Starting phenix.real_space_refine
on Sat Jul 26 01:54:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pdv_17622/07_2025/8pdv_17622.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pdv_17622/07_2025/8pdv_17622.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pdv_17622/07_2025/8pdv_17622.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pdv_17622/07_2025/8pdv_17622.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pdv_17622/07_2025/8pdv_17622.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pdv_17622/07_2025/8pdv_17622.cif"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001 sd=   0.022
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       1      5.49       5
     S      43      5.16       5
     C    5317      2.51       5
     N    1352      2.21       5
     O    1427      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8140
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1027, 8117
          Classifications: {'peptide': 1027}
          Link IDs: {'PTRANS': 30, 'TRANS': 996}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'PCG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.33, per 1000 atoms: 0.65
  Number of scatterers: 8140
  At special positions: 0
  Unit cell: (84.826, 118.552, 123.662, 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      43     16.00
     P       1     15.00
     O    1427      8.00
     N    1352      7.00
     C    5317      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: 2.36
  Conformation dependent library (CDL) restraints added in 975.3 milliseconds
  

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1938

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 4 sheets defined
      76.6% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 95
      removed outlier: 3.853A  pdb=" N   PHE A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 120
      removed outlier: 3.953A  pdb=" N   VAL A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ASN A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.531A  pdb=" N   GLU A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 153
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 155 through 161
    Processing helix  chain 'A' and resid 162 through 171
    Processing helix  chain 'A' and resid 171 through 188
    Processing helix  chain 'A' and resid 194 through 206
    Processing helix  chain 'A' and resid 210 through 221
      removed outlier: 3.607A  pdb=" N   ASP A 219 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 254
      removed outlier: 3.618A  pdb=" N   LYS A 250 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   MET A 251 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 273
      removed outlier: 3.520A  pdb=" N   ASN A 264 " --> pdb=" O   THR A 260 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VAL A 265 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 266 " --> pdb=" O   GLY A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 291
    Processing helix  chain 'A' and resid 296 through 317
      removed outlier: 3.582A  pdb=" N   TYR A 312 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 337
    Processing helix  chain 'A' and resid 338 through 341
    Processing helix  chain 'A' and resid 342 through 376
      removed outlier: 3.553A  pdb=" N   PHE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   THR A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 380
      removed outlier: 3.612A  pdb=" N   VAL A 380 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 377 through 380'
    Processing helix  chain 'A' and resid 381 through 406
      removed outlier: 4.023A  pdb=" N   TRP A 385 " --> pdb=" O   ASP A 381 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   PHE A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 413
      removed outlier: 3.538A  pdb=" N   ARG A 412 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 432 through 447
