Starting phenix.real_space_refine
on Wed Feb  4 06:50:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jl1_61575/02_2026/9jl1_61575.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jl1_61575/02_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jl1_61575/02_2026/9jl1_61575.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jl1_61575/02_2026/9jl1_61575.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jl1_61575/02_2026/9jl1_61575.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jl1_61575/02_2026/9jl1_61575.map"
  }
  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-2.0-5952/lib/python3.9/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: 2.08, per 1000 atoms: 0.23
  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: 0.83
  Conformation dependent library (CDL) restraints added in 577.3 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: 0.93
  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: 1.41

  Time building geometry restraints manager: 1.05 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.840
  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:         0.030
  Set scattering table:                    0.060
  Process input model:                     10.500
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
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= 0.192
  Angle     :  0.668   8.184  12534  Z= 0.396
  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
  covalent geometry    : bond        0.00337 ( 9215)
  covalent geometry    : angle       0.66811 (12534)
  hydrogen bonds       : bond        0.13513 (  432)
  hydrogen bonds       : angle       5.87315 ( 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  : 0.251 
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: 0.1201
  time to fit residues: 32.5254
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  : 0.223 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
A 329 HIS
A 739 GLN
A 817 GLN
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 980 ASN
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1177 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 = 0.4160 r_free = 0.4160 target = 0.115972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.091592 restraints weight = 30223.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.094015 restraints weight = 16554.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.095569 restraints weight = 11417.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.096517 restraints weight = 9096.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.097137 restraints weight = 7940.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9215  Z= 0.139
  Angle     :  0.643  10.373  12534  Z= 0.332
  Chirality :  0.042   0.210   1421
  Planarity :  0.005   0.071   1491
  Dihedral  : 12.793  73.667   1582
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.16 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  9.48 %
    Favored  : 88.56 %
  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:  0.68 (0.23), residues: 515
  sheet: -0.04 (0.56), residues: 87
  loop : -0.78 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 895 
 TYR   0.021   0.002   TYR A  72 
 PHE   0.028   0.002   PHE A1008 
 TRP   0.019   0.002   TRP A 883 
 HIS   0.005   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9215)
  covalent geometry    : angle       0.64322 (12534)
  hydrogen bonds       : bond        0.04920 (  432)
  hydrogen bonds       : angle       4.85177 ( 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
  129 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.242 
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   74 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8429 (ppt-90)
REVERT: A   80 CYS cc_start: 0.9388 (m) cc_final: 0.9029 (p)
REVERT: A  195 LEU cc_start: 0.9119 (tp) cc_final: 0.8842 (tt)
REVERT: A 1057 ILE cc_start: 0.8317 (mm) cc_final: 0.8079 (tp)
REVERT: A 1160 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7119 (p)
REVERT: A 1161 LYS cc_start: 0.6871 (ttmt) cc_final: 0.6671 (ttpt)
REVERT: A 1169 MET cc_start: 0.8404 (mpp) cc_final: 0.7940 (mmm)
  outliers start: 18
  outliers final: 12
  residues processed: 125
  average time/residue: 0.0915
  time to fit residues: 15.5542
Evaluate side-chains
  103 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ARG
Chi-restraints excluded: chain A residue  179 SER
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 1338 SER
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:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 61 optimal weight:    0.1980
   chunk 57 optimal weight:    8.9990
   chunk 11 optimal weight:   20.0000
   chunk 82 optimal weight:    0.3980
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1177 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.113293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.089118 restraints weight = 29954.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.091418 restraints weight = 16554.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.092843 restraints weight = 11508.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.093720 restraints weight = 9286.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.094070 restraints weight = 8170.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9215  Z= 0.201
