Starting phenix.real_space_refine
on Fri Oct 23 01:18:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/21im_67696/10_2026/21im_67696.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/21im_67696/10_2026/21im_67696.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/21im_67696/10_2026/21im_67696.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/21im_67696/10_2026/21im_67696.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/21im_67696/10_2026/21im_67696.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/21im_67696/10_2026/21im_67696.map"
  }
  resolution = 3.0
  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=   0.037
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      11      5.16       5
     C    4662      2.51       5
     N    1197      2.21       5
     O    1439      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7309
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 919, 7309
          Classifications: {'peptide': 919}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 889}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 1.64, per 1000 atoms: 0.22
  Number of scatterers: 7309
  At special positions: 0
  Unit cell: (77.19, 91.14, 128.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      11     16.00
     O    1439      8.00
     N    1197      7.00
     C    4662      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 354.7 milliseconds
  

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1738

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 12 sheets defined
      38.2% alpha, 20.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 19
      removed outlier: 3.540A  pdb=" N   GLN A   6 " --> pdb=" O   GLY A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 38
      removed outlier: 3.721A  pdb=" N   THR A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 43
    Processing helix  chain 'A' and resid 81 through 88
    Processing helix  chain 'A' and resid 89 through 92
    Processing helix  chain 'A' and resid 95 through 97
      No H-bonds generated for 'chain 'A' and resid 95 through 97'
    Processing helix  chain 'A' and resid 98 through 102
      removed outlier: 4.330A  pdb=" N   SER A 102 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 98 through 102'
    Processing helix  chain 'A' and resid 123 through 133
      removed outlier: 3.502A  pdb=" N   LYS A 133 " --> pdb=" O   HIS A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 151
    Processing helix  chain 'A' and resid 151 through 173
      removed outlier: 3.517A  pdb=" N   PHE A 155 " --> pdb=" O   TYR A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 190
      removed outlier: 3.779A  pdb=" N   LEU A 188 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ASN A 189 " --> pdb=" O   MET A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 246
    Processing helix  chain 'A' and resid 248 through 257
      removed outlier: 3.850A  pdb=" N   GLN A 257 " --> pdb=" O   GLN A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 265
    Processing helix  chain 'A' and resid 272 through 283
    Processing helix  chain 'A' and resid 287 through 291
    Processing helix  chain 'A' and resid 302 through 325
      removed outlier: 3.754A  pdb=" N   SER A 310 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 316 " --> pdb=" O   LYS A 312 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER A 317 " --> pdb=" O   LYS A 313 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASP A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 337
      removed outlier: 3.609A  pdb=" N   THR A 336 " --> pdb=" O   TYR A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 357 through 362
      removed outlier: 4.010A  pdb=" N   GLY A 362 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 378
    Processing helix  chain 'A' and resid 381 through 386
      removed outlier: 3.712A  pdb=" N   SER A 386 " --> pdb=" O   GLU A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 402
    Processing helix  chain 'A' and resid 402 through 421
      removed outlier: 3.729A  pdb=" N   ALA A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   SER A 420 " --> pdb=" O   GLU A 416 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   VAL A 421 " --> pdb=" O   VAL A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 441
    Processing helix  chain 'A' and resid 471 through 474
      removed outlier: 4.305A  pdb=" N   ASP A 474 " --> pdb=" O   SER A 471 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 471 through 474'
    Processing helix  chain 'A' and resid 575 through 583
    Processing helix  chain 'A' and resid 601 through 612
    Processing helix  chain 'A' and resid 642 through 650
    Processing helix  chain 'A' and resid 709 through 717
    Processing helix  chain 'A' and resid 721 through 734
    Processing helix  chain 'A' and resid 737 through 741
    Processing helix  chain 'A' and resid 893 through 908
    Processing helix  chain 'A' and resid 921 through 932
    Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 80
      removed outlier: 6.876A  pdb=" N   CYS A  54 " --> pdb=" O   THR A  76 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   VAL A  78 " --> pdb=" O   PHE A  52 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   PHE A  52 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60
    Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 201
      removed outlier: 11.045A  pdb=" N   SER A 195 " --> pdb=" O   PHE A 210 " (cutoff:3.500A)
      removed outlier: 10.345A  pdb=" N   PHE A 210 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
      removed outlier: 10.115A  pdb=" N   LEU A 197 " --> pdb=" O   ASP A 208 " (cutoff:3.500A)
      removed outlier: 9.307A  pdb=" N   ASP A 208 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   PHE A 199 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   PHE A 210 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 365
      removed outlier: 3.599A  pdb=" N   ILE A 364 " --> pdb=" O   SER A 371 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 454 through 457
    Processing sheet with id=AA6, first strand: chain 'A' and resid 490 through 492
      removed outlier: 5.802A  pdb=" N   ARG A 503 " --> pdb=" O   GLU A 491 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510
    Processing sheet with id=AA8, first strand: chain 'A' and resid 537 through 540
      removed outlier: 6.448A  pdb=" N   VAL A 537 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   ASP A 691 " --> pdb=" O   VAL A 537 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   PHE A 539 " --> pdb=" O   ASP A 691 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   VAL A 686 " --> pdb=" O   LYS A 659 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LYS A 659 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 537 through 540
      removed outlier: 6.448A  pdb=" N   VAL A 537 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   ASP A 691 " --> pdb=" O   VAL A 537 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   PHE A 539 " --> pdb=" O   ASP A 691 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   VAL A 686 " --> pdb=" O   LYS A 659 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LYS A 659 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 636 through 640
    Processing sheet with id=AB2, first strand: chain 'A' and resid 759 through 761
      removed outlier: 3.584A  pdb=" N   GLU A 759 " --> pdb=" O   LYS A 844 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY A 842 " --> pdb=" O   ALA A 761 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLY A 839 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ASP A 934 " --> pdb=" O   ARG A 872 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   SER A 935 " --> pdb=" O   SER A 958 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   PHE A 960 " --> pdb=" O   SER A 935 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ILE A 937 " --> pdb=" O   PHE A 960 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 800 through 804
      removed outlier: 4.230A  pdb=" N   VAL A 988 " --> pdb=" O   PHE A1014 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LYS A1008 " --> pdb=" O   SER A 994 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   SER A 996 " --> pdb=" O   VAL A1006 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   VAL A1006 " --> pdb=" O   SER A 996 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   ASN A 998 " --> pdb=" O   ILE A1004 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ILE A1004 " --> pdb=" O   ASN A 998 " (cutoff:3.500A)

    313 hydrogen bonds defined for protein.