      removed outlier: 3.538A  pdb=" N   GLY A 447 " --> pdb=" O   GLU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 469
      removed outlier: 4.042A  pdb=" N   SER A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 481
      removed outlier: 4.936A  pdb=" N   GLN A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   THR A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 514
    Processing helix  chain 'A' and resid 522 through 530
    Processing helix  chain 'A' and resid 571 through 600
      removed outlier: 4.268A  pdb=" N   ASP A 577 " --> pdb=" O   ARG A 573 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   MET A 578 " --> pdb=" O   GLU A 574 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS A 600 " --> pdb=" O   LYS A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 621
      removed outlier: 3.517A  pdb=" N   GLU A 621 " --> pdb=" O   VAL A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 632
    Processing helix  chain 'A' and resid 639 through 652
      removed outlier: 3.735A  pdb=" N   ILE A 652 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 657
      removed outlier: 4.226A  pdb=" N   LYS A 656 " --> pdb=" O   SER A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 677
    Processing helix  chain 'A' and resid 677 through 691
      removed outlier: 3.962A  pdb=" N   GLU A 681 " --> pdb=" O   HIS A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 706
      removed outlier: 3.707A  pdb=" N   PHE A 699 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 755
    Processing helix  chain 'A' and resid 756 through 760
      removed outlier: 3.874A  pdb=" N   ILE A 759 " --> pdb=" O   ARG A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 778
      removed outlier: 3.841A  pdb=" N   LEU A 771 " --> pdb=" O   ASP A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 812
      removed outlier: 3.991A  pdb=" N   LEU A 804 " --> pdb=" O   LYS A 800 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   LEU A 808 " --> pdb=" O   LEU A 804 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ARG A 809 " --> pdb=" O   LEU A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 858
      Proline residue:  A 819  - end of helix
      removed outlier: 3.952A  pdb=" N   LYS A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ASP A 855 " --> pdb=" O   GLY A 851 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   ARG A 856 " --> pdb=" O   LYS A 852 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   MET A 857 " --> pdb=" O   ILE A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 889
      removed outlier: 3.603A  pdb=" N   LEU A 885 " --> pdb=" O   GLU A 881 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLN A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG A 887 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 919
      removed outlier: 3.555A  pdb=" N   ILE A 913 " --> pdb=" O   SER A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 941
      removed outlier: 3.721A  pdb=" N   THR A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 944
      No H-bonds generated for 'chain 'A' and resid 942 through 944'
    Processing helix  chain 'A' and resid 952 through 960
      removed outlier: 3.526A  pdb=" N   LEU A 956 " --> pdb=" O   PRO A 952 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS A 958 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 975
    Processing helix  chain 'A' and resid 1043 through 1048
      removed outlier: 3.531A  pdb=" N   VAL A1047 " --> pdb=" O   GLY A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1070 through 1080
    Processing helix  chain 'A' and resid 1085 through 1108
      removed outlier: 3.548A  pdb=" N   ARG A1097 " --> pdb=" O   VAL A1093 " (cutoff:3.500A)
      Proline residue:  A1101  - end of helix
    Processing helix  chain 'A' and resid 1113 through 1123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982
