Starting phenix.real_space_refine
on Thu Jul  2 16:45:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jl1_61575/07_2026/9jl1_61575.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jl1_61575/07_2026/9jl1_61575.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jl1_61575/07_2026/9jl1_61575.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jl1_61575/07_2026/9jl1_61575.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jl1_61575/07_2026/9jl1_61575.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jl1_61575/07_2026/9jl1_61575.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
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      30      5.49       5
     S      16      5.16       5
     C    5601      2.51       5
     N    1579      2.21       5
     O    1777      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9003
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1026, 8358
          Classifications: {'peptide': 1026}
          Link IDs: {'PTRANS': 26, 'TRANS': 999}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 645
          Classifications: {'RNA': 30}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 4, 'rna3p': 25}
  Time building chain proxies: 1.91, per 1000 atoms: 0.21
  Number of scatterers: 9003
  At special positions: 0
  Unit cell: (91.74, 108.24, 111.54, 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      16     16.00
     P      30     15.00
     O    1777      8.00
     N    1579      7.00
     C    5601      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 274.3 milliseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 7 sheets defined
      55.7% alpha, 9.6% beta
      8 base pairs and 18 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 64
    Processing helix  chain 'A' and resid 67 through 92
    Processing helix  chain 'A' and resid 125 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.765A  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 175 through 179
    Processing helix  chain 'A' and resid 180 through 197
    Processing helix  chain 'A' and resid 207 through 213
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 3.632A  pdb=" N   LEU A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 247
    Processing helix  chain 'A' and resid 252 through 257
    Processing helix  chain 'A' and resid 270 through 283
    Processing helix  chain 'A' and resid 286 through 306
    Processing helix  chain 'A' and resid 315 through 339
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 369 through 383
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 388 through 395
    Processing helix  chain 'A' and resid 411 through 426
      removed outlier: 4.040A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.724A  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 719 through 726
    Processing helix  chain 'A' and resid 732 through 751
    Processing helix  chain 'A' and resid 771 through 792
      removed outlier: 3.874A  pdb=" N   LYS A 775 " --> pdb=" O   GLN A 771 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   SER A 777 " --> pdb=" O   GLY A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 799
    Processing helix  chain 'A' and resid 802 through 807
    Processing helix  chain 'A' and resid 808 through 817
    Processing helix  chain 'A' and resid 829 through 836
      removed outlier: 3.575A  pdb=" N   ARG A 832 " --> pdb=" O   ASP A 829 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   LEU A 833 " --> pdb=" O   ILE A 830 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   SER A 834 " --> pdb=" O   ASN A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 853
      No H-bonds generated for 'chain 'A' and resid 851 through 853'
    Processing helix  chain 'A' and resid 860 through 865
      removed outlier: 3.506A  pdb=" N   ASN A 863 " --> pdb=" O   SER A 860 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 889
      removed outlier: 3.719A  pdb=" N   VAL A 876 " --> pdb=" O   SER A 872 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS A 878 " --> pdb=" O   GLU A 874 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   ASN A 881 " --> pdb=" O   LYS A 877 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   TYR A 882 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 902
    Processing helix  chain 'A' and resid 909 through 922
    Processing helix  chain 'A' and resid 925 through 940
    Processing helix  chain 'A' and resid 959 through 971
      removed outlier: 4.289A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 1001
      removed outlier: 4.442A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1009
      removed outlier: 4.088A  pdb=" N   PHE A1008 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1043 through 1047
      removed outlier: 3.706A  pdb=" N   PHE A1046 " --> pdb=" O   MET A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1089
    Processing helix  chain 'A' and resid 1168 through 1177
      removed outlier: 4.379A  pdb=" N   SER A1172 " --> pdb=" O   ILE A1168 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   SER A1173 " --> pdb=" O   MET A1169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1186
    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 1249 through 1262
    Processing helix  chain 'A' and resid 1263 through 1281
      removed outlier: 4.396A  pdb=" N   ASP A1267 " --> pdb=" O   LYS A1263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1313
    Processing helix  chain 'A' and resid 1340 through 1344
    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: 5.925A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   TYR A   5 " --> pdb=" O   ASN A 758 " (cutoff:3.500A)
      removed outlier: 9.069A  pdb=" N   VAL A 760 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 8.403A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   LEU A   9 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 4.341A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 837 through 840
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1049 through 1051
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1063 through 1066
      removed outlier: 6.302A  pdb=" N   GLU A1064 " --> pdb=" O   VAL A1073 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLU A1071 " --> pdb=" O   ASN A1066 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.580A  pdb=" N   VAL A1149 " --> pdb=" O   LYS A1158 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL A1160 " --> pdb=" O   ALA A1147 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA A1147 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLU A1162 " --> pdb=" O   VAL A1145 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL A1145 " --> pdb=" O   GLU A1162 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325

    412 hydrogen bonds defined for protein.