    870 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.08

  Time building geometry restraints manager: 0.86 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: 2333
        1.34 -     1.46: 1230
        1.46 -     1.57: 3873
        1.57 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 7454
  Sorted by residual:
  bond pdb=" N   ILE A 235 "
       pdb=" CA  ILE A 235 "
    ideal  model  delta    sigma   weight residual
    1.460  1.503 -0.044 1.21e-02 6.83e+03 1.31e+01
  bond pdb=" N   THR A 828 "
       pdb=" CA  THR A 828 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.23e-02 6.61e+03 8.09e+00
  bond pdb=" N   ILE A 246 "
       pdb=" CA  ILE A 246 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.030 1.06e-02 8.90e+03 7.91e+00
  bond pdb=" N   LEU A 255 "
       pdb=" CA  LEU A 255 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.21e-02 6.83e+03 7.82e+00
  bond pdb=" N   TYR A 716 "
       pdb=" CA  TYR A 716 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.29e-02 6.01e+03 7.23e+00
  ... (remaining 7449 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 9740
        2.12 -     4.25: 293
        4.25 -     6.37: 46
        6.37 -     8.49: 14
        8.49 -    10.61: 4
  Bond angle restraints: 10097
  Sorted by residual:
  angle pdb=" C   ALA A 403 "
        pdb=" N   ILE A 404 "
        pdb=" CA  ILE A 404 "
      ideal   model   delta    sigma   weight residual
     120.24  123.35   -3.11 6.30e-01 2.52e+00 2.44e+01
  angle pdb=" C   THR A 825 "
        pdb=" CA  THR A 825 "
        pdb=" CB  THR A 825 "
      ideal   model   delta    sigma   weight residual
     110.40  120.37   -9.97 2.07e+00 2.33e-01 2.32e+01
  angle pdb=" CB  ARG A 734 "
        pdb=" CG  ARG A 734 "
        pdb=" CD  ARG A 734 "
      ideal   model   delta    sigma   weight residual
     111.30  121.91  -10.61 2.30e+00 1.89e-01 2.13e+01
  angle pdb=" C   SER A 720 "
        pdb=" N   ILE A 721 "
        pdb=" CA  ILE A 721 "
      ideal   model   delta    sigma   weight residual
     121.97  129.56   -7.59 1.80e+00 3.09e-01 1.78e+01
  angle pdb=" CB  GLU A 288 "
        pdb=" CG  GLU A 288 "
        pdb=" CD  GLU A 288 "
      ideal   model   delta    sigma   weight residual
     112.60  119.53   -6.93 1.70e+00 3.46e-01 1.66e+01
  ... (remaining 10092 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.09: 3760
       18.09 -    36.17: 510
       36.17 -    54.26: 140
       54.26 -    72.34: 33
       72.34 -    90.43: 8
  Dihedral angle restraints: 4451
    sinusoidal: 1752
      harmonic: 2699
  Sorted by residual:
  dihedral pdb=" CA  TYR A 290 "
           pdb=" C   TYR A 290 "
           pdb=" N   PHE A 291 "
           pdb=" CA  PHE A 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.38   25.62     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" C   THR A 825 "
           pdb=" N   THR A 825 "
           pdb=" CA  THR A 825 "
           pdb=" CB  THR A 825 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.48   11.48     0      2.50e+00 1.60e-01 2.11e+01
  dihedral pdb=" CA  ARG A 598 "
           pdb=" C   ARG A 598 "
           pdb=" N   GLY A 599 "
           pdb=" CA  GLY A 599 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.42   20.58     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 4448 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 945
       0.070 -    0.139: 173
       0.139 -    0.209: 13
       0.209 -    0.279: 5
       0.279 -    0.348: 2
  Chirality restraints: 1138
  Sorted by residual:
  chirality pdb=" CB  ILE A 246 "
            pdb=" CA  ILE A 246 "
            pdb=" CG1 ILE A 246 "
            pdb=" CG2 ILE A 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CB  ILE A 488 "
            pdb=" CA  ILE A 488 "
            pdb=" CG1 ILE A 488 "
            pdb=" CG2 ILE A 488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CA  THR A 825 "
            pdb=" N   THR A 825 "
            pdb=" C   THR A 825 "
            pdb=" CB  THR A 825 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.81e+00
  ... (remaining 1135 not shown)

  Planarity restraints: 1292
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 821 "    0.013 2.00e-02 2.50e+03   2.67e-02 7.14e+00
        pdb=" C   LYS A 821 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   LYS A 821 "    0.017 2.00e-02 2.50e+03
        pdb=" N   TYR A 822 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 960 "   -0.040 5.00e-02 4.00e+02   6.04e-02 5.83e+00
        pdb=" N   PRO A 961 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 961 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 961 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 535 "    0.040 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO A 536 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 536 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 536 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1289 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 3359
        2.99 -     3.47: 7350
        3.47 -     3.95: 12441
        3.95 -     4.42: 14629
        4.42 -     4.90: 23511
  Nonbonded interactions: 61290
  Sorted by model distance:
  nonbonded pdb=" N   THR A 428 "
            pdb=" OG1 THR A 428 "
     model   vdw
     2.514 2.496
  nonbonded pdb=" N   LEU A 824 "
            pdb=" O   LEU A 824 "