      removed outlier: 6.043A  pdb=" N   GLN A1064 " --> pdb=" O   VAL A1002 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989
      removed outlier: 6.872A  pdb=" N   VAL A1057 " --> pdb=" O   ILE A 988 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126
      removed outlier: 6.078A  pdb=" N   ARG A1185 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP A1144 " --> pdb=" O   VAL A1189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136
      removed outlier: 3.751A  pdb=" N   ALA A1152 " --> pdb=" O   ILE A1161 " (cutoff:3.500A)

    578 hydrogen bonds defined for protein.
    1704 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.74

  Time building geometry restraints manager: 2.73 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1770
        1.33 -     1.45: 1665
        1.45 -     1.57: 4784
        1.57 -     1.69: 2
        1.69 -     1.81: 79
  Bond restraints: 8300
  Sorted by residual:
  bond pdb=" O1A PCG A1401 "
       pdb=" PA  PCG A1401 "
    ideal  model  delta    sigma   weight residual
    1.582  1.468  0.114 2.00e-02 2.50e+03 3.24e+01
  bond pdb=" C5  PCG A1401 "
       pdb=" C6  PCG A1401 "
    ideal  model  delta    sigma   weight residual
    1.425  1.322  0.103 2.00e-02 2.50e+03 2.67e+01
  bond pdb=" CA  SER A 995 "
       pdb=" CB  SER A 995 "
    ideal  model  delta    sigma   weight residual
    1.527  1.470  0.057 1.44e-02 4.82e+03 1.55e+01
  bond pdb=" N   VAL A1041 "
       pdb=" CA  VAL A1041 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.20e-02 6.94e+03 9.27e+00
  bond pdb=" C4  PCG A1401 "
       pdb=" C5  PCG A1401 "
    ideal  model  delta    sigma   weight residual
    1.381  1.327  0.054 2.00e-02 2.50e+03 7.29e+00
  ... (remaining 8295 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 11098
        1.94 -     3.87: 128
        3.87 -     5.81: 22
        5.81 -     7.74: 6
        7.74 -     9.68: 4
  Bond angle restraints: 11258
  Sorted by residual:
  angle pdb=" N   VAL A1047 "
        pdb=" CA  VAL A1047 "
        pdb=" C   VAL A1047 "
      ideal   model   delta    sigma   weight residual
     111.45  107.63    3.82 9.30e-01 1.16e+00 1.69e+01
  angle pdb=" CA  LEU A 998 "
        pdb=" C   LEU A 998 "
        pdb=" O   LEU A 998 "
      ideal   model   delta    sigma   weight residual
     121.99  117.73    4.26 1.14e+00 7.69e-01 1.40e+01
  angle pdb=" N   MET A1045 "
        pdb=" CA  MET A1045 "
        pdb=" C   MET A1045 "
      ideal   model   delta    sigma   weight residual
     113.02  108.57    4.45 1.20e+00 6.94e-01 1.38e+01
  angle pdb=" CB  MET A 925 "
        pdb=" CG  MET A 925 "
        pdb=" SD  MET A 925 "
      ideal   model   delta    sigma   weight residual
     112.70  122.38   -9.68 3.00e+00 1.11e-01 1.04e+01
  angle pdb=" CA  VAL A1041 "
        pdb=" C   VAL A1041 "
        pdb=" O   VAL A1041 "
      ideal   model   delta    sigma   weight residual
     120.72  117.08    3.64 1.14e+00 7.69e-01 1.02e+01
  ... (remaining 11253 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.31: 4876
       33.31 -    66.62: 91
       66.62 -    99.93: 8
       99.93 -   133.25: 1
      133.25 -   166.56: 2
  Dihedral angle restraints: 4978
    sinusoidal: 1990
      harmonic: 2988
  Sorted by residual:
  dihedral pdb=" C3' PCG A1401 "
           pdb=" O3' PCG A1401 "
           pdb=" PA  PCG A1401 "
           pdb=" O2A PCG A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     279.09  112.53  166.56     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" C5' PCG A1401 "
           pdb=" O5' PCG A1401 "
           pdb=" PA  PCG A1401 "
           pdb=" O2A PCG A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      81.13  -56.54  137.67     1      3.00e+01 1.11e-03 1.86e+01
  dihedral pdb=" C5' PCG A1401 "
           pdb=" O5' PCG A1401 "
           pdb=" PA  PCG A1401 "
           pdb=" O3' PCG A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -45.54   60.33 -105.87     1      3.00e+01 1.11e-03 1.36e+01