  Angle     :  0.632   8.006  12534  Z= 0.334
  Chirality :  0.042   0.180   1421
  Planarity :  0.005   0.073   1491
  Dihedral  : 12.916  73.661   1582
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.65 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.87 %
    Favored  : 85.95 %
  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: -0.04 (0.26), residues: 1014
  helix:  0.78 (0.23), residues: 507
  sheet: -0.53 (0.50), residues: 107
  loop : -0.83 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1060 
 TYR   0.025   0.002   TYR A 814 
 PHE   0.024   0.002   PHE A1174 
 TRP   0.030   0.003   TRP A 883 
 HIS   0.006   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 9215)
  covalent geometry    : angle       0.63170 (12534)
  hydrogen bonds       : bond        0.05122 (  432)
  hydrogen bonds       : angle       4.83587 ( 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
  116 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.275 
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: 0.9391 (m) cc_final: 0.9102 (p)
REVERT: A  132 TYR cc_start: 0.8021 (m-80) cc_final: 0.7657 (m-10)
REVERT: A  328 HIS cc_start: 0.3992 (OUTLIER) cc_final: 0.3300 (t-90)
REVERT: A  888 ASN cc_start: 0.7687 (m-40) cc_final: 0.7444 (p0)
REVERT: A 1062 LEU cc_start: 0.8004 (tp) cc_final: 0.7750 (mt)
REVERT: A 1160 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7646 (p)
REVERT: A 1161 LYS cc_start: 0.7187 (ttmt) cc_final: 0.6878 (ttpt)
REVERT: A 1169 MET cc_start: 0.8339 (mpp) cc_final: 0.7926 (mmm)
  outliers start: 20
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0903
  time to fit residues: 13.9217
Evaluate side-chains
  98 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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  328 HIS
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 1073 VAL
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1160 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 1351 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 52 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9980
   chunk 104 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 102 optimal weight:   10.0000
   chunk 95 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.113188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.088774 restraints weight = 30008.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.091091 restraints weight = 16450.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.092517 restraints weight = 11463.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.093412 restraints weight = 9226.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.093837 restraints weight = 8101.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9215  Z= 0.160
  Angle     :  0.583   6.713  12534  Z= 0.310
  Chirality :  0.040   0.171   1421
  Planarity :  0.004   0.068   1491
  Dihedral  : 12.887  73.682   1582
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.65 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 12.53 %
    Favored  : 84.97 %
  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:  0.71 (0.23), residues: 520
  sheet: -0.67 (0.48), residues: 106
  loop : -0.75 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  71 
 TYR   0.016   0.001   TYR A 815 
 PHE   0.021   0.001   PHE A1174 
 TRP   0.013   0.002   TRP A 883 
 HIS   0.004   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9215)
  covalent geometry    : angle       0.58348 (12534)
  hydrogen bonds       : bond        0.04743 (  432)
  hydrogen bonds       : angle       4.76256 ( 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
  111 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.345 
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   71 ARG cc_start: 0.8085 (mmp80) cc_final: 0.7843 (mmp-170)
REVERT: A   80 CYS cc_start: 0.9400 (m) cc_final: 0.9116 (p)
REVERT: A  132 TYR cc_start: 0.7942 (m-80) cc_final: 0.7664 (m-10)
REVERT: A  328 HIS cc_start: 0.3950 (OUTLIER) cc_final: 0.3276 (t-90)
REVERT: A 1062 LEU cc_start: 0.8038 (tp) cc_final: 0.7765 (mt)
REVERT: A 1160 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7885 (p)
REVERT: A 1169 MET cc_start: 0.8226 (mpp) cc_final: 0.7886 (mmm)
  outliers start: 23
  outliers final: 15
  residues processed: 105
  average time/residue: 0.0926
  time to fit residues: 13.7846
Evaluate side-chains
  96 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  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 1160 VAL
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:    4.9990
   chunk 21 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.113866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.089660 restraints weight = 29834.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.091985 restraints weight = 16392.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.093462 restraints weight = 11363.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.094373 restraints weight = 9110.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.094831 restraints weight = 7996.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9215  Z= 0.123