     model   vdw
     2.539 2.496
  nonbonded pdb=" C   SER A 713 "
            pdb=" OG  SER A 713 "
     model   vdw
     2.580 2.616
  nonbonded pdb=" N   THR A 825 "
            pdb=" O   THR A 825 "
     model   vdw
     2.596 2.496
  nonbonded pdb=" C   THR A 882 "
            pdb=" OG1 THR A 882 "
     model   vdw
     2.600 2.616
  ... (remaining 61285 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.810
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
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      :  0.005   0.051   7454  Z= 0.257
  Angle     :  0.872  10.613  10097  Z= 0.505
  Chirality :  0.056   0.348   1138
  Planarity :  0.006   0.060   1292
  Dihedral  : 18.227  90.427   2713
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 32.07 %
    Favored  : 63.41 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -2.61 (0.25), residues: 899
  helix: -2.72 (0.20), residues: 318
  sheet: -1.14 (0.37), residues: 185
  loop : -0.91 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  25 
 TYR   0.026   0.002   TYR A 803 
 PHE   0.014   0.002   PHE A 304 
 TRP   0.007   0.001   TRP A 676 
 HIS   0.005   0.001   HIS A 675 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00482 /  0.26 ( 7454)
  covalent geometry    : angle       0.87194 /  0.50 (10097)
  hydrogen bonds       : bond        0.25219 / 15.60 (  307)
  hydrogen bonds       : angle       9.90783 /  6.99 (  870)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 86
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.8054 (tpt-90) cc_final: 0.7582 (tpm170)
REVERT: A   57 GLN cc_start: 0.7014 (tt0) cc_final: 0.6511 (mt0)
REVERT: A   58 ASN cc_start: 0.6843 (OUTLIER) cc_final: 0.6571 (m-40)
REVERT: A   69 ASP cc_start: 0.5344 (p0) cc_final: 0.5132 (p0)
REVERT: A   93 PHE cc_start: 0.6697 (m-80) cc_final: 0.6494 (m-80)
REVERT: A  246 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6104 (mp)
REVERT: A  287 ASN cc_start: 0.8095 (m-40) cc_final: 0.7884 (p0)
REVERT: A  324 LYS cc_start: 0.7207 (mttp) cc_final: 0.6282 (ptmt)
REVERT: A  384 ARG cc_start: 0.5738 (mmm160) cc_final: 0.4620 (mtm180)
REVERT: A  440 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6952 (tm-30)
REVERT: A  504 ARG cc_start: 0.5909 (ttt-90) cc_final: 0.5546 (ttp-170)
REVERT: A  541 ASP cc_start: 0.6741 (t0) cc_final: 0.5864 (t70)
REVERT: A  563 TYR cc_start: 0.6975 (t80) cc_final: 0.6440 (t80)
REVERT: A  592 ARG cc_start: 0.6760 (pmt170) cc_final: 0.6437 (pmt170)
REVERT: A  638 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6372 (mp0)
REVERT: A  860 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8350 (t)
REVERT: A  963 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.6321 (OUTLIER)
  outliers start: 37
  outliers final: 18
  residues processed: 112
  average time/residue: 0.4368
  time to fit residues: 52.4337
Evaluate side-chains
  96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ASN
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  440 GLU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  577 MET
Chi-restraints excluded: chain A residue  601 THR
Chi-restraints excluded: chain A residue  638 GLU
Chi-restraints excluded: chain A residue  713 SER
Chi-restraints excluded: chain A residue  745 SER
Chi-restraints excluded: chain A residue  807 ILE
Chi-restraints excluded: chain A residue  825 THR
Chi-restraints excluded: chain A residue  860 SER
Chi-restraints excluded: chain A residue  882 THR
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74]
   chunk 49 optimal weight:    0.0470
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.9280

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.213747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.171285 restraints weight = 7178.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 1.86
r_work: 0.3820 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3661 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7454  Z= 0.151
  Angle     :  0.522   5.421  10097  Z= 0.280
  Chirality :  0.044   0.145   1138
  Planarity :  0.004   0.044   1292
  Dihedral  :  7.518  83.994   1032
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 29.88 %
    Favored  : 64.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -1.03 (0.26), residues: 899
  helix: -0.46 (0.26), residues: 322
  sheet: -0.99 (0.37), residues: 184
  loop : -0.51 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 507 
 TYR   0.012   0.001   TYR A 163 
 PHE   0.011   0.001   PHE A 304 
 TRP   0.009   0.001   TRP A 148 
 HIS   0.003   0.001   HIS A  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 7454)
  covalent geometry    : angle       0.52233 /  0.28 (10097)
  hydrogen bonds       : bond        0.03499 /  2.17 (  307)
  hydrogen bonds       : angle       5.90605 /  4.24 (  870)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 82
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.7085 (tt0) cc_final: 0.6409 (mt0)
REVERT: A   58 ASN cc_start: 0.7266 (p0) cc_final: 0.6847 (m-40)
REVERT: A   69 ASP cc_start: 0.5610 (p0) cc_final: 0.5170 (p0)
REVERT: A  208 ASP cc_start: 0.7733 (p0) cc_final: 0.6903 (p0)
REVERT: A  296 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7744 (tttt)
REVERT: A  324 LYS cc_start: 0.7102 (mttp) cc_final: 0.6482 (ptpt)
REVERT: A  384 ARG cc_start: 0.6369 (mmm160) cc_final: 0.4604 (mtm180)