    1182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      20 hydrogen bonds
      36 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      18 stacking parallelities
  Total time for adding SS restraints: 1.71

  Time building geometry restraints manager: 1.12 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: 2713
        1.34 -     1.45: 1367
        1.45 -     1.57: 5045
        1.57 -     1.69: 59
        1.69 -     1.81: 31
  Bond restraints: 9215
  Sorted by residual:
  bond pdb=" N   ASN A1177 "
       pdb=" CA  ASN A1177 "
    ideal  model  delta    sigma   weight residual
    1.463  1.490 -0.027 8.80e-03 1.29e+04 9.32e+00
  bond pdb=" N   ASP A 180 "
       pdb=" CA  ASP A 180 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.28e-02 6.10e+03 9.28e+00
  bond pdb=" N   VAL A 801 "
       pdb=" CA  VAL A 801 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.60e+00
  bond pdb=" N   ASN A 803 "
       pdb=" CA  ASN A 803 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.033 1.23e-02 6.61e+03 7.36e+00
  bond pdb=" N   GLU A 802 "
       pdb=" CA  GLU A 802 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.25e-02 6.40e+03 6.80e+00
  ... (remaining 9210 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 12128
        1.64 -     3.27: 336
        3.27 -     4.91: 60
        4.91 -     6.55: 6
        6.55 -     8.18: 4
  Bond angle restraints: 12534
  Sorted by residual:
  angle pdb=" C   VAL A 339 "
        pdb=" N   ARG A 340 "
        pdb=" CA  ARG A 340 "
      ideal   model   delta    sigma   weight residual
     121.54  129.04   -7.50 1.91e+00 2.74e-01 1.54e+01
  angle pdb=" N   ASN A 407 "
        pdb=" CA  ASN A 407 "
        pdb=" C   ASN A 407 "
      ideal   model   delta    sigma   weight residual
     114.56  109.80    4.76 1.27e+00 6.20e-01 1.40e+01
  angle pdb=" CA  ARG A  74 "
        pdb=" CB  ARG A  74 "
        pdb=" CG  ARG A  74 "
      ideal   model   delta    sigma   weight residual
     114.10  120.34   -6.24 2.00e+00 2.50e-01 9.74e+00
  angle pdb=" C   LYS A 183 "
        pdb=" N   LEU A 184 "
        pdb=" CA  LEU A 184 "
      ideal   model   delta    sigma   weight residual
     120.28  116.19    4.09 1.34e+00 5.57e-01 9.32e+00
  angle pdb=" CB  ARG A  74 "
        pdb=" CG  ARG A  74 "
        pdb=" CD  ARG A  74 "
      ideal   model   delta    sigma   weight residual
     111.30  104.65    6.65 2.30e+00 1.89e-01 8.36e+00
  ... (remaining 12529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.68: 5068
       16.68 -    33.36: 448
       33.36 -    50.05: 123
       50.05 -    66.73: 56
       66.73 -    83.41: 14
  Dihedral angle restraints: 5709
    sinusoidal: 2689
      harmonic: 3020
  Sorted by residual:
  dihedral pdb=" CA  GLU A 197 "
           pdb=" C   GLU A 197 "
           pdb=" N   GLU A 198 "
           pdb=" CA  GLU A 198 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.33   18.67     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  ARG A 925 "
           pdb=" C   ARG A 925 "
           pdb=" N   GLN A 926 "
           pdb=" CA  GLN A 926 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.05  -17.95     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  VAL A 339 "
           pdb=" C   VAL A 339 "
           pdb=" N   ARG A 340 "
           pdb=" CA  ARG A 340 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.37  -17.63     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 5706 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 978
       0.034 -    0.069: 302
       0.069 -    0.103: 110
       0.103 -    0.138: 27
       0.138 -    0.172: 4
  Chirality restraints: 1421
  Sorted by residual:
  chirality pdb=" CG  LEU A 184 "
            pdb=" CB  LEU A 184 "
            pdb=" CD1 LEU A 184 "
            pdb=" CD2 LEU A 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.43e-01
  chirality pdb=" CA  VAL A 801 "
            pdb=" N   VAL A 801 "
            pdb=" C   VAL A 801 "
            pdb=" CB  VAL A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CB  ILE A1057 "
            pdb=" CA  ILE A1057 "
            pdb=" CG1 ILE A1057 "
            pdb=" CG2 ILE A1057 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 1418 not shown)

  Planarity restraints: 1491
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1060 "    0.058 5.00e-02 4.00e+02   8.72e-02 1.22e+01
        pdb=" N   PRO A1061 "   -0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO A1061 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A1061 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 315 "   -0.044 5.00e-02 4.00e+02   6.69e-02 7.16e+00