  ... (remaining 4975 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1281
       0.080 -    0.159: 68
       0.159 -    0.239: 3
       0.239 -    0.318: 1
       0.318 -    0.398: 1
  Chirality restraints: 1354
  Sorted by residual:
  chirality pdb=" PA  PCG A1401 "
            pdb=" O2A PCG A1401 "
            pdb=" O3' PCG A1401 "
            pdb=" O5' PCG A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.70   -3.10   -0.40 2.00e-01 2.50e+01 3.96e+00
  chirality pdb=" C3' PCG A1401 "
            pdb=" C2' PCG A1401 "
            pdb=" C4' PCG A1401 "
            pdb=" O3' PCG A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.69    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ILE A1042 "
            pdb=" N   ILE A1042 "
            pdb=" C   ILE A1042 "
            pdb=" CB  ILE A1042 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 1351 not shown)

  Planarity restraints: 1379
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1097 "   -0.191 9.50e-02 1.11e+02   8.56e-02 4.50e+00
        pdb=" NE  ARG A1097 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1097 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1097 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1097 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1096 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   ILE A1096 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ILE A1096 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A1097 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1045 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.64e+00
        pdb=" C   MET A1045 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   MET A1045 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLY A1046 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1376 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1695
        2.78 -     3.31: 8387
        3.31 -     3.84: 12727
        3.84 -     4.37: 15049
        4.37 -     4.90: 25629
  Nonbonded interactions: 63487
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A1144 "
            pdb=" N   VAL A1145 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" OD1 ASP A 923 "
            pdb=" N   GLU A 924 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OH  TYR A 392 "
            pdb=" OD1 ASN A 470 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   ASN A1154 "
            pdb=" N   ARG A1158 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" O   VAL A 468 "
            pdb=" OG1 THR A 472 "
     model   vdw
     2.391 3.040
  ... (remaining 63482 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.100
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.114   8300  Z= 0.212
  Angle     :  0.594   9.677  11258  Z= 0.327
  Chirality :  0.040   0.398   1354
  Planarity :  0.004   0.086   1379
  Dihedral  : 14.127 166.557   3040
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.80 %
    Favored  : 93.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.27), residues: 1015
  helix:  1.49 (0.19), residues: 727
  sheet:  0.62 (0.72), residues: 48
  loop :  0.12 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 278 
 HIS   0.002   0.001   HIS A 676 
 PHE   0.017   0.001   PHE A 201 
 TYR   0.010   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A 733 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18955 (  578)
  hydrogen bonds       : angle       6.74787 ( 1704)
  covalent geometry    : bond        0.00397 ( 8300)
  covalent geometry    : angle       0.59426 (11258)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 264
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7905 (mttm) cc_final: 0.7689 (mttm)
REVERT: A   84 SER cc_start: 0.7750 (p) cc_final: 0.7485 (t)
REVERT: A  116 VAL cc_start: 0.6947 (p) cc_final: 0.6681 (m)
REVERT: A  120 VAL cc_start: 0.7218 (t) cc_final: 0.7001 (p)