REVERT: A  476 GLN cc_start: 0.5722 (OUTLIER) cc_final: 0.5361 (tm-30)
REVERT: A  504 ARG cc_start: 0.6330 (ttt-90) cc_final: 0.5796 (ttp-170)
REVERT: A  592 ARG cc_start: 0.6598 (pmt170) cc_final: 0.6236 (pmt-80)
REVERT: A  638 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6339 (mp0)
REVERT: A  672 TYR cc_start: 0.6733 (t80) cc_final: 0.5481 (m-80)
REVERT: A  902 GLU cc_start: 0.7842 (tp30) cc_final: 0.7548 (tp30)
REVERT: A  963 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6210 (OUTLIER)
  outliers start: 46
  outliers final: 18
  residues processed: 119
  average time/residue: 0.3598
  time to fit residues: 46.5381
Evaluate side-chains
  97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  476 GLN
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  638 GLU
Chi-restraints excluded: chain A residue  825 THR
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  882 THR
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks: [27, 38, 10, 26, 20, 30, 73, 89, 55, 81, 41]
   chunk 27 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    0.2980
   chunk 30 optimal weight:    0.5980
   chunk 73 optimal weight:    9.9990
   chunk 89 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 81 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 GLN
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.216299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.174617 restraints weight = 7109.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 1.85
r_work: 0.3851 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7454  Z= 0.111
  Angle     :  0.468   5.360  10097  Z= 0.250
  Chirality :  0.043   0.141   1138
  Planarity :  0.003   0.040   1292
  Dihedral  :  6.599  80.931   1013
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 30.73 %
    Favored  : 64.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.13 (0.27), residues: 899
  helix:  0.79 (0.29), residues: 312
  sheet: -0.82 (0.37), residues: 178
  loop : -0.29 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  25 
 TYR   0.011   0.001   TYR A 163 
 PHE   0.026   0.001   PHE A 972 
 TRP   0.006   0.001   TRP A 148 
 HIS   0.002   0.001   HIS A 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 ( 7454)
  covalent geometry    : angle       0.46837 /  0.25 (10097)
  hydrogen bonds       : bond        0.03071 /  1.90 (  307)
  hydrogen bonds       : angle       5.32715 /  3.84 (  870)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 85
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.7157 (tt0) cc_final: 0.6409 (mt0)
REVERT: A   58 ASN cc_start: 0.7273 (p0) cc_final: 0.6767 (m-40)
REVERT: A   69 ASP cc_start: 0.5449 (p0) cc_final: 0.5067 (p0)
REVERT: A  156 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6796 (ttmt)
REVERT: A  208 ASP cc_start: 0.7700 (p0) cc_final: 0.6907 (p0)
REVERT: A  244 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7113 (pt0)
REVERT: A  324 LYS cc_start: 0.7008 (mttp) cc_final: 0.6381 (ptpt)
REVERT: A  384 ARG cc_start: 0.6314 (mmm160) cc_final: 0.4571 (mtm180)
REVERT: A  592 ARG cc_start: 0.6526 (pmt170) cc_final: 0.6177 (pmt-80)
REVERT: A  672 TYR cc_start: 0.6684 (t80) cc_final: 0.5518 (m-80)
REVERT: A  902 GLU cc_start: 0.7876 (tp30) cc_final: 0.7559 (tp30)
REVERT: A  963 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.6265 (m-80)
  outliers start: 41
  outliers final: 13
  residues processed: 116
  average time/residue: 0.3736
  time to fit residues: 46.9362
Evaluate side-chains
  94 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  156 LYS
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  244 GLU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  577 MET
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  979 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks: [82, 36, 30, 20, 18, 84, 5, 47, 39, 32, 8]
   chunk 82 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0570
   chunk 5 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.217675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.180106 restraints weight = 7180.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 1.77
r_work: 0.3828 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7454  Z= 0.113
  Angle     :  0.474   5.306  10097  Z= 0.253
  Chirality :  0.043   0.147   1138
  Planarity :  0.003   0.052   1292
  Dihedral  :  5.426  59.897   1003
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 30.24 %
    Favored  : 63.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.28 (0.28), residues: 899
  helix:  1.34 (0.29), residues: 306
  sheet: -0.64 (0.37), residues: 185
  loop : -0.19 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  25 
 TYR   0.010   0.001   TYR A 163 
 PHE   0.012   0.001   PHE A 654 
 TRP   0.006   0.001   TRP A 148 
 HIS   0.002   0.001   HIS A 675 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 7454)
  covalent geometry    : angle       0.47377 /  0.25 (10097)
  hydrogen bonds       : bond        0.02950 /  1.84 (  307)
  hydrogen bonds       : angle       5.13766 /  3.70 (  870)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 79
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.7022 (mmtt)
REVERT: A   57 GLN cc_start: 0.7218 (tt0) cc_final: 0.6561 (mt0)
REVERT: A   58 ASN cc_start: 0.7138 (p0) cc_final: 0.6754 (m-40)
