Starting phenix.real_space_refine
on Wed Aug  5 20:08:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k4d_62055/08_2026/9k4d_62055.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k4d_62055/08_2026/9k4d_62055.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k4d_62055/08_2026/9k4d_62055.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k4d_62055/08_2026/9k4d_62055.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k4d_62055/08_2026/9k4d_62055.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k4d_62055/08_2026/9k4d_62055.cif"
  }
  resolution = 3.53
  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=   0.006 sd=   0.090
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: 5
    Type Number    sf(0)   Gaussians
     P     146      5.49       5
     S      19      5.16       5
     C    6745      2.51       5
     N    2024      2.21       5
     O    2524      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11458
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1017, 8325
          Classifications: {'peptide': 1017}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 989}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 719
          Classifications: {'DNA': 35}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 34}
    Chain: "C"
      Number of atoms: 325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 325
          Classifications: {'DNA': 16}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 15}
    Chain: "D"
      Number of atoms: 2089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2089
          Classifications: {'RNA': 98}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 39}
          Link IDs: {'rna2p': 11, 'rna3p': 86}
  Time building chain proxies: 2.21, per 1000 atoms: 0.19
  Number of scatterers: 11458
  At special positions: 0
  Unit cell: (119.658, 104.566, 143.374, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P     146     15.00
     O    2524      8.00
     N    2024      7.00
     C    6745      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: 1.10
  Conformation dependent library (CDL) restraints added in 419.2 milliseconds
  

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 7 sheets defined
      54.7% alpha, 11.3% beta
      58 base pairs and 95 stacking pairs defined.
    Time for finding SS restraints: 1.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.771A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.646A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 293 through 306
      removed outlier: 3.904A  pdb=" N   ASP A 304 " --> pdb=" O   ILE A 300 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.696A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 382
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.809A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 426
      removed outlier: 4.281A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.786A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 474 through 476
      No H-bonds generated for 'chain 'A' and resid 474 through 476'
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 3.561A  pdb=" N   VAL A 481 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 496
      removed outlier: 4.422A  pdb=" N   MET A 495 " --> pdb=" O   PHE A 491 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   THR A 496 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 3.995A  pdb=" N   LYS A 526 " --> pdb=" O   ASN A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 603 through 609
      removed outlier: 3.533A  pdb=" N   LEU A 607 " --> pdb=" O   ASP A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 663 through 669
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 702 through 712
      removed outlier: 4.470A  pdb=" N   GLU A 706 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 727
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.645A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 940
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 4.028A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 999
      removed outlier: 4.557A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.587A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1313
      removed outlier: 3.518A  pdb=" N   PHE A1313 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1344
      removed outlier: 3.718A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 6.583A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ASN A 758 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 10.369A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539
      removed outlier: 3.672A  pdb=" N   LYS A 528 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1121
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.586A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.586A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1326
      removed outlier: 3.578A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    411 hydrogen bonds defined for protein.
    1194 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      146 hydrogen bonds
      284 hydrogen bond angles
      0 basepair planarities
      58 basepair parallelities
      95 stacking parallelities
  Total time for adding SS restraints: 2.77

  Time building geometry restraints manager: 1.38 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: 3089