  Angle     :  0.554   6.228  12534  Z= 0.292
  Chirality :  0.040   0.202   1421
  Planarity :  0.004   0.065   1491
  Dihedral  : 12.826  73.652   1582
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.65 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.27 %
    Favored  : 83.66 %
  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:  0.82 (0.23), residues: 520
  sheet: -0.74 (0.48), residues: 108
  loop : -0.68 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 895 
 TYR   0.021   0.001   TYR A 814 
 PHE   0.021   0.001   PHE A1174 
 TRP   0.008   0.001   TRP A 883 
 HIS   0.004   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9215)
  covalent geometry    : angle       0.55443 (12534)
  hydrogen bonds       : bond        0.04418 (  432)
  hydrogen bonds       : angle       4.73028 ( 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
  106 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 ARG cc_start: 0.8016 (mmp80) cc_final: 0.7554 (mmp-170)
REVERT: A   74 ARG cc_start: 0.8079 (ttp80) cc_final: 0.6296 (ttp80)
REVERT: A   80 CYS cc_start: 0.9381 (m) cc_final: 0.9102 (p)
REVERT: A  132 TYR cc_start: 0.7914 (m-80) cc_final: 0.7704 (m-10)
REVERT: A 1062 LEU cc_start: 0.7980 (tp) cc_final: 0.7703 (mt)
REVERT: A 1160 VAL cc_start: 0.8106 (p) cc_final: 0.7763 (p)
REVERT: A 1169 MET cc_start: 0.8205 (mpp) cc_final: 0.7833 (mmm)
  outliers start: 19
  outliers final: 16
  residues processed: 102
  average time/residue: 0.0827
  time to fit residues: 12.1295
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  : 0.340 
-------------------------------------------------------------------------------
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  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  946 ASN
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1211 LYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 926 GLN
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1177 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.112472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.088082 restraints weight = 29898.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.090378 restraints weight = 16429.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.091842 restraints weight = 11462.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.092735 restraints weight = 9203.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.093185 restraints weight = 8089.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9215  Z= 0.153
  Angle     :  0.559   6.113  12534  Z= 0.297
  Chirality :  0.040   0.132   1421
  Planarity :  0.004   0.065   1491
  Dihedral  : 12.817  73.606   1580
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.94 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.92 %
    Favored  : 83.01 %
  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:  0.04 (0.26), residues: 1014
  helix:  0.88 (0.23), residues: 523
  sheet: -1.01 (0.46), residues: 108
  loop : -0.73 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 895 
 TYR   0.020   0.001   TYR A1036 
 PHE   0.008   0.001   PHE A1181 
 TRP   0.007   0.001   TRP A 883 
 HIS   0.004   0.001   HIS A 799 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9215)
  covalent geometry    : angle       0.55886 (12534)
  hydrogen bonds       : bond        0.04517 (  432)
  hydrogen bonds       : angle       4.68363 ( 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
  107 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 CYS cc_start: 0.9391 (m) cc_final: 0.9069 (p)
REVERT: A  328 HIS cc_start: 0.3973 (OUTLIER) cc_final: 0.3301 (t-90)
REVERT: A  822 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6421 (ttm)
REVERT: A 1160 VAL cc_start: 0.8314 (p) cc_final: 0.7874 (p)
REVERT: A 1169 MET cc_start: 0.8265 (mpp) cc_final: 0.7864 (mmm)
  outliers start: 19
  outliers final: 14
  residues processed: 103
  average time/residue: 0.0855
  time to fit residues: 12.4409
Evaluate side-chains
  94 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
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  328 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  822 MET
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 1211 LYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 844 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.110015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.085753 restraints weight = 30144.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.087988 restraints weight = 17028.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.089367 restraints weight = 11994.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.090234 restraints weight = 9703.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.090622 restraints weight = 8560.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.4525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9215  Z= 0.200