REVERT: A   69 ASP cc_start: 0.5509 (p0) cc_final: 0.5175 (p0)
REVERT: A  156 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6736 (ttmt)
REVERT: A  208 ASP cc_start: 0.7556 (p0) cc_final: 0.6810 (p0)
REVERT: A  296 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7713 (tttt)
REVERT: A  324 LYS cc_start: 0.6929 (mttp) cc_final: 0.6575 (ptpt)
REVERT: A  384 ARG cc_start: 0.6313 (mmm160) cc_final: 0.4644 (mtm180)
REVERT: A  476 GLN cc_start: 0.5852 (OUTLIER) cc_final: 0.5226 (tm-30)
REVERT: A  592 ARG cc_start: 0.6722 (pmt170) cc_final: 0.6432 (pmt-80)
REVERT: A  672 TYR cc_start: 0.6719 (t80) cc_final: 0.5757 (m-80)
REVERT: A  693 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6913 (mtp180)
REVERT: A  963 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.6287 (OUTLIER)
  outliers start: 49
  outliers final: 21
  residues processed: 119
  average time/residue: 0.3660
  time to fit residues: 47.3037
Evaluate side-chains
  98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  156 LYS
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  476 GLN
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  577 MET
Chi-restraints excluded: chain A residue  693 ARG
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks: [20, 37, 35, 66, 27, 70, 25, 63, 34, 14, 29]
   chunk 20 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 35 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 823 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.214702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.176786 restraints weight = 7181.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 1.75
r_work: 0.3770 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7454  Z= 0.155
  Angle     :  0.521   5.783  10097  Z= 0.274
  Chirality :  0.044   0.143   1138
  Planarity :  0.003   0.040   1292
  Dihedral  :  5.509  59.353   1003
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  6.22 %
    Allowed  : 30.98 %
    Favored  : 62.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.31 (0.28), residues: 899
  helix:  1.37 (0.29), residues: 311
  sheet: -0.69 (0.38), residues: 186
  loop : -0.14 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  25 
 TYR   0.011   0.001   TYR A 333 
 PHE   0.013   0.002   PHE A 304 
 TRP   0.009   0.001   TRP A 148 
 HIS   0.002   0.001   HIS A  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.16 ( 7454)
  covalent geometry    : angle       0.52087 /  0.27 (10097)
  hydrogen bonds       : bond        0.03188 /  1.99 (  307)
  hydrogen bonds       : angle       5.18729 /  3.74 (  870)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 76
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6983 (mmtt)
REVERT: A   57 GLN cc_start: 0.7127 (tt0) cc_final: 0.6564 (mt0)
REVERT: A   58 ASN cc_start: 0.7261 (p0) cc_final: 0.6847 (m-40)
REVERT: A   69 ASP cc_start: 0.5617 (p0) cc_final: 0.5354 (p0)
REVERT: A  156 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6740 (ttmt)
REVERT: A  208 ASP cc_start: 0.7635 (p0) cc_final: 0.6925 (p0)
REVERT: A  240 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7429 (mm)
REVERT: A  296 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7777 (tttt)
REVERT: A  324 LYS cc_start: 0.6831 (mttp) cc_final: 0.6406 (ptpt)
REVERT: A  476 GLN cc_start: 0.5765 (OUTLIER) cc_final: 0.5389 (pp30)
REVERT: A  592 ARG cc_start: 0.6741 (pmt170) cc_final: 0.6415 (pmt-80)
REVERT: A  638 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6566 (mp0)
REVERT: A  672 TYR cc_start: 0.6920 (t80) cc_final: 0.5845 (m-80)
REVERT: A  693 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6961 (mtp180)
REVERT: A  963 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6330 (OUTLIER)
REVERT: A  995 TYR cc_start: 0.8424 (m-80) cc_final: 0.8160 (m-80)
  outliers start: 51
  outliers final: 25
  residues processed: 120
  average time/residue: 0.3874
  time to fit residues: 50.3517
Evaluate side-chains
  103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 71
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  156 LYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  476 GLN
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  577 MET
Chi-restraints excluded: chain A residue  638 GLU
Chi-restraints excluded: chain A residue  693 ARG
Chi-restraints excluded: chain A residue  724 THR
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks: [83, 53, 76, 77, 52, 67, 42, 63, 87, 39, 23]
   chunk 83 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0970
   chunk 63 optimal weight:    0.8980
   chunk 87 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 282 ASN
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 823 ASN
A 826 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.213923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.176682 restraints weight = 7152.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 1.90
r_work: 0.3847 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7454  Z= 0.158
  Angle     :  0.526   7.283  10097  Z= 0.275
  Chirality :  0.044   0.139   1138
  Planarity :  0.004   0.045   1292
  Dihedral  :  5.536  59.548   1003
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 32.32 %
    Favored  : 62.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.40 (0.28), residues: 899
  helix:  1.42 (0.29), residues: 311
  sheet: -0.58 (0.39), residues: 180