        1.34 -     1.46: 2808
        1.46 -     1.58: 5761
        1.58 -     1.69: 292
        1.69 -     1.81: 36
  Bond restraints: 11986
  Sorted by residual:
  bond pdb=" C3'  DC C  10 "
       pdb=" C2'  DC C  10 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.03e+01
  bond pdb=" C3'  DC B  14 "
       pdb=" C2'  DC B  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.01e+01
  bond pdb=" C3'  DA B  27 "
       pdb=" C2'  DA B  27 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.70e+00
  bond pdb=" C3'  DG B  12 "
       pdb=" C2'  DG B  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.05e+00
  bond pdb=" C3'  DG B   7 "
       pdb=" C2'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.72e+00
  ... (remaining 11981 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 16048
        1.37 -     2.74: 699
        2.74 -     4.12: 78
        4.12 -     5.49: 5
        5.49 -     6.86: 1
  Bond angle restraints: 16831
  Sorted by residual:
  angle pdb=" O4'  DG B  18 "
        pdb=" C4'  DG B  18 "
        pdb=" C3'  DG B  18 "
      ideal   model   delta    sigma   weight residual
     106.00  103.13    2.87 6.00e-01 2.78e+00 2.29e+01
  angle pdb=" O4'  DG B  23 "
        pdb=" C4'  DG B  23 "
        pdb=" C3'  DG B  23 "
      ideal   model   delta    sigma   weight residual
     106.00  103.15    2.85 6.00e-01 2.78e+00 2.26e+01
  angle pdb=" O4'  DA B  22 "
        pdb=" C4'  DA B  22 "
        pdb=" C3'  DA B  22 "
      ideal   model   delta    sigma   weight residual
     106.00  103.33    2.67 6.00e-01 2.78e+00 1.98e+01
  angle pdb=" O4'  DT B  19 "
        pdb=" C4'  DT B  19 "
        pdb=" C3'  DT B  19 "
      ideal   model   delta    sigma   weight residual
     106.00  103.41    2.59 6.00e-01 2.78e+00 1.87e+01
  angle pdb=" N3   DT B   4 "
        pdb=" C4   DT B   4 "
        pdb=" O4   DT B   4 "
      ideal   model   delta    sigma   weight residual
     119.90  122.45   -2.55 6.00e-01 2.78e+00 1.80e+01
  ... (remaining 16826 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.55: 6883
       35.55 -    71.10: 332
       71.10 -   106.65: 24
      106.65 -   142.20: 0
      142.20 -   177.76: 1
  Dihedral angle restraints: 7240
    sinusoidal: 4253
      harmonic: 2987
  Sorted by residual:
  dihedral pdb=" C4'  DG B   7 "
           pdb=" C3'  DG B   7 "
           pdb=" O3'  DG B   7 "
           pdb=" P    DA B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.24  177.76     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  PHE A 446 "
           pdb=" C   PHE A 446 "
           pdb=" N   ARG A 447 "
           pdb=" CA  ARG A 447 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.17   16.83     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CG  ARG A1359 "
           pdb=" CD  ARG A1359 "
           pdb=" NE  ARG A1359 "
           pdb=" CZ  ARG A1359 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.60  -43.40     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 7237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1261
       0.031 -    0.062: 395
       0.062 -    0.092: 136
       0.092 -    0.123: 60
       0.123 -    0.154: 92
  Chirality restraints: 1944
  Sorted by residual:
  chirality pdb=" C3'  DG B   7 "
            pdb=" C4'  DG B   7 "
            pdb=" O3'  DG B   7 "
            pdb=" C2'  DG B   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.58   -0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" C2'   G D  33 "
            pdb=" C3'   G D  33 "
            pdb=" O2'   G D  33 "
            pdb=" C1'   G D  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.76    0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" C2'   G D   6 "
            pdb=" C3'   G D   6 "
            pdb=" O2'   G D   6 "
            pdb=" C1'   G D   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.76    0.14 2.00e-01 2.50e+01 5.04e-01
  ... (remaining 1941 not shown)

  Planarity restraints: 1601
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  42 "    0.022 2.00e-02 2.50e+03   1.01e-02 2.79e+00
        pdb=" N9    A D  42 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8    A D  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  42 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A D  42 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A D  42 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A D  42 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    A D  42 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A D  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  42 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  42 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G D  54 "    0.018 2.00e-02 2.50e+03   8.10e-03 1.97e+00
        pdb=" N9    G D  54 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8    G D  54 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G D  54 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    G D  54 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G D  54 "   -0.000 2.00e-02 2.50e+03