REVERT: A  124 GLU cc_start: 0.7468 (tt0) cc_final: 0.6974 (tm-30)
REVERT: A  155 ASP cc_start: 0.7711 (t70) cc_final: 0.7258 (t0)
REVERT: A  175 VAL cc_start: 0.7056 (t) cc_final: 0.6828 (m)
REVERT: A  187 ASN cc_start: 0.7318 (m-40) cc_final: 0.6808 (m-40)
REVERT: A  263 GLN cc_start: 0.6218 (mm-40) cc_final: 0.5954 (mm-40)
REVERT: A  289 PHE cc_start: 0.8187 (m-80) cc_final: 0.7983 (m-80)
REVERT: A  295 ASN cc_start: 0.8260 (t0) cc_final: 0.7937 (t0)
REVERT: A  344 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7454 (mm-30)
REVERT: A  354 GLU cc_start: 0.7928 (tt0) cc_final: 0.7699 (mt-10)
REVERT: A  355 MET cc_start: 0.7773 (tmm) cc_final: 0.7509 (tmm)
REVERT: A  383 MET cc_start: 0.7899 (mmm) cc_final: 0.7540 (mmm)
REVERT: A  474 ILE cc_start: 0.7717 (tp) cc_final: 0.7420 (tt)
REVERT: A  485 ASP cc_start: 0.7604 (m-30) cc_final: 0.7344 (m-30)
REVERT: A  511 MET cc_start: 0.7457 (tmm) cc_final: 0.7019 (tmm)
REVERT: A  531 GLU cc_start: 0.7532 (tt0) cc_final: 0.7214 (tp30)
REVERT: A  579 MET cc_start: 0.6495 (tpt) cc_final: 0.6271 (tpt)
REVERT: A  585 ARG cc_start: 0.6990 (mtt-85) cc_final: 0.6460 (mtt-85)
REVERT: A  588 LYS cc_start: 0.7849 (ttpp) cc_final: 0.7512 (ttpp)
REVERT: A  628 VAL cc_start: 0.7706 (m) cc_final: 0.7354 (t)
REVERT: A  634 SER cc_start: 0.8034 (m) cc_final: 0.7706 (p)
REVERT: A  646 ARG cc_start: 0.7598 (ttp-170) cc_final: 0.7357 (ttp-170)
REVERT: A  647 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7424 (mptt)
REVERT: A  684 ILE cc_start: 0.7197 (mm) cc_final: 0.6752 (pt)
REVERT: A  697 MET cc_start: 0.5542 (tpp) cc_final: 0.5107 (tpp)
REVERT: A  815 LYS cc_start: 0.8364 (tttm) cc_final: 0.8092 (tttp)
REVERT: A  828 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8204 (mmmt)
REVERT: A  838 ASP cc_start: 0.7577 (m-30) cc_final: 0.7228 (m-30)
REVERT: A  841 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7410 (tptt)
REVERT: A  845 ILE cc_start: 0.8044 (mt) cc_final: 0.7810 (mm)
REVERT: A  862 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7556 (tppt)
REVERT: A  865 ARG cc_start: 0.6725 (tmm-80) cc_final: 0.6519 (tmm-80)
REVERT: A  866 GLU cc_start: 0.7360 (tp30) cc_final: 0.6711 (tp30)
REVERT: A  867 LEU cc_start: 0.7761 (mp) cc_final: 0.7441 (mm)
REVERT: A  868 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7373 (mtmm)
REVERT: A  870 ILE cc_start: 0.8005 (mt) cc_final: 0.7634 (mt)
REVERT: A  877 GLN cc_start: 0.7815 (mt0) cc_final: 0.7540 (tt0)
REVERT: A  888 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7252 (mm-30)
REVERT: A  911 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7244 (mm-30)
REVERT: A  931 GLU cc_start: 0.7583 (tt0) cc_final: 0.7356 (tt0)
REVERT: A  946 SER cc_start: 0.8169 (p) cc_final: 0.7956 (t)
REVERT: A  961 SER cc_start: 0.8303 (m) cc_final: 0.7975 (p)
REVERT: A  972 PHE cc_start: 0.7915 (t80) cc_final: 0.7625 (t80)
REVERT: A  974 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7566 (mtpp)
REVERT: A  999 PHE cc_start: 0.7627 (m-80) cc_final: 0.7298 (m-80)
REVERT: A 1003 SER cc_start: 0.8647 (t) cc_final: 0.8266 (t)
REVERT: A 1033 GLU cc_start: 0.7258 (tt0) cc_final: 0.6978 (tt0)
REVERT: A 1096 ILE cc_start: 0.7975 (mt) cc_final: 0.7677 (mm)
REVERT: A 1107 MET cc_start: 0.6480 (mtm) cc_final: 0.6141 (mtp)
REVERT: A 1118 LYS cc_start: 0.3998 (tmtt) cc_final: 0.2876 (mttm)
REVERT: A 1122 GLU cc_start: 0.7677 (tp30) cc_final: 0.7370 (tt0)
REVERT: A 1133 HIS cc_start: 0.6864 (t-170) cc_final: 0.6622 (t-90)
REVERT: A 1143 GLU cc_start: 0.7176 (tt0) cc_final: 0.6759 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7138 (t0) cc_final: 0.6626 (t0)
REVERT: A 1182 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6179 (mp0)
REVERT: A 1186 LEU cc_start: 0.8455 (tp) cc_final: 0.8189 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 265
  average time/residue: 0.2291
  time to fit residues: 78.8258
Evaluate side-chains