  loop : -0.11 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 384 
 TYR   0.014   0.001   TYR A 205 
 PHE   0.013   0.002   PHE A 304 
 TRP   0.008   0.001   TRP A 148 
 HIS   0.003   0.001   HIS A  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 ( 7454)
  covalent geometry    : angle       0.52618 /  0.28 (10097)
  hydrogen bonds       : bond        0.03125 /  1.95 (  307)
  hydrogen bonds       : angle       5.20441 /  3.75 (  870)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 78
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.7174 (tt0) cc_final: 0.6517 (mt0)
REVERT: A   58 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.6932 (m-40)
REVERT: A   69 ASP cc_start: 0.5774 (p0) cc_final: 0.5122 (p0)
REVERT: A  156 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6789 (ttmt)
REVERT: A  208 ASP cc_start: 0.7753 (p0) cc_final: 0.7029 (p0)
REVERT: A  240 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7369 (mm)
REVERT: A  296 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8148 (ttmt)
REVERT: A  324 LYS cc_start: 0.6938 (mttp) cc_final: 0.6376 (ptpt)
REVERT: A  440 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7742 (tm-30)
REVERT: A  476 GLN cc_start: 0.5811 (OUTLIER) cc_final: 0.5379 (pp30)
REVERT: A  504 ARG cc_start: 0.6314 (ttt-90) cc_final: 0.5993 (ttt180)
REVERT: A  592 ARG cc_start: 0.6733 (pmt170) cc_final: 0.6320 (pmt-80)
REVERT: A  638 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6616 (mp0)
REVERT: A  672 TYR cc_start: 0.7026 (t80) cc_final: 0.5873 (m-80)
REVERT: A  691 ASP cc_start: 0.5959 (t70) cc_final: 0.5322 (t0)
REVERT: A  693 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6963 (mtp180)
REVERT: A  963 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6426 (OUTLIER)
REVERT: A  995 TYR cc_start: 0.8491 (m-80) cc_final: 0.8276 (m-80)
  outliers start: 44
  outliers final: 24
  residues processed: 114
  average time/residue: 0.3640
  time to fit residues: 45.0535
Evaluate side-chains
  103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 72
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ASN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  156 LYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  476 GLN
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  577 MET
Chi-restraints excluded: chain A residue  638 GLU
Chi-restraints excluded: chain A residue  693 ARG
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks: [61, 26, 32, 56, 79, 64, 35, 52, 34, 24, 28]
   chunk 61 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 823 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.213998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.175827 restraints weight = 7169.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.4026 rms_B_bonded: 1.94
r_work: 0.3820 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3663 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7454  Z= 0.167
  Angle     :  0.541   8.832  10097  Z= 0.283
  Chirality :  0.045   0.148   1138
  Planarity :  0.004   0.049   1292
  Dihedral  :  5.593  59.727   1003
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 31.95 %
    Favored  : 62.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.40 (0.28), residues: 899
  helix:  1.38 (0.29), residues: 311
  sheet: -0.56 (0.39), residues: 180
  loop : -0.09 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 384 
 TYR   0.012   0.002   TYR A 205 
 PHE   0.025   0.002   PHE A 729 
 TRP   0.008   0.001   TRP A 148 
 HIS   0.003   0.001   HIS A 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00395 /  0.17 ( 7454)
  covalent geometry    : angle       0.54125 /  0.28 (10097)
  hydrogen bonds       : bond        0.03210 /  2.03 (  307)
  hydrogen bonds       : angle       5.21912 /  3.76 (  870)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 77
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.7146 (tt0) cc_final: 0.6423 (mt0)
REVERT: A   58 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.6932 (m-40)
REVERT: A   69 ASP cc_start: 0.5756 (p0) cc_final: 0.5049 (p0)
REVERT: A   97 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8170 (m-30)
REVERT: A  156 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6810 (ttmt)
REVERT: A  208 ASP cc_start: 0.7819 (p0) cc_final: 0.7082 (p0)
REVERT: A  240 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7285 (mm)
REVERT: A  296 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7856 (tttt)
REVERT: A  324 LYS cc_start: 0.6973 (mttp) cc_final: 0.6335 (ptpt)
REVERT: A  504 ARG cc_start: 0.6326 (ttt-90) cc_final: 0.5520 (ttp-170)
REVERT: A  592 ARG cc_start: 0.6689 (pmt170) cc_final: 0.6260 (pmt-80)
REVERT: A  638 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6648 (mp0)
REVERT: A  672 TYR cc_start: 0.7066 (t80) cc_final: 0.5827 (m-80)
REVERT: A  693 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6907 (mtp180)
REVERT: A  963 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.6388 (OUTLIER)
  outliers start: 47
  outliers final: 28
  residues processed: 117
  average time/residue: 0.3787
  time to fit residues: 48.0715
Evaluate side-chains
  107 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 72
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ASN
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  156 LYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  577 MET