        pdb=" N   PRO A 316 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 316 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 316 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 180 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.93e+00
        pdb=" C   ASP A 180 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ASP A 180 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 181 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1488 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1578
        2.77 -     3.30: 9058
        3.30 -     3.84: 15225
        3.84 -     4.37: 17409
        4.37 -     4.90: 28993
  Nonbonded interactions: 72263
  Sorted by model distance:
  nonbonded pdb=" O   PHE A1045 "
            pdb=" NZ  LYS A1076 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" N2    G B  87 "
            pdb=" O2    C B  91 "
     model   vdw
     2.264 2.496
  nonbonded pdb=" ND2 ASN A 240 "
            pdb=" OD1 ASN A 255 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" O   GLN A 817 "
            pdb=" OH  TYR A 882 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OE1 GLN A1272 "
            pdb=" N1    G B  89 "
     model   vdw
     2.280 3.120
  ... (remaining 72258 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:             5.560
  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:          0.290
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.180
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
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   0.053   9215  Z= 0.194
  Angle     :  0.668   8.184  12534  Z= 0.400
  Chirality :  0.040   0.172   1421
  Planarity :  0.005   0.087   1491
  Dihedral  : 15.098  83.411   3753
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.04 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  0.87 %
    Favored  : 98.37 %
  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: -0.03 (0.26), residues: 1014
  helix:  0.69 (0.23), residues: 509
  sheet: -0.25 (0.53), residues: 107
  loop : -0.77 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  71 
 TYR   0.022   0.001   TYR A  72 
 PHE   0.017   0.001   PHE A 970 
 TRP   0.010   0.001   TRP A 883 
 HIS   0.005   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.19 ( 9215)
  covalent geometry    : angle       0.66812 /  0.40 (12534)
  hydrogen bonds       : bond        0.13513 /  8.89 (  432)
  hydrogen bonds       : angle       5.87315 /  4.23 ( 1218)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 209
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8243 (tp) cc_final: 0.8036 (tt)
REVERT: A  195 LEU cc_start: 0.9010 (tp) cc_final: 0.8653 (tt)
REVERT: A 1169 MET cc_start: 0.7838 (mpp) cc_final: 0.7599 (mmm)
  outliers start: 7
  outliers final: 1
  residues processed: 213
  average time/residue: 0.1109
  time to fit residues: 30.3400
Evaluate side-chains
  106 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  912 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0980
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 329 HIS
A 726 ASN
** A 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 817 GLN
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 980 ASN
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1305 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.116231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.091827 restraints weight = 30264.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.094242 restraints weight = 16603.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.095706 restraints weight = 11473.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.096733 restraints weight = 9168.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.097248 restraints weight = 7989.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9215  Z= 0.159
  Angle     :  0.670  10.714  12534  Z= 0.352
  Chirality :  0.043   0.270   1421
  Planarity :  0.005   0.071   1491
  Dihedral  : 12.797  73.330   1582
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.16 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.02 %
    Favored  : 88.24 %
  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: -0.14 (0.25), residues: 1014
  helix:  0.56 (0.22), residues: 512
  sheet: -0.07 (0.54), residues: 99
  loop : -0.86 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG A 925 
 TYR   0.020   0.002   TYR A 815 