        pdb=" O6    G D  54 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G D  54 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G D  54 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G D  54 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G D  54 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G D  54 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 315 "    0.022 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO A 316 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 316 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 316 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1598 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 4
        2.02 -     2.74: 880
        2.74 -     3.46: 15390
        3.46 -     4.18: 29092
        4.18 -     4.90: 46980
  Nonbonded interactions: 92346
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 510 "
            pdb=" OP1   G D   6 "
     model   vdw
     1.297 3.120
  nonbonded pdb=" NZ  LYS A  44 "
            pdb=" O6    G D  92 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" ND2 ASN A  77 "
            pdb=" O2    U D  59 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" C5    C D  18 "
     model   vdw
     1.431 3.420
  nonbonded pdb=" N2   DG B   9 "
            pdb=" O2   DC C   8 "
     model   vdw
     2.126 2.496
  ... (remaining 92341 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.720
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
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      :  0.003   0.031  11986  Z= 0.263
  Angle     :  0.606   6.861  16831  Z= 0.481
  Chirality :  0.046   0.154   1944
  Planarity :  0.003   0.034   1601
  Dihedral  : 16.931 177.755   5306
  Min Nonbonded Distance : 1.297

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.68 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.26), residues: 1009
  helix:  1.76 (0.24), residues: 506
  sheet:  1.12 (0.53), residues: 105
  loop :  0.17 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 494 
 TYR   0.009   0.001   TYR A  72 
 PHE   0.009   0.001   PHE A 432 
 TRP   0.010   0.001   TRP A1126 
 HIS   0.004   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.26 (11986)
  covalent geometry    : angle       0.60577 /  0.48 (16831)
  hydrogen bonds       : bond        0.14550 / 10.04 (  546)
  hydrogen bonds       : angle       5.64256 /  4.06 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  441 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8013 (mt-10)
REVERT: A  511 HIS cc_start: 0.7288 (m90) cc_final: 0.6204 (m-70)
REVERT: A  534 MET cc_start: -0.0525 (mtt) cc_final: -0.2080 (tpt)
REVERT: A  618 ASP cc_start: 0.8720 (t70) cc_final: 0.8349 (t0)
REVERT: A  623 LEU cc_start: 0.9401 (mt) cc_final: 0.9167 (mt)
REVERT: A  630 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8546 (mt-10)
REVERT: A  653 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7734 (mtm-85)
REVERT: A  654 ARG cc_start: 0.7393 (tpt170) cc_final: 0.6701 (ttm170)
REVERT: A  656 TYR cc_start: 0.8101 (m-80) cc_final: 0.7862 (m-10)
REVERT: A  709 GLN cc_start: 0.7939 (mt0) cc_final: 0.7613 (mt0)
REVERT: A  762 GLU cc_start: 0.7669 (pp20) cc_final: 0.7038 (tm-30)
REVERT: A  954 LYS cc_start: 0.8294 (mttt) cc_final: 0.8054 (mttm)
REVERT: A  962 LEU cc_start: 0.8939 (mt) cc_final: 0.8243 (tp)
REVERT: A  979 ASN cc_start: 0.8427 (p0) cc_final: 0.8109 (p0)
REVERT: A 1148 LYS cc_start: 0.8270 (mttt) cc_final: 0.7791 (mtpp)
REVERT: A 1169 MET cc_start: 0.8891 (ttp) cc_final: 0.8617 (ttm)
REVERT: A 1230 SER cc_start: 0.7697 (m) cc_final: 0.7447 (t)
REVERT: A 1261 GLN cc_start: 0.9029 (mt0) cc_final: 0.8728 (mt0)
REVERT: A 1325 LYS cc_start: 0.8858 (mttt) cc_final: 0.8443 (ttmm)
REVERT: A 1326 TYR cc_start: 0.8507 (t80) cc_final: 0.7942 (t80)
REVERT: A 1339 THR cc_start: 0.9245 (p) cc_final: 0.8948 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1337
  time to fit residues: 39.8199
Evaluate side-chains
  110 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:   40.0000
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:   30.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    3.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 178 ASN
A 595 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.160952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.109607 restraints weight = 18400.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.107489 restraints weight = 11523.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.108855 restraints weight = 10238.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.108907 restraints weight = 7720.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.109281 restraints weight = 7315.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  11986  Z= 0.231
  Angle     :  0.597   8.516  16831  Z= 0.340
  Chirality :  0.042   0.245   1944
  Planarity :  0.005   0.067   1601
  Dihedral  : 19.405 179.206   3143
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.27 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  7.56 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.26), residues: 1009
  helix:  1.63 (0.23), residues: 516
  sheet:  1.05 (0.51), residues: 104
  loop :  0.03 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A  71 
 TYR   0.022   0.002   TYR A   5 
 PHE   0.018   0.002   PHE A1258 
 TRP   0.008   0.002   TRP A1126 
 HIS   0.007   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00501 /  0.23 (11986)
  covalent geometry    : angle       0.59685 /  0.34 (16831)