Chi-restraints excluded: chain A residue  638 GLU
Chi-restraints excluded: chain A residue  693 ARG
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue  908 THR
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks: [53, 16, 8, 18, 38, 90, 79, 60, 59, 17, 34]
   chunk 53 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 38 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 282 ASN
A 823 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.215074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.177762 restraints weight = 7142.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 1.85
r_work: 0.3858 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7454  Z= 0.149
  Angle     :  0.530   8.993  10097  Z= 0.276
  Chirality :  0.044   0.142   1138
  Planarity :  0.004   0.040   1292
  Dihedral  :  5.520  59.200   1003
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 31.83 %
    Favored  : 62.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.52 (0.28), residues: 899
  helix:  1.54 (0.29), residues: 305
  sheet: -0.54 (0.39), residues: 180
  loop : -0.03 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 384 
 TYR   0.012   0.001   TYR A 803 
 PHE   0.022   0.002   PHE A 729 
 TRP   0.007   0.001   TRP A 148 
 HIS   0.002   0.001   HIS A  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 ( 7454)
  covalent geometry    : angle       0.53008 /  0.28 (10097)
  hydrogen bonds       : bond        0.03068 /  1.93 (  307)
  hydrogen bonds       : angle       5.17310 /  3.72 (  870)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 76
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.7134 (tt0) cc_final: 0.6408 (mt0)
REVERT: A   58 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6891 (m-40)
REVERT: A   69 ASP cc_start: 0.5725 (p0) cc_final: 0.5028 (p0)
REVERT: A   97 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8124 (m-30)
REVERT: A  156 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6776 (ttmt)
REVERT: A  208 ASP cc_start: 0.7727 (p0) cc_final: 0.6960 (p0)
REVERT: A  240 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7252 (mm)
REVERT: A  246 ILE cc_start: 0.6057 (OUTLIER) cc_final: 0.5837 (tp)
REVERT: A  296 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8106 (ttmt)
REVERT: A  324 LYS cc_start: 0.7013 (mttp) cc_final: 0.6289 (ptpt)
REVERT: A  504 ARG cc_start: 0.6263 (ttt-90) cc_final: 0.5879 (ttt180)
REVERT: A  592 ARG cc_start: 0.6696 (pmt170) cc_final: 0.6234 (pmt-80)
REVERT: A  638 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6562 (mp0)
REVERT: A  672 TYR cc_start: 0.7001 (t80) cc_final: 0.5767 (m-80)
REVERT: A  691 ASP cc_start: 0.5869 (t70) cc_final: 0.5277 (t0)
REVERT: A  693 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6903 (mtp180)
REVERT: A  963 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.6334 (OUTLIER)
  outliers start: 43
  outliers final: 28
  residues processed: 112
  average time/residue: 0.3412
  time to fit residues: 41.7232
Evaluate side-chains
  108 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 72
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ASN
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  156 LYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  577 MET
Chi-restraints excluded: chain A residue  638 GLU
Chi-restraints excluded: chain A residue  693 ARG
Chi-restraints excluded: chain A residue  724 THR
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue  908 THR
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks: [65, 5, 4, 82, 50, 15, 11, 23, 2, 81, 51]
   chunk 65 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 15 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 81 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0020
   overall best weight:    0.4788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.217034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.179585 restraints weight = 7036.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 2.05
r_work: 0.3893 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3742 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7454  Z= 0.111
  Angle     :  0.505   8.748  10097  Z= 0.262
  Chirality :  0.043   0.141   1138
  Planarity :  0.003   0.039   1292
  Dihedral  :  5.352  59.184   1003
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 34.02 %
    Favored  : 62.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.62 (0.28), residues: 899
  helix:  1.60 (0.29), residues: 311
  sheet: -0.43 (0.40), residues: 172
  loop : -0.00 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 384 
 TYR   0.012   0.001   TYR A 803 
 PHE   0.018   0.001   PHE A 729 
 TRP   0.005   0.001   TRP A   5 
 HIS   0.002   0.001   HIS A 675 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 7454)
  covalent geometry    : angle       0.50470 /  0.26 (10097)
  hydrogen bonds       : bond        0.02787 /  1.75 (  307)
  hydrogen bonds       : angle       5.00282 /  3.60 (  870)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 75
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.7184 (tt0) cc_final: 0.6465 (mt0)
REVERT: A   58 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6805 (m-40)
REVERT: A   69 ASP cc_start: 0.5529 (p0) cc_final: 0.5224 (p0)
REVERT: A  208 ASP cc_start: 0.7621 (p0) cc_final: 0.6803 (p0)