 PHE   0.028   0.002   PHE A1008 
 TRP   0.023   0.003   TRP A 883 
 HIS   0.004   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 ( 9215)
  covalent geometry    : angle       0.66983 /  0.35 (12534)
  hydrogen bonds       : bond        0.05638 /  3.52 (  432)
  hydrogen bonds       : angle       4.97667 /  3.52 ( 1218)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASN cc_start: 0.8360 (p0) cc_final: 0.8143 (p0)
REVERT: A   74 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8320 (ppt-90)
REVERT: A   80 CYS cc_start: 0.9355 (m) cc_final: 0.9045 (p)
REVERT: A  195 LEU cc_start: 0.9111 (tp) cc_final: 0.8805 (tt)
REVERT: A 1057 ILE cc_start: 0.8281 (mm) cc_final: 0.8013 (tp)
REVERT: A 1160 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.6976 (m)
REVERT: A 1169 MET cc_start: 0.8346 (mpp) cc_final: 0.7926 (mmm)
REVERT: A 1266 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7764 (tp)
  outliers start: 16
  outliers final: 9
  residues processed: 120
  average time/residue: 0.0935
  time to fit residues: 15.5015
Evaluate side-chains
  106 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ARG
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  288 ASP
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue  946 ASN
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1310 ILE
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 28 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0020
   chunk 75 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 57 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.3792

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 726 ASN
A 739 GLN
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN
A1177 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.114853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.090264 restraints weight = 29999.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.092624 restraints weight = 16611.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.094123 restraints weight = 11523.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.095078 restraints weight = 9230.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.095680 restraints weight = 8068.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9215  Z= 0.156
  Angle     :  0.623   9.024  12534  Z= 0.330
  Chirality :  0.042   0.206   1421
  Planarity :  0.005   0.068   1491
  Dihedral  : 12.828  73.472   1582
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.04 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.11 %
    Favored  : 87.15 %
  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: -0.01 (0.26), residues: 1014
  helix:  0.73 (0.23), residues: 500
  sheet: -0.13 (0.56), residues: 87
  loop : -0.79 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 895 
 TYR   0.026   0.002   TYR A  72 
 PHE   0.026   0.002   PHE A1174 
 TRP   0.029   0.003   TRP A 883 
 HIS   0.005   0.001   HIS A1262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.16 ( 9215)
  covalent geometry    : angle       0.62304 /  0.33 (12534)
  hydrogen bonds       : bond        0.05239 /  3.25 (  432)
  hydrogen bonds       : angle       4.82774 /  3.40 ( 1218)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 CYS cc_start: 0.9351 (m) cc_final: 0.9054 (p)
REVERT: A  132 TYR cc_start: 0.8027 (m-80) cc_final: 0.7494 (m-10)
REVERT: A 1062 LEU cc_start: 0.7881 (tp) cc_final: 0.7675 (mt)
REVERT: A 1169 MET cc_start: 0.8390 (mpp) cc_final: 0.7951 (mmm)
  outliers start: 16
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0818
  time to fit residues: 12.7269
Evaluate side-chains
  99 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  288 ASP
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue  946 ASN
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1310 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 97 optimal weight:    0.6980
   chunk 104 optimal weight:   10.0000
   chunk 62 optimal weight:    0.6980
   chunk 102 optimal weight:   20.0000
   chunk 95 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 87 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 160 HIS
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.115489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.090894 restraints weight = 29966.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.093276 restraints weight = 16487.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.094795 restraints weight = 11398.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.095728 restraints weight = 9092.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.096287 restraints weight = 7930.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9215  Z= 0.127