  224 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    0.1980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 691 ASN
A 900 GLN
A 908 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.142648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.116317 restraints weight = 11948.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.81
r_work: 0.3291 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8300  Z= 0.164
  Angle     :  0.554   7.845  11258  Z= 0.292
  Chirality :  0.041   0.188   1354
  Planarity :  0.004   0.047   1379
  Dihedral  :  9.664 169.318   1127
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.33 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.27), residues: 1015
  helix:  1.75 (0.19), residues: 731
  sheet:  0.67 (0.69), residues: 51
  loop :  0.45 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 278 
 HIS   0.003   0.001   HIS A 676 
 PHE   0.013   0.001   PHE A 575 
 TYR   0.017   0.002   TYR A 743 
 ARG   0.003   0.000   ARG A 733 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05537 (  578)
  hydrogen bonds       : angle       4.60628 ( 1704)
  covalent geometry    : bond        0.00361 ( 8300)
  covalent geometry    : angle       0.55375 (11258)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 230
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 SER cc_start: 0.8420 (p) cc_final: 0.7996 (t)
REVERT: A  120 VAL cc_start: 0.8170 (t) cc_final: 0.7808 (p)
REVERT: A  169 LEU cc_start: 0.8526 (tp) cc_final: 0.8302 (tp)
REVERT: A  187 ASN cc_start: 0.7886 (m-40) cc_final: 0.7496 (m-40)
REVERT: A  205 MET cc_start: 0.8296 (tpp) cc_final: 0.8093 (mmt)
REVERT: A  295 ASN cc_start: 0.8302 (t0) cc_final: 0.7983 (t0)
REVERT: A  344 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7977 (mm-30)
REVERT: A  354 GLU cc_start: 0.8333 (tt0) cc_final: 0.8004 (mt-10)
REVERT: A  355 MET cc_start: 0.8432 (tmm) cc_final: 0.7844 (tmm)
REVERT: A  375 LYS cc_start: 0.7895 (mttt) cc_final: 0.7687 (mttt)
REVERT: A  383 MET cc_start: 0.8419 (mmm) cc_final: 0.8137 (mmm)
REVERT: A  443 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7746 (tp30)
REVERT: A  474 ILE cc_start: 0.8479 (tp) cc_final: 0.8233 (tt)
REVERT: A  503 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7686 (mt-10)
REVERT: A  511 MET cc_start: 0.8293 (tmm) cc_final: 0.7937 (tmm)
REVERT: A  579 MET cc_start: 0.7008 (tpt) cc_final: 0.6778 (tpt)
REVERT: A  588 LYS cc_start: 0.7954 (ttpp) cc_final: 0.7720 (ttpp)
REVERT: A  628 VAL cc_start: 0.7906 (m) cc_final: 0.7576 (t)
REVERT: A  629 ASP cc_start: 0.7905 (p0) cc_final: 0.7649 (p0)
REVERT: A  633 LYS cc_start: 0.8416 (mttt) cc_final: 0.8156 (mmtm)
REVERT: A  634 SER cc_start: 0.8144 (m) cc_final: 0.7821 (p)
REVERT: A  646 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7635 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7349 (mm) cc_final: 0.6997 (pt)
REVERT: A  697 MET cc_start: 0.5602 (tpp) cc_final: 0.5208 (tpp)
REVERT: A  862 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7895 (ttmt)
REVERT: A  866 GLU cc_start: 0.7492 (tp30) cc_final: 0.7113 (tp30)
REVERT: A  870 ILE cc_start: 0.8498 (mt) cc_final: 0.7971 (mt)
REVERT: A  974 LYS cc_start: 0.8464 (ttmt) cc_final: 0.8108 (mtpp)
REVERT: A 1102 LEU cc_start: 0.8326 (mt) cc_final: 0.8126 (mp)
REVERT: A 1118 LYS cc_start: 0.5230 (tmtt) cc_final: 0.3693 (mttm)
REVERT: A 1143 GLU cc_start: 0.7162 (tt0) cc_final: 0.6888 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7618 (t0) cc_final: 0.7168 (t0)
REVERT: A 1182 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6350 (mp0)
REVERT: A 1186 LEU cc_start: 0.8797 (tp) cc_final: 0.8588 (tp)
  outliers start: 16
  outliers final: 8
  residues processed: 238
  average time/residue: 0.2160
  time to fit residues: 68.3866
Evaluate side-chains
  230 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 222
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 84 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0270