  hydrogen bonds       : bond        0.06160 /  3.99 (  546)
  hydrogen bonds       : angle       4.56999 /  3.32 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 ASP cc_start: 0.8671 (m-30) cc_final: 0.8357 (p0)
REVERT: A  465 MET cc_start: 0.8274 (ttp) cc_final: 0.8041 (tmm)
REVERT: A  618 ASP cc_start: 0.8775 (t70) cc_final: 0.8280 (t0)
REVERT: A  630 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8259 (mt-10)
REVERT: A  654 ARG cc_start: 0.7504 (tpt170) cc_final: 0.7085 (ttm170)
REVERT: A  762 GLU cc_start: 0.7812 (pp20) cc_final: 0.7195 (tm-30)
REVERT: A  942 LYS cc_start: 0.8423 (mmmt) cc_final: 0.7522 (mtpt)
REVERT: A  954 LYS cc_start: 0.8456 (mttt) cc_final: 0.8229 (mttm)
REVERT: A 1148 LYS cc_start: 0.8546 (mttt) cc_final: 0.7997 (mtpp)
REVERT: A 1230 SER cc_start: 0.7748 (m) cc_final: 0.7528 (t)
REVERT: A 1261 GLN cc_start: 0.8980 (mt0) cc_final: 0.8688 (mt0)
REVERT: A 1325 LYS cc_start: 0.8760 (mttt) cc_final: 0.8376 (ttmm)
REVERT: A 1326 TYR cc_start: 0.8332 (t80) cc_final: 0.8122 (t80)
REVERT: A 1339 THR cc_start: 0.9212 (p) cc_final: 0.8925 (t)
  outliers start: 20
  outliers final: 13
  residues processed: 132
  average time/residue: 0.0858
  time to fit residues: 16.3216
Evaluate side-chains
  102 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1106 SER
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 90 optimal weight:    5.9990
   chunk 112 optimal weight:   30.0000
   overall best weight:    2.6586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS
A 511 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.166662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.108561 restraints weight = 19348.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.112490 restraints weight = 9070.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.114859 restraints weight = 6303.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.116203 restraints weight = 5266.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.116535 restraints weight = 4800.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  11986  Z= 0.179
  Angle     :  0.534   9.653  16831  Z= 0.311
  Chirality :  0.041   0.254   1944
  Planarity :  0.004   0.056   1601
  Dihedral  : 19.446 178.723   3143
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.97 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  8.32 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.26), residues: 1009
  helix:  1.63 (0.23), residues: 516
  sheet:  0.94 (0.50), residues: 102
  loop : -0.10 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  71 
 TYR   0.026   0.001   TYR A   5 
 PHE   0.011   0.002   PHE A 478 
 TRP   0.006   0.001   TRP A1126 
 HIS   0.006   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.18 (11986)
  covalent geometry    : angle       0.53370 /  0.31 (16831)
  hydrogen bonds       : bond        0.05642 /  3.64 (  546)
  hydrogen bonds       : angle       4.31981 /  3.15 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.7990 (m-30) cc_final: 0.7367 (m-30)
REVERT: A  304 ASP cc_start: 0.8608 (m-30) cc_final: 0.8340 (p0)
REVERT: A  465 MET cc_start: 0.8341 (ttp) cc_final: 0.8016 (tmm)
REVERT: A  508 LEU cc_start: 0.8400 (mm) cc_final: 0.8188 (mp)
REVERT: A  618 ASP cc_start: 0.8801 (t70) cc_final: 0.8280 (t0)
REVERT: A  630 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8432 (mt-10)
REVERT: A  631 MET cc_start: 0.8486 (mmm) cc_final: 0.7783 (mmm)
REVERT: A  654 ARG cc_start: 0.7329 (tpt170) cc_final: 0.7018 (ttm170)
REVERT: A  762 GLU cc_start: 0.7868 (pp20) cc_final: 0.7074 (tm-30)
REVERT: A  954 LYS cc_start: 0.8397 (mttt) cc_final: 0.8032 (ttmm)
REVERT: A 1148 LYS cc_start: 0.8487 (mttt) cc_final: 0.8064 (mtpp)
REVERT: A 1226 LEU cc_start: 0.8982 (tt) cc_final: 0.8778 (tp)
REVERT: A 1261 GLN cc_start: 0.8951 (mt0) cc_final: 0.8659 (mt0)
REVERT: A 1339 THR cc_start: 0.9244 (p) cc_final: 0.8964 (t)
  outliers start: 20
  outliers final: 15
  residues processed: 116
  average time/residue: 0.0946
  time to fit residues: 16.2443
Evaluate side-chains
  103 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 106 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 96 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 111 optimal weight:    9.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 116 HIS
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1234 ASN
** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.161581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.103558 restraints weight = 19247.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.107176 restraints weight = 9146.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.109340 restraints weight = 6378.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.110560 restraints weight = 5354.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.110977 restraints weight = 4893.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  11986  Z= 0.314
  Angle     :  0.680   6.367  16831  Z= 0.377
  Chirality :  0.048   0.252   1944
  Planarity :  0.005   0.057   1601
  Dihedral  : 19.669 179.338   3143
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.77 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  :  9.42 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.26), residues: 1009
  helix:  1.27 (0.23), residues: 515
  sheet:  0.22 (0.48), residues: 112