  Angle     :  0.580   8.019  12534  Z= 0.307
  Chirality :  0.040   0.241   1421
  Planarity :  0.004   0.066   1491
  Dihedral  : 12.795  73.501   1582
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.75 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.87 %
    Favored  : 86.27 %
  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: -0.00 (0.26), residues: 1014
  helix:  0.66 (0.23), residues: 512
  sheet: -0.45 (0.52), residues: 98
  loop : -0.62 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  71 
 TYR   0.016   0.001   TYR A 815 
 PHE   0.025   0.002   PHE A1174 
 TRP   0.032   0.003   TRP A 883 
 HIS   0.004   0.001   HIS A1262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 9215)
  covalent geometry    : angle       0.58034 /  0.31 (12534)
  hydrogen bonds       : bond        0.04850 /  3.01 (  432)
  hydrogen bonds       : angle       4.80749 /  3.39 ( 1218)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 CYS cc_start: 0.9354 (m) cc_final: 0.9070 (p)
REVERT: A  132 TYR cc_start: 0.8016 (m-80) cc_final: 0.7621 (m-10)
REVERT: A 1169 MET cc_start: 0.8380 (mpp) cc_final: 0.7941 (mmm)
  outliers start: 17
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0786
  time to fit residues: 11.5132
Evaluate side-chains
  91 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  779 GLU
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue  946 ASN
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1175 GLU
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1310 ILE
Chi-restraints excluded: chain A residue 1338 SER
Chi-restraints excluded: chain A residue 1347 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 23 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 83 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 92 optimal weight:    0.4980
   chunk 100 optimal weight:    0.0970
   chunk 64 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.2580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.114559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.089858 restraints weight = 30025.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.092212 restraints weight = 16536.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.093720 restraints weight = 11441.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.094667 restraints weight = 9162.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.095276 restraints weight = 7988.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9215  Z= 0.146
  Angle     :  0.579   8.081  12534  Z= 0.307
  Chirality :  0.042   0.270   1421
  Planarity :  0.004   0.066   1491
  Dihedral  : 12.798  73.561   1582
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.65 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.51 %
    Favored  : 84.20 %
  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:  0.06 (0.26), residues: 1014
  helix:  0.75 (0.23), residues: 511
  sheet: -0.58 (0.51), residues: 98
  loop : -0.59 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  71 
 TYR   0.032   0.001   TYR A1036 
 PHE   0.028   0.002   PHE A1008 
 TRP   0.040   0.004   TRP A 883 
 HIS   0.006   0.001   HIS A 137 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.15 ( 9215)
  covalent geometry    : angle       0.57878 /  0.31 (12534)
  hydrogen bonds       : bond        0.04771 /  2.98 (  432)
  hydrogen bonds       : angle       4.78832 /  3.36 ( 1218)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 CYS cc_start: 0.9362 (m) cc_final: 0.9069 (p)
REVERT: A  132 TYR cc_start: 0.8048 (m-80) cc_final: 0.7704 (m-10)
REVERT: A  328 HIS cc_start: 0.3949 (OUTLIER) cc_final: 0.3215 (t-170)
REVERT: A 1169 MET cc_start: 0.8425 (mpp) cc_final: 0.7988 (mmm)
  outliers start: 21
  outliers final: 15
  residues processed: 110
  average time/residue: 0.0888
  time to fit residues: 13.9530
Evaluate side-chains
  95 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  779 GLU
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue  946 ASN
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1175 GLU
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1310 ILE
Chi-restraints excluded: chain A residue 1347 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 10 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 96 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 412 HIS
