TYR
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  500 MET
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1164 SER
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1298 LEU
Chi-restraints excluded: chain A residue 1324 GLN
Chi-restraints excluded: chain A residue 1354 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 93 optimal weight:    0.3980
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.8184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.166455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.135253 restraints weight = 12705.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.138486 restraints weight = 8261.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.140633 restraints weight = 6295.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.142040 restraints weight = 5276.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.142821 restraints weight = 4698.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8755  Z= 0.135
  Angle     :  0.580   8.642  11886  Z= 0.298
  Chirality :  0.043   0.153   1360
  Planarity :  0.004   0.046   1485
  Dihedral  :  4.684  18.945   1171
  Min Nonbonded Distance : 1.437

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.85 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.89 (0.26), residues: 1056
  helix:  1.11 (0.25), residues: 435
  sheet: -1.15 (0.42), residues: 164
  loop : -2.10 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1366 
 TYR   0.033   0.001   TYR A 233 
 PHE   0.015   0.001   PHE A1083 
 TRP   0.028   0.001   TRP A1237 
 HIS   0.002   0.000   HIS A 761 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8755)
  covalent geometry    : angle       0.58003 (11886)
  hydrogen bonds       : bond        0.04046 (  368)
  hydrogen bonds       : angle       4.27702 ( 1050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1702.40 seconds
wall clock time: 30 minutes 9.05 seconds (1809.05 seconds total)