  loop : -0.33 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1122 
 TYR   0.022   0.002   TYR A 988 
 PHE   0.023   0.002   PHE A 682 
 TRP   0.008   0.002   TRP A1126 
 HIS   0.006   0.002   HIS A1349 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00687 /  0.31 (11986)
  covalent geometry    : angle       0.68023 /  0.38 (16831)
  hydrogen bonds       : bond        0.07170 /  4.70 (  546)
  hydrogen bonds       : angle       4.51180 /  3.28 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 89
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.7970 (m-30) cc_final: 0.7345 (m-30)
REVERT: A  304 ASP cc_start: 0.8665 (m-30) cc_final: 0.8380 (p0)
REVERT: A  321 MET cc_start: 0.8990 (mmt) cc_final: 0.8592 (mmt)
REVERT: A  441 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7782 (mt-10)
REVERT: A  465 MET cc_start: 0.8397 (ttp) cc_final: 0.8163 (tmm)
REVERT: A  618 ASP cc_start: 0.8815 (t70) cc_final: 0.8329 (t0)
REVERT: A  630 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8368 (mt-10)
REVERT: A  631 MET cc_start: 0.8459 (mmm) cc_final: 0.7574 (mmm)
REVERT: A  653 ARG cc_start: 0.8215 (mtm-85) cc_final: 0.7870 (mtm-85)
REVERT: A  654 ARG cc_start: 0.7316 (tpt170) cc_final: 0.7052 (ttm170)
REVERT: A  954 LYS cc_start: 0.8463 (mttt) cc_final: 0.8090 (ttmm)
REVERT: A 1148 LYS cc_start: 0.8509 (mttt) cc_final: 0.8104 (mtpp)
REVERT: A 1261 GLN cc_start: 0.8929 (mt0) cc_final: 0.8667 (mt0)
REVERT: A 1303 ARG cc_start: 0.7686 (ptm-80) cc_final: 0.7439 (ptm-80)
REVERT: A 1325 LYS cc_start: 0.8855 (tttt) cc_final: 0.8381 (ttmm)
REVERT: A 1339 THR cc_start: 0.9289 (p) cc_final: 0.8997 (t)
  outliers start: 27
  outliers final: 20
  residues processed: 112
  average time/residue: 0.0983
  time to fit residues: 16.1276
Evaluate side-chains
  103 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1106 SER
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 107 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 110 optimal weight:   10.0000
   chunk 66 optimal weight:    8.9990
   chunk 73 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.6182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.166181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.107958 restraints weight = 19303.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.111892 restraints weight = 9087.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.114246 restraints weight = 6310.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.115267 restraints weight = 5273.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.116183 restraints weight = 4856.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11986  Z= 0.135
  Angle     :  0.506   7.496  16831  Z= 0.299
  Chirality :  0.039   0.253   1944
  Planarity :  0.004   0.052   1601
  Dihedral  : 19.564 177.641   3143
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.38 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 11.17 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.26), residues: 1009
  helix:  1.48 (0.23), residues: 515
  sheet:  0.32 (0.48), residues: 112
  loop : -0.36 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 951 
 TYR   0.027   0.001   TYR A   5 
 PHE   0.012   0.001   PHE A 164 
 TRP   0.005   0.001   TRP A 464 
 HIS   0.004   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.14 (11986)
  covalent geometry    : angle       0.50645 /  0.30 (16831)
  hydrogen bonds       : bond        0.05431 /  3.47 (  546)
  hydrogen bonds       : angle       4.18625 /  3.07 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.7948 (m-30) cc_final: 0.7262 (m-30)
REVERT: A  178 ASN cc_start: 0.6587 (m-40) cc_final: 0.6304 (m-40)
REVERT: A  304 ASP cc_start: 0.8609 (m-30) cc_final: 0.8346 (p0)
REVERT: A  321 MET cc_start: 0.9041 (mmt) cc_final: 0.8679 (mmt)
REVERT: A  465 MET cc_start: 0.8263 (ttp) cc_final: 0.8043 (tmm)
REVERT: A  508 LEU cc_start: 0.8533 (mp) cc_final: 0.8301 (mp)
REVERT: A  618 ASP cc_start: 0.8834 (t70) cc_final: 0.8341 (t0)
REVERT: A  630 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8380 (mt-10)
REVERT: A  631 MET cc_start: 0.8424 (mmm) cc_final: 0.7667 (mmm)
REVERT: A  648 MET cc_start: 0.7875 (mmt) cc_final: 0.7608 (mmt)
REVERT: A  654 ARG cc_start: 0.7288 (tpt170) cc_final: 0.7005 (ttm170)
REVERT: A  762 GLU cc_start: 0.7904 (pp20) cc_final: 0.7200 (tp30)
REVERT: A  954 LYS cc_start: 0.8421 (mttt) cc_final: 0.8046 (ttmm)
REVERT: A 1148 LYS cc_start: 0.8454 (mttt) cc_final: 0.7997 (mtpp)
REVERT: A 1261 GLN cc_start: 0.8885 (mt0) cc_final: 0.8600 (mt0)
REVERT: A 1303 ARG cc_start: 0.7586 (ptm-80) cc_final: 0.7345 (ptm-80)
REVERT: A 1325 LYS cc_start: 0.8815 (tttt) cc_final: 0.8354 (ttmm)
REVERT: A 1339 THR cc_start: 0.9257 (p) cc_final: 0.8958 (t)
  outliers start: 18
  outliers final: 14
  residues processed: 109
  average time/residue: 0.0906
  time to fit residues: 14.4818
Evaluate side-chains
  98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 22 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 112 optimal weight:   30.0000