  Angle     :  0.624  14.259  12534  Z= 0.332
  Chirality :  0.043   0.243   1421
  Planarity :  0.004   0.065   1491
  Dihedral  : 12.937  73.571   1580
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.80 %
    Favored  : 81.70 %
  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: -0.15 (0.26), residues: 1014
  helix:  0.72 (0.23), residues: 516
  sheet: -1.26 (0.44), residues: 112
  loop : -0.73 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 778 
 TYR   0.017   0.002   TYR A 271 
 PHE   0.020   0.002   PHE A1174 
 TRP   0.005   0.002   TRP A  18 
 HIS   0.005   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 9215)
  covalent geometry    : angle       0.62352 (12534)
  hydrogen bonds       : bond        0.04882 (  432)
  hydrogen bonds       : angle       4.93574 ( 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
  102 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 CYS cc_start: 0.9410 (m) cc_final: 0.9112 (p)
REVERT: A  328 HIS cc_start: 0.3974 (OUTLIER) cc_final: 0.3287 (t-90)
REVERT: A  436 ASN cc_start: 0.8685 (t0) cc_final: 0.7621 (p0)
REVERT: A 1160 VAL cc_start: 0.8377 (p) cc_final: 0.8015 (p)
REVERT: A 1169 MET cc_start: 0.8370 (mpp) cc_final: 0.8004 (mmm)
  outliers start: 23
  outliers final: 18
  residues processed: 96
  average time/residue: 0.0865
  time to fit residues: 11.8774
Evaluate side-chains
  95 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
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  288 ASP
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  946 ASN
Chi-restraints excluded: chain A residue 1043 MET
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 1211 LYS
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:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 92 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.112030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.087486 restraints weight = 30850.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.089820 restraints weight = 17333.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.091258 restraints weight = 12164.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.092197 restraints weight = 9842.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.092751 restraints weight = 8640.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9215  Z= 0.123
  Angle     :  0.578  14.614  12534  Z= 0.303
  Chirality :  0.041   0.202   1421
  Planarity :  0.004   0.063   1491
  Dihedral  : 12.857  73.550   1580
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.45 %
    Favored  : 81.37 %
  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: -0.01 (0.26), residues: 1014
  helix:  0.82 (0.23), residues: 516
  sheet: -0.98 (0.46), residues: 108
  loop : -0.72 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 403 
 TYR   0.016   0.001   TYR A 814 
 PHE   0.011   0.001   PHE A1174 
 TRP   0.006   0.001   TRP A  18 
 HIS   0.004   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9215)
  covalent geometry    : angle       0.57826 (12534)
  hydrogen bonds       : bond        0.04336 (  432)
  hydrogen bonds       : angle       4.82985 ( 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
  94 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 CYS cc_start: 0.9419 (m) cc_final: 0.9130 (p)
REVERT: A  328 HIS cc_start: 0.3960 (OUTLIER) cc_final: 0.3339 (t-90)
REVERT: A  436 ASN cc_start: 0.8569 (t0) cc_final: 0.7688 (p0)
REVERT: A 1169 MET cc_start: 0.8328 (mpp) cc_final: 0.7967 (mmm)
  outliers start: 20
  outliers final: 14
  residues processed: 89
  average time/residue: 0.0799
  time to fit residues: 10.6563
Evaluate side-chains
  88 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
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  838 VAL
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 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:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A1305 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.109448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.085127 restraints weight = 29958.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.087389 restraints weight = 16467.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.088776 restraints weight = 11502.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.089681 restraints weight = 9280.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.090068 restraints weight = 8151.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9215  Z= 0.204
  Angle     :  0.645  14.532  12534  Z= 0.340
  Chirality :  0.043   0.185   1421
  Planarity :  0.005   0.063   1491
  Dihedral  : 13.016  73.566   1580
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.78 %
    Favored  : 81.59 %
  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: -0.22 (0.26), residues: 1014
  helix:  0.65 (0.23), residues: 527
  sheet: -1.29 (0.46), residues: 112
  loop : -0.79 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1303 
 TYR   0.019   0.002   TYR A 814 
 PHE   0.011   0.002   PHE A1235 