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.114111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.089334 restraints weight = 30202.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.091636 restraints weight = 16736.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.093076 restraints weight = 11736.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.093988 restraints weight = 9476.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.094542 restraints weight = 8322.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9215  Z= 0.195
  Angle     :  0.603   8.635  12534  Z= 0.319
  Chirality :  0.042   0.198   1421
  Planarity :  0.005   0.067   1491
  Dihedral  : 12.851  73.613   1582
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.24 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.05 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.26), residues: 1014
  helix:  0.73 (0.23), residues: 515
  sheet: -0.89 (0.48), residues: 108
  loop : -0.61 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  74 
 TYR   0.017   0.001   TYR A 815 
 PHE   0.021   0.002   PHE A1008 
 TRP   0.044   0.004   TRP A 883 
 HIS   0.005   0.001   HIS A 137 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00444 /  0.19 ( 9215)
  covalent geometry    : angle       0.60255 /  0.32 (12534)
  hydrogen bonds       : bond        0.05017 /  3.12 (  432)
  hydrogen bonds       : angle       4.86952 /  3.43 ( 1218)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8720 (p)
REVERT: A   80 CYS cc_start: 0.9354 (m) cc_final: 0.9085 (p)
REVERT: A  132 TYR cc_start: 0.8059 (m-80) cc_final: 0.7761 (m-10)
REVERT: A  328 HIS cc_start: 0.3955 (OUTLIER) cc_final: 0.3212 (t-90)
REVERT: A 1169 MET cc_start: 0.8248 (mpp) cc_final: 0.7886 (mmm)
  outliers start: 20
  outliers final: 15
  residues processed: 99
  average time/residue: 0.0898
  time to fit residues: 13.1173
Evaluate side-chains
  93 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  779 GLU
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue  946 ASN
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1175 GLU
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1310 ILE
Chi-restraints excluded: chain A residue 1338 SER
Chi-restraints excluded: chain A residue 1347 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 86 optimal weight:    0.6980
   chunk 101 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 888 ASN
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.113623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.089058 restraints weight = 29833.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.091343 restraints weight = 16488.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.092802 restraints weight = 11508.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.093729 restraints weight = 9255.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.094249 restraints weight = 8092.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9215  Z= 0.177
  Angle     :  0.607  13.861  12534  Z= 0.318
  Chirality :  0.042   0.207   1421
  Planarity :  0.004   0.067   1491
  Dihedral  : 12.887  73.634   1582
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.25 %
    Favored  : 82.46 %
  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: -0.06 (0.26), residues: 1014
  helix:  0.73 (0.23), residues: 515
  sheet: -1.10 (0.45), residues: 113
  loop : -0.60 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  78 
 TYR   0.018   0.001   TYR A 814 
 PHE   0.027   0.002   PHE A1008 
 TRP   0.036   0.004   TRP A 883 
 HIS   0.005   0.001   HIS A 137 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.18 ( 9215)
  covalent geometry    : angle       0.60749 /  0.32 (12534)
  hydrogen bonds       : bond        0.04938 /  3.08 (  432)
  hydrogen bonds       : angle       4.90378 /  3.45 ( 1218)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8739 (p)
REVERT: A   80 CYS cc_start: 0.9350 (m) cc_final: 0.9084 (p)
REVERT: A  132 TYR cc_start: 0.8040 (m-80) cc_final: 0.7779 (m-10)
REVERT: A  328 HIS cc_start: 0.3878 (OUTLIER) cc_final: 0.3151 (t-90)
REVERT: A 1169 MET cc_start: 0.8274 (mpp) cc_final: 0.7922 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 93
  average time/residue: 0.0853
  time to fit residues: 11.8853
Evaluate side-chains
  96 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  779 GLU
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue  946 ASN
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1175 GLU
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1310 ILE