   chunk 89 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   overall best weight:    2.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1234 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.164074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.106302 restraints weight = 19166.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.110080 restraints weight = 8956.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.112318 restraints weight = 6190.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.113573 restraints weight = 5162.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.114164 restraints weight = 4712.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11986  Z= 0.174
  Angle     :  0.535   9.568  16831  Z= 0.309
  Chirality :  0.041   0.252   1944
  Planarity :  0.004   0.050   1601
  Dihedral  : 19.525 178.050   3143
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.17 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.16 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.26), residues: 1009
  helix:  1.46 (0.23), residues: 515
  sheet:  0.28 (0.48), residues: 112
  loop : -0.42 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1122 
 TYR   0.024   0.001   TYR A   5 
 PHE   0.010   0.001   PHE A1258 
 TRP   0.004   0.001   TRP A1126 
 HIS   0.004   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.17 (11986)
  covalent geometry    : angle       0.53542 /  0.31 (16831)
  hydrogen bonds       : bond        0.05630 /  3.62 (  546)
  hydrogen bonds       : angle       4.18583 /  3.07 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.7958 (m-30) cc_final: 0.7254 (m-30)
REVERT: A  178 ASN cc_start: 0.6372 (m-40) cc_final: 0.6044 (m-40)
REVERT: A  304 ASP cc_start: 0.8512 (m-30) cc_final: 0.8293 (p0)
REVERT: A  321 MET cc_start: 0.9004 (mmt) cc_final: 0.8798 (mmt)
REVERT: A  508 LEU cc_start: 0.8646 (mp) cc_final: 0.8378 (mp)
REVERT: A  618 ASP cc_start: 0.8834 (t70) cc_final: 0.8341 (t0)
REVERT: A  630 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8347 (mt-10)
REVERT: A  631 MET cc_start: 0.8383 (mmm) cc_final: 0.7729 (mmm)
REVERT: A  648 MET cc_start: 0.7888 (mmt) cc_final: 0.7637 (mmt)
REVERT: A  654 ARG cc_start: 0.7297 (tpt170) cc_final: 0.7029 (ttm170)
REVERT: A  762 GLU cc_start: 0.7837 (pp20) cc_final: 0.7215 (tp30)
REVERT: A  951 ARG cc_start: 0.6769 (mtt-85) cc_final: 0.6564 (mtt-85)
REVERT: A  954 LYS cc_start: 0.8474 (mttt) cc_final: 0.8111 (ttmm)
REVERT: A 1148 LYS cc_start: 0.8462 (mttt) cc_final: 0.8187 (mtpp)
REVERT: A 1261 GLN cc_start: 0.8890 (mt0) cc_final: 0.8583 (mt0)
REVERT: A 1303 ARG cc_start: 0.7650 (ptm-80) cc_final: 0.7402 (ptm-80)
REVERT: A 1325 LYS cc_start: 0.8829 (tttt) cc_final: 0.8363 (ttmm)
REVERT: A 1339 THR cc_start: 0.9276 (p) cc_final: 0.8978 (t)
  outliers start: 21
  outliers final: 18
  residues processed: 107
  average time/residue: 0.0992
  time to fit residues: 15.6391
Evaluate side-chains
  104 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1106 SER
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1240 SER
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 102 optimal weight:   20.0000
   chunk 81 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 52 optimal weight:    0.4980
   chunk 3 optimal weight:    7.9990
   chunk 77 optimal weight:    0.0970
   chunk 51 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1234 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.158668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.108464 restraints weight = 18979.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.105919 restraints weight = 10492.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.108068 restraints weight = 9396.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.107590 restraints weight = 7165.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.110048 restraints weight = 6681.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11986  Z= 0.116
  Angle     :  0.485  10.733  16831  Z= 0.284
  Chirality :  0.038   0.251   1944
  Planarity :  0.004   0.048   1601
  Dihedral  : 19.448 177.132   3143
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.68 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.60 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.26), residues: 1009
  helix:  1.60 (0.24), residues: 515
  sheet:  0.51 (0.49), residues: 110
  loop : -0.37 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 653 
 TYR   0.026   0.001   TYR A   5 
 PHE   0.013   0.001   PHE A 164 
 TRP   0.005   0.001   TRP A 464 
 HIS   0.003   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.12 (11986)
  covalent geometry    : angle       0.48484 /  0.28 (16831)
  hydrogen bonds       : bond        0.04797 /  3.01 (  546)
  hydrogen bonds       : angle       3.98983 /  2.94 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.7916 (m-30) cc_final: 0.7205 (m-30)
REVERT: A  178 ASN cc_start: 0.6158 (m-40) cc_final: 0.5906 (m-40)
REVERT: A  321 MET cc_start: 0.8949 (mmt) cc_final: 0.8723 (mmt)
REVERT: A  508 LEU cc_start: 0.8874 (mp) cc_final: 0.8548 (mp)
REVERT: A  618 ASP cc_start: 0.8842 (t70) cc_final: 0.8326 (t0)
REVERT: A  630 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8356 (mt-10)
REVERT: A  631 MET cc_start: 0.8343 (mmm) cc_final: 0.7635 (mmm)
REVERT: A  653 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.8083 (mtm-85)
REVERT: A  762 GLU cc_start: 0.7827 (pp20) cc_final: 0.7203 (tp30)
REVERT: A  954 LYS cc_start: 0.8497 (mttt) cc_final: 0.8178 (ttmm)
REVERT: A 1261 GLN cc_start: 0.8896 (mt0) cc_final: 0.8569 (mt0)