REVERT: A  240 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7243 (mm)
REVERT: A  324 LYS cc_start: 0.6968 (mttp) cc_final: 0.6326 (ptpt)
REVERT: A  384 ARG cc_start: 0.6570 (mmm160) cc_final: 0.4330 (mpp80)
REVERT: A  563 TYR cc_start: 0.6904 (t80) cc_final: 0.6347 (t80)
REVERT: A  592 ARG cc_start: 0.6735 (pmt170) cc_final: 0.6386 (pmt-80)
REVERT: A  638 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6437 (mp0)
REVERT: A  672 TYR cc_start: 0.6909 (t80) cc_final: 0.5753 (m-80)
REVERT: A  693 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6832 (mtp180)
REVERT: A  963 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6304 (OUTLIER)
  outliers start: 28
  outliers final: 19
  residues processed: 99
  average time/residue: 0.3432
  time to fit residues: 37.1151
Evaluate side-chains
  95 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ASN
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  638 GLU
Chi-restraints excluded: chain A residue  693 ARG
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks: [45, 67, 53, 33, 57, 25, 58, 54, 60, 18, 87]
   chunk 45 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0470
   chunk 33 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    0.6280

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 823 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.216040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.176823 restraints weight = 7117.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 1.77
r_work: 0.3830 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7454  Z= 0.125
  Angle     :  0.529   9.051  10097  Z= 0.274
  Chirality :  0.044   0.141   1138
  Planarity :  0.003   0.041   1292
  Dihedral  :  5.178  59.279   1001
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 34.02 %
    Favored  : 62.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.69 (0.29), residues: 899
  helix:  1.81 (0.29), residues: 304
  sheet: -0.54 (0.39), residues: 178
  loop :  0.01 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 384 
 TYR   0.013   0.001   TYR A 803 
 PHE   0.018   0.001   PHE A 729 
 TRP   0.005   0.001   TRP A 148 
 HIS   0.002   0.001   HIS A 258 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.12 ( 7454)
  covalent geometry    : angle       0.52872 /  0.27 (10097)
  hydrogen bonds       : bond        0.02878 /  1.80 (  307)
  hydrogen bonds       : angle       5.00664 /  3.60 (  870)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.7180 (mtm110) cc_final: 0.6705 (mtm-85)
REVERT: A   57 GLN cc_start: 0.7193 (tt0) cc_final: 0.6591 (mt0)
REVERT: A   58 ASN cc_start: 0.7134 (p0) cc_final: 0.6767 (m-40)
REVERT: A   69 ASP cc_start: 0.5549 (p0) cc_final: 0.5154 (p0)
REVERT: A  208 ASP cc_start: 0.7485 (p0) cc_final: 0.6733 (p0)
REVERT: A  240 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7337 (mm)
REVERT: A  324 LYS cc_start: 0.6911 (mttp) cc_final: 0.6461 (ptpt)
REVERT: A  384 ARG cc_start: 0.6541 (mmm160) cc_final: 0.4365 (mpp80)
REVERT: A  504 ARG cc_start: 0.6220 (ttt-90) cc_final: 0.5881 (ttt180)
REVERT: A  592 ARG cc_start: 0.6826 (pmt170) cc_final: 0.6503 (pmt-80)
REVERT: A  638 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6481 (mp0)
REVERT: A  672 TYR cc_start: 0.6812 (t80) cc_final: 0.5761 (m-80)
REVERT: A  693 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6898 (mtp180)
REVERT: A  963 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6376 (OUTLIER)
  outliers start: 28
  outliers final: 23
  residues processed: 96
  average time/residue: 0.3861
  time to fit residues: 40.2742
Evaluate side-chains
  97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 71
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  577 MET
Chi-restraints excluded: chain A residue  638 GLU
Chi-restraints excluded: chain A residue  693 ARG
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue  908 THR
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks: [64, 13, 24, 3, 5, 23, 52, 70, 86, 17, 22]
   chunk 64 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 823 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.214698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.176067 restraints weight = 7121.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.4025 rms_B_bonded: 1.75
r_work: 0.3807 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7454  Z= 0.141
  Angle     :  0.539   9.064  10097  Z= 0.280
  Chirality :  0.045   0.151   1138
  Planarity :  0.004   0.041   1292
  Dihedral  :  5.233  59.259   1001
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 33.29 %
    Favored  : 62.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.28), residues: 899
  helix:  1.64 (0.29), residues: 310
  sheet: -0.52 (0.40), residues: 178
  loop : -0.03 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 384 
 TYR   0.013   0.001   TYR A 803 
 PHE   0.019   0.002   PHE A 729 
 TRP   0.007   0.001   TRP A 148 
 HIS   0.002   0.001   HIS A  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 7454)
  covalent geometry    : angle       0.53948 /  0.28 (10097)
  hydrogen bonds       : bond        0.02990 /  1.87 (  307)
  hydrogen bonds       : angle       5.05102 /  3.63 (  870)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2325.08 seconds
wall clock time: 40 minutes 29.77 seconds (2429.77 seconds total)