Chi-restraints excluded: chain A residue 1338 SER
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 93 optimal weight:    0.7980
   chunk 82 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 92 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.114611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.090129 restraints weight = 29697.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.092473 restraints weight = 16390.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.093963 restraints weight = 11357.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.094851 restraints weight = 9100.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.095404 restraints weight = 8007.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.3783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9215  Z= 0.126
  Angle     :  0.585  15.204  12534  Z= 0.306
  Chirality :  0.041   0.238   1421
  Planarity :  0.004   0.064   1491
  Dihedral  : 12.864  73.653   1582
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.14 %
    Favored  : 82.68 %
  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:  0.02 (0.26), residues: 1014
  helix:  0.75 (0.23), residues: 516
  sheet: -0.90 (0.47), residues: 107
  loop : -0.59 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  78 
 TYR   0.017   0.001   TYR A 815 
 PHE   0.031   0.001   PHE A1008 
 TRP   0.025   0.003   TRP A 883 
 HIS   0.004   0.001   HIS A 137 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 9215)
  covalent geometry    : angle       0.58518 /  0.31 (12534)
  hydrogen bonds       : bond        0.04625 /  2.88 (  432)
  hydrogen bonds       : angle       4.82396 /  3.39 ( 1218)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8756 (p)
REVERT: A   80 CYS cc_start: 0.9366 (m) cc_final: 0.9085 (p)
REVERT: A  132 TYR cc_start: 0.8020 (m-80) cc_final: 0.7744 (m-10)
REVERT: A  328 HIS cc_start: 0.3848 (OUTLIER) cc_final: 0.3149 (t-90)
REVERT: A 1169 MET cc_start: 0.8319 (mpp) cc_final: 0.7939 (mmm)
  outliers start: 20
  outliers final: 16
  residues processed: 96
  average time/residue: 0.0857
  time to fit residues: 12.2741
Evaluate side-chains
  93 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  779 GLU
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue  946 ASN
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1175 GLU
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1310 ILE
Chi-restraints excluded: chain A residue 1338 SER
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0870
   chunk 92 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 63 optimal weight:    0.0370
   overall best weight:    0.5836

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.115001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.090621 restraints weight = 29452.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.092977 restraints weight = 16249.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.094467 restraints weight = 11223.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.095399 restraints weight = 8965.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.095848 restraints weight = 7841.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.3884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9215  Z= 0.114
  Angle     :  0.574  15.315  12534  Z= 0.299
  Chirality :  0.040   0.198   1421
  Planarity :  0.004   0.062   1491
  Dihedral  : 12.832  73.635   1582
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.58 %
    Favored  : 82.35 %
  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:  0.08 (0.26), residues: 1014
  helix:  0.78 (0.23), residues: 516
  sheet: -0.81 (0.48), residues: 107
  loop : -0.54 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  78 
 TYR   0.020   0.001   TYR A 814 
 PHE   0.031   0.001   PHE A1008 
 TRP   0.021   0.002   TRP A 883 
 HIS   0.004   0.001   HIS A1262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 ( 9215)
  covalent geometry    : angle       0.57393 /  0.30 (12534)
  hydrogen bonds       : bond        0.04449 /  2.78 (  432)
  hydrogen bonds       : angle       4.78353 /  3.36 ( 1218)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8765 (p)
REVERT: A   80 CYS cc_start: 0.9352 (m) cc_final: 0.9070 (p)
REVERT: A  132 TYR cc_start: 0.8012 (m-80) cc_final: 0.7797 (m-10)
REVERT: A  328 HIS cc_start: 0.3823 (OUTLIER) cc_final: 0.3170 (t-90)
REVERT: A 1169 MET cc_start: 0.8335 (mpp) cc_final: 0.7949 (mmm)
  outliers start: 19
  outliers final: 17
  residues processed: 94
  average time/residue: 0.0766