REVERT: A 1303 ARG cc_start: 0.7546 (ptm-80) cc_final: 0.7299 (ptm-80)
REVERT: A 1317 ASN cc_start: 0.8247 (t0) cc_final: 0.8012 (t0)
REVERT: A 1325 LYS cc_start: 0.8812 (tttt) cc_final: 0.8439 (ttmm)
REVERT: A 1327 PHE cc_start: 0.7965 (m-80) cc_final: 0.7745 (m-80)
REVERT: A 1339 THR cc_start: 0.9237 (p) cc_final: 0.8880 (t)
  outliers start: 14
  outliers final: 8
  residues processed: 105
  average time/residue: 0.0903
  time to fit residues: 14.0476
Evaluate side-chains
  94 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0370
   chunk 69 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    1.3262

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.167103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.117523 restraints weight = 19152.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.119184 restraints weight = 10555.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.118612 restraints weight = 9079.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.118787 restraints weight = 6371.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.119814 restraints weight = 5960.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11986  Z= 0.123
  Angle     :  0.482   9.554  16831  Z= 0.282
  Chirality :  0.038   0.252   1944
  Planarity :  0.004   0.049   1601
  Dihedral  : 19.416 177.461   3143
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.68 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.60 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.27), residues: 1009
  helix:  1.62 (0.24), residues: 515
  sheet:  0.52 (0.49), residues: 111
  loop : -0.40 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 951 
 TYR   0.040   0.001   TYR A   5 
 PHE   0.010   0.001   PHE A 164 
 TRP   0.002   0.001   TRP A1126 
 HIS   0.003   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.12 (11986)
  covalent geometry    : angle       0.48159 /  0.28 (16831)
  hydrogen bonds       : bond        0.04812 /  3.02 (  546)
  hydrogen bonds       : angle       3.98374 /  2.92 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.7923 (m-30) cc_final: 0.7207 (m-30)
REVERT: A  618 ASP cc_start: 0.8794 (t70) cc_final: 0.8296 (t0)
REVERT: A  630 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8201 (pt0)
REVERT: A  631 MET cc_start: 0.8214 (mmm) cc_final: 0.7539 (mmm)
REVERT: A  653 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7998 (mtm-85)
REVERT: A  762 GLU cc_start: 0.7847 (pp20) cc_final: 0.7228 (tp30)
REVERT: A  954 LYS cc_start: 0.8479 (mttt) cc_final: 0.8177 (ttmm)
REVERT: A 1261 GLN cc_start: 0.8899 (mt0) cc_final: 0.8587 (mt0)
REVERT: A 1303 ARG cc_start: 0.7564 (ptm-80) cc_final: 0.7327 (ptm-80)
REVERT: A 1317 ASN cc_start: 0.8237 (t0) cc_final: 0.8016 (t0)
REVERT: A 1325 LYS cc_start: 0.8805 (tttt) cc_final: 0.8434 (ttmm)
REVERT: A 1327 PHE cc_start: 0.7926 (m-80) cc_final: 0.7706 (m-80)
REVERT: A 1339 THR cc_start: 0.9250 (p) cc_final: 0.8891 (t)
  outliers start: 13
  outliers final: 10
  residues processed: 97
  average time/residue: 0.0939
  time to fit residues: 13.5311
Evaluate side-chains
  93 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0970
   chunk 97 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 70 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.3782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.166481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.109320 restraints weight = 18921.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.113136 restraints weight = 8830.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.115445 restraints weight = 6088.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.116644 restraints weight = 5076.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.117151 restraints weight = 4646.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11986  Z= 0.124
  Angle     :  0.482   6.836  16831  Z= 0.282
  Chirality :  0.037   0.252   1944
  Planarity :  0.003   0.048   1601
  Dihedral  : 19.400 177.470   3143
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.97 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.03 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.27), residues: 1009
  helix:  1.66 (0.24), residues: 514
  sheet:  0.49 (0.49), residues: 111
  loop : -0.41 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 951 
 TYR   0.013   0.001   TYR A   5 
 PHE   0.010   0.001   PHE A 164 
 TRP   0.005   0.001   TRP A 464 
 HIS   0.003   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.12 (11986)
  covalent geometry    : angle       0.48159 /  0.28 (16831)
  hydrogen bonds       : bond        0.04760 /  2.99 (  546)
  hydrogen bonds       : angle       3.93932 /  2.89 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.7922 (m-30) cc_final: 0.7198 (m-30)
REVERT: A  618 ASP cc_start: 0.8867 (t70) cc_final: 0.8360 (t0)
REVERT: A  630 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8223 (pt0)
REVERT: A  631 MET cc_start: 0.8260 (mmm) cc_final: 0.7619 (mmm)
REVERT: A  653 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7867 (mtm-85)
REVERT: A  762 GLU cc_start: 0.7933 (pp20) cc_final: 0.7120 (tp30)
REVERT: A  954 LYS cc_start: 0.8472 (mttt) cc_final: 0.8144 (ttmm)
REVERT: A 1234 ASN cc_start: 0.8778 (m-40) cc_final: 0.8317 (m110)
REVERT: A 1261 GLN cc_start: 0.8900 (mt0) cc_final: 0.8610 (mt0)