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 886 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.144925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.118472 restraints weight = 12085.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.81
r_work: 0.3311 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8300  Z= 0.134
  Angle     :  0.505   8.001  11258  Z= 0.265
  Chirality :  0.039   0.198   1354
  Planarity :  0.004   0.054   1379
  Dihedral  :  9.681 174.726   1127
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.52 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.26), residues: 1015
  helix:  1.89 (0.19), residues: 732
  sheet:  0.80 (0.69), residues: 51
  loop :  0.37 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.014   0.002   PHE A1136 
 TYR   0.013   0.001   TYR A 743 
 ARG   0.003   0.000   ARG A1169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04530 (  578)
  hydrogen bonds       : angle       4.20793 ( 1704)
  covalent geometry    : bond        0.00290 ( 8300)
  covalent geometry    : angle       0.50465 (11258)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 227
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 SER cc_start: 0.8287 (p) cc_final: 0.7937 (t)
REVERT: A  120 VAL cc_start: 0.8134 (t) cc_final: 0.7755 (p)
REVERT: A  124 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7340 (tp30)
REVERT: A  161 ARG cc_start: 0.8061 (mtm180) cc_final: 0.7848 (mtt180)
REVERT: A  187 ASN cc_start: 0.7931 (m-40) cc_final: 0.7506 (m-40)
REVERT: A  256 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7832 (tm-30)
REVERT: A  354 GLU cc_start: 0.8339 (tt0) cc_final: 0.8012 (mt-10)
REVERT: A  355 MET cc_start: 0.8427 (tmm) cc_final: 0.7850 (tmm)
REVERT: A  383 MET cc_start: 0.8443 (mmm) cc_final: 0.8212 (mmm)
REVERT: A  443 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7671 (tp30)
REVERT: A  474 ILE cc_start: 0.8456 (tp) cc_final: 0.8206 (tt)
REVERT: A  511 MET cc_start: 0.8182 (tmm) cc_final: 0.7823 (tmm)
REVERT: A  531 GLU cc_start: 0.7379 (tp30) cc_final: 0.7124 (tp30)
REVERT: A  532 ILE cc_start: 0.8234 (mm) cc_final: 0.7537 (mt)
REVERT: A  588 LYS cc_start: 0.7953 (ttpp) cc_final: 0.7730 (ttpp)
REVERT: A  628 VAL cc_start: 0.7877 (m) cc_final: 0.7651 (t)
REVERT: A  629 ASP cc_start: 0.7885 (p0) cc_final: 0.7661 (p0)
REVERT: A  633 LYS cc_start: 0.8392 (mttt) cc_final: 0.8159 (mmtm)
REVERT: A  634 SER cc_start: 0.8119 (m) cc_final: 0.7806 (p)
REVERT: A  646 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7608 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7362 (mm) cc_final: 0.6980 (pt)
REVERT: A  697 MET cc_start: 0.5609 (tpp) cc_final: 0.5296 (tpp)
REVERT: A  828 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8330 (mmtm)
REVERT: A  841 LYS cc_start: 0.7913 (tptt) cc_final: 0.7612 (mptt)
REVERT: A  847 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7080 (mm-30)
REVERT: A  862 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7932 (tppt)
REVERT: A  900 GLN cc_start: 0.7751 (mm110) cc_final: 0.7538 (mm-40)
REVERT: A  931 GLU cc_start: 0.7992 (tt0) cc_final: 0.7671 (mt-10)
REVERT: A  974 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8052 (mtpp)
REVERT: A 1033 GLU cc_start: 0.7559 (tt0) cc_final: 0.7225 (tt0)
REVERT: A 1118 LYS cc_start: 0.5519 (tmtt) cc_final: 0.3597 (tppt)
REVERT: A 1122 GLU cc_start: 0.6380 (tt0) cc_final: 0.6022 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7455 (t0) cc_final: 0.7035 (t0)
REVERT: A 1182 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6318 (mp0)
  outliers start: 20
  outliers final: 12
  residues processed: 237
  average time/residue: 0.2253
  time to fit residues: 70.5854
Evaluate side-chains
  230 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 218
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.144533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.117791 restraints weight = 11762.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.79