  time to fit residues: 10.8816
Evaluate side-chains
  94 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  779 GLU
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue  946 ASN
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1175 GLU
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1310 ILE
Chi-restraints excluded: chain A residue 1338 SER
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0670
   chunk 32 optimal weight:    9.9990
   chunk 59 optimal weight:    0.0050
   chunk 98 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 97 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    1.8138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.113580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.089083 restraints weight = 29667.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.091377 restraints weight = 16487.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.092804 restraints weight = 11493.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.093738 restraints weight = 9237.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.094090 restraints weight = 8087.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9215  Z= 0.168
  Angle     :  0.598  14.500  12534  Z= 0.314
  Chirality :  0.041   0.196   1421
  Planarity :  0.004   0.064   1491
  Dihedral  : 12.866  73.603   1582
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.58 %
    Favored  : 82.46 %
  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:  0.05 (0.26), residues: 1014
  helix:  0.81 (0.23), residues: 516
  sheet: -1.10 (0.46), residues: 113
  loop : -0.53 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  78 
 TYR   0.018   0.001   TYR A 271 
 PHE   0.021   0.002   PHE A1008 
 TRP   0.019   0.002   TRP A 883 
 HIS   0.004   0.001   HIS A1262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.17 ( 9215)
  covalent geometry    : angle       0.59750 /  0.31 (12534)
  hydrogen bonds       : bond        0.04692 /  2.93 (  432)
  hydrogen bonds       : angle       4.81192 /  3.37 ( 1218)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8772 (p)
REVERT: A   80 CYS cc_start: 0.9370 (m) cc_final: 0.9076 (p)
REVERT: A  132 TYR cc_start: 0.8037 (m-80) cc_final: 0.7836 (m-10)
REVERT: A  328 HIS cc_start: 0.3949 (OUTLIER) cc_final: 0.3247 (t-90)
REVERT: A 1169 MET cc_start: 0.8358 (mpp) cc_final: 0.7972 (mmm)
  outliers start: 18
  outliers final: 14
  residues processed: 92
  average time/residue: 0.0716
  time to fit residues: 9.8746
Evaluate side-chains
  89 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue  946 ASN
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1175 GLU
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1310 ILE
Chi-restraints excluded: chain A residue 1338 SER
Chi-restraints excluded: chain A residue 1347 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 10 optimal weight:    0.1980
   chunk 19 optimal weight:    0.3980
   chunk 89 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 844 GLN
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.114687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.090381 restraints weight = 29199.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.092692 restraints weight = 16164.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.094166 restraints weight = 11243.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.095076 restraints weight = 9004.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.095647 restraints weight = 7880.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9215  Z= 0.117
  Angle     :  0.589  15.297  12534  Z= 0.308
  Chirality :  0.041   0.178   1421
  Planarity :  0.004   0.062   1491
  Dihedral  : 12.843  73.630   1582
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.90 %
    Favored  : 82.35 %
  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:  0.07 (0.26), residues: 1014
  helix:  0.78 (0.23), residues: 516
  sheet: -0.91 (0.48), residues: 107
  loop : -0.53 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  78 
 TYR   0.021   0.001   TYR A 814 
 PHE   0.030   0.001   PHE A1008 
 TRP   0.019   0.002   TRP A 883 
 HIS   0.004   0.001   HIS A1262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 9215)
  covalent geometry    : angle       0.58890 /  0.31 (12534)
  hydrogen bonds       : bond        0.04441 /  2.79 (  432)
  hydrogen bonds       : angle       4.81763 /  3.38 ( 1218)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1723.62 seconds
wall clock time: 30 minutes 40.11 seconds (1840.11 seconds total)