REVERT: A 1268 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7794 (mt-10)
REVERT: A 1303 ARG cc_start: 0.7568 (ptm-80) cc_final: 0.7333 (ptm-80)
REVERT: A 1317 ASN cc_start: 0.8291 (t0) cc_final: 0.8052 (t0)
REVERT: A 1325 LYS cc_start: 0.8813 (tttt) cc_final: 0.8431 (ttmm)
REVERT: A 1339 THR cc_start: 0.9250 (p) cc_final: 0.8894 (t)
  outliers start: 11
  outliers final: 9
  residues processed: 95
  average time/residue: 0.0893
  time to fit residues: 12.6411
Evaluate side-chains
  94 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 111 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 112 optimal weight:   30.0000
   chunk 65 optimal weight:    3.9990
   chunk 46 optimal weight:   50.0000
   chunk 80 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   chunk 113 optimal weight:   30.0000
   overall best weight:    1.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.165517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.108155 restraints weight = 19204.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.111940 restraints weight = 8934.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.114242 restraints weight = 6178.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.115324 restraints weight = 5138.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.116129 restraints weight = 4712.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11986  Z= 0.144
  Angle     :  0.497   7.442  16831  Z= 0.288
  Chirality :  0.038   0.251   1944
  Planarity :  0.003   0.049   1601
  Dihedral  : 19.407 177.544   3143
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.57 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.36 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.26), residues: 1009
  helix:  1.60 (0.24), residues: 513
  sheet:  0.62 (0.49), residues: 110
  loop : -0.41 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 664 
 TYR   0.010   0.001   TYR A 988 
 PHE   0.018   0.001   PHE A1327 
 TRP   0.003   0.001   TRP A 464 
 HIS   0.003   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 (11986)
  covalent geometry    : angle       0.49734 /  0.29 (16831)
  hydrogen bonds       : bond        0.04959 /  3.13 (  546)
  hydrogen bonds       : angle       3.96979 /  2.91 ( 1478)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.7944 (m-30) cc_final: 0.7215 (m-30)
REVERT: A  618 ASP cc_start: 0.8893 (t70) cc_final: 0.8392 (t0)
REVERT: A  630 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8232 (pt0)
REVERT: A  631 MET cc_start: 0.8273 (mmm) cc_final: 0.7588 (mmm)
REVERT: A  762 GLU cc_start: 0.7949 (pp20) cc_final: 0.7210 (tp30)
REVERT: A  954 LYS cc_start: 0.8485 (mttt) cc_final: 0.8158 (ttmm)
REVERT: A 1234 ASN cc_start: 0.8785 (m-40) cc_final: 0.8337 (m110)
REVERT: A 1261 GLN cc_start: 0.8904 (mt0) cc_final: 0.8617 (mt0)
REVERT: A 1268 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7819 (mt-10)
REVERT: A 1303 ARG cc_start: 0.7591 (ptm-80) cc_final: 0.7355 (ptm-80)
REVERT: A 1325 LYS cc_start: 0.8824 (tttt) cc_final: 0.8433 (ttmm)
REVERT: A 1327 PHE cc_start: 0.7994 (m-80) cc_final: 0.7776 (m-80)
REVERT: A 1339 THR cc_start: 0.9266 (p) cc_final: 0.8920 (t)
  outliers start: 13
  outliers final: 12
  residues processed: 95
  average time/residue: 0.0889
  time to fit residues: 12.4355
Evaluate side-chains
  96 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  751 MET
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1268 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 61 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 41 optimal weight:   30.0000
   chunk 55 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    0.5980
   chunk 95 optimal weight:   10.0000
   chunk 105 optimal weight:   50.0000
   chunk 63 optimal weight:    0.9980
   overall best weight:    2.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.157456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.098917 restraints weight = 18992.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.102752 restraints weight = 9010.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.105080 restraints weight = 6280.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.106437 restraints weight = 5242.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.106967 restraints weight = 4773.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11986  Z= 0.159
  Angle     :  0.527  11.802  16831  Z= 0.297
  Chirality :  0.039   0.250   1944
  Planarity :  0.003   0.048   1601
  Dihedral  : 19.435 177.424   3143
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.27 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.36 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.26), residues: 1009
  helix:  1.55 (0.23), residues: 514
  sheet:  0.44 (0.49), residues: 112
  loop : -0.40 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 653 
 TYR   0.010   0.001   TYR A 155 
 PHE   0.014   0.001   PHE A1327 
 TRP   0.003   0.001   TRP A1126 
 HIS   0.003   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.16 (11986)
  covalent geometry    : angle       0.52726 /  0.30 (16831)
  hydrogen bonds       : bond        0.05147 /  3.26 (  546)
  hydrogen bonds       : angle       3.98560 /  2.93 ( 1478)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1839.07 seconds
wall clock time: 32 minutes 23.56 seconds (1943.56 seconds total)