 TRP   0.007   0.002   TRP A1074 
 HIS   0.007   0.001   HIS A 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 9215)
  covalent geometry    : angle       0.64546 (12534)
  hydrogen bonds       : bond        0.05011 (  432)
  hydrogen bonds       : angle       4.93972 ( 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
  87 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 CYS cc_start: 0.9394 (m) cc_final: 0.9080 (p)
REVERT: A  132 TYR cc_start: 0.8095 (m-10) cc_final: 0.7875 (m-80)
REVERT: A  328 HIS cc_start: 0.3950 (OUTLIER) cc_final: 0.3261 (t-90)
REVERT: A  436 ASN cc_start: 0.8573 (t0) cc_final: 0.7677 (p0)
REVERT: A 1169 MET cc_start: 0.8306 (mpp) cc_final: 0.8104 (mmm)
  outliers start: 15
  outliers final: 14
  residues processed: 84
  average time/residue: 0.0754
  time to fit residues: 9.3723
Evaluate side-chains
  85 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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  328 HIS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  841 ILE
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 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:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   chunk 68 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 415 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.109588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.083834 restraints weight = 30547.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.086156 restraints weight = 17195.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.087624 restraints weight = 12136.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.088537 restraints weight = 9854.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.089055 restraints weight = 8686.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.5121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9215  Z= 0.191
  Angle     :  0.635  14.483  12534  Z= 0.332
  Chirality :  0.042   0.172   1421
  Planarity :  0.005   0.063   1491
  Dihedral  : 13.042  73.424   1580
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.99 %
    Favored  : 81.15 %
  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: -0.29 (0.26), residues: 1014
  helix:  0.64 (0.23), residues: 528
  sheet: -1.19 (0.47), residues: 106
  loop : -0.95 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 403 
 TYR   0.018   0.001   TYR A 814 
 PHE   0.012   0.002   PHE A 375 
 TRP   0.005   0.002   TRP A 883 
 HIS   0.004   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 9215)
  covalent geometry    : angle       0.63465 (12534)
  hydrogen bonds       : bond        0.04806 (  432)
  hydrogen bonds       : angle       4.95253 ( 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
  88 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 CYS cc_start: 0.9446 (m) cc_final: 0.9120 (p)
REVERT: A  328 HIS cc_start: 0.3966 (OUTLIER) cc_final: 0.3420 (t-90)
REVERT: A 1169 MET cc_start: 0.8402 (mpp) cc_final: 0.8021 (mmm)
  outliers start: 17
  outliers final: 15
  residues processed: 85
  average time/residue: 0.0767
  time to fit residues: 9.5808
Evaluate side-chains
  83 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
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  288 ASP
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  838 VAL
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 1073 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
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 93 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 342 GLN
** A1305 GLN ** 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 = 0.4065 r_free = 0.4065 target = 0.109493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.084875 restraints weight = 30407.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.087145 restraints weight = 17150.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.088591 restraints weight = 12124.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.089486 restraints weight = 9804.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.089919 restraints weight = 8625.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.5283

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= 0.174
  Angle     :  0.629  14.915  12534  Z= 0.331
  Chirality :  0.042   0.306   1421
  Planarity :  0.004   0.063   1491
  Dihedral  : 13.013  73.399   1580
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.21 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.26), residues: 1014
  helix:  0.72 (0.23), residues: 521
  sheet: -1.37 (0.46), residues: 114
  loop : -0.83 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 403 
 TYR   0.016   0.002   TYR A 815 
 PHE   0.017   0.002   PHE A1008 
 TRP   0.007   0.002   TRP A 883 
 HIS   0.004   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 9215)
  covalent geometry    : angle       0.62875 (12534)
  hydrogen bonds       : bond        0.04669 (  432)
  hydrogen bonds       : angle       4.97229 ( 1218)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1593.73 seconds
wall clock time: 28 minutes 20.39 seconds (1700.39 seconds total)