r_work: 0.3291 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8300  Z= 0.169
  Angle     :  0.523   6.954  11258  Z= 0.274
  Chirality :  0.040   0.216   1354
  Planarity :  0.004   0.055   1379
  Dihedral  :  9.698 175.122   1127
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.97 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.26), residues: 1015
  helix:  1.80 (0.19), residues: 733
  sheet:  1.08 (0.70), residues: 51
  loop :  0.31 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 643 
 HIS   0.004   0.001   HIS A1133 
 PHE   0.016   0.001   PHE A 575 
 TYR   0.012   0.001   TYR A 309 
 ARG   0.003   0.000   ARG A1169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04582 (  578)
  hydrogen bonds       : angle       4.17116 ( 1704)
  covalent geometry    : bond        0.00382 ( 8300)
  covalent geometry    : angle       0.52257 (11258)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 221
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 SER cc_start: 0.8278 (p) cc_final: 0.7955 (t)
REVERT: A  108 ILE cc_start: 0.8167 (mm) cc_final: 0.7871 (mt)
REVERT: A  120 VAL cc_start: 0.8102 (t) cc_final: 0.7705 (p)
REVERT: A  155 ASP cc_start: 0.8347 (t0) cc_final: 0.8056 (t0)
REVERT: A  160 MET cc_start: 0.8109 (mmm) cc_final: 0.7808 (mmm)
REVERT: A  161 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7775 (mtt180)
REVERT: A  187 ASN cc_start: 0.7902 (m-40) cc_final: 0.7531 (m-40)
REVERT: A  256 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: A  355 MET cc_start: 0.8499 (tmm) cc_final: 0.7883 (tmm)
REVERT: A  443 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7651 (tp30)
REVERT: A  474 ILE cc_start: 0.8426 (tp) cc_final: 0.8161 (tt)
REVERT: A  500 ARG cc_start: 0.6540 (ttp-170) cc_final: 0.6321 (ttp-170)
REVERT: A  511 MET cc_start: 0.8156 (tmm) cc_final: 0.7797 (tmm)
REVERT: A  588 LYS cc_start: 0.7989 (ttpp) cc_final: 0.7755 (ttpp)
REVERT: A  633 LYS cc_start: 0.8423 (mttt) cc_final: 0.8145 (mmtm)
REVERT: A  634 SER cc_start: 0.8115 (m) cc_final: 0.7829 (p)
REVERT: A  646 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.7484 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7418 (mm) cc_final: 0.6945 (pt)
REVERT: A  697 MET cc_start: 0.5615 (tpp) cc_final: 0.5322 (tpp)
REVERT: A  847 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7011 (mm-30)
REVERT: A  862 LYS cc_start: 0.8232 (ttmm) cc_final: 0.8027 (ttmt)
REVERT: A  876 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8418 (mt)
REVERT: A  900 GLN cc_start: 0.7797 (mm110) cc_final: 0.7596 (mm-40)
REVERT: A  931 GLU cc_start: 0.8099 (tt0) cc_final: 0.7773 (mt-10)
REVERT: A  974 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8038 (mtpp)
REVERT: A 1118 LYS cc_start: 0.5095 (tmtt) cc_final: 0.2751 (tppt)
REVERT: A 1122 GLU cc_start: 0.7038 (tt0) cc_final: 0.5789 (tt0)
REVERT: A 1143 GLU cc_start: 0.7082 (tt0) cc_final: 0.6837 (mt-10)
REVERT: A 1154 ASN cc_start: 0.7471 (t0) cc_final: 0.7049 (t0)
REVERT: A 1182 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6389 (mp0)
  outliers start: 30
  outliers final: 24
  residues processed: 235
  average time/residue: 0.2244
  time to fit residues: 70.1691
Evaluate side-chains
  241 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 216
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  867 LEU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  924 GLU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0000
   chunk 12 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 95 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 726 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.146260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.119759 restraints weight = 11642.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.78
r_work: 0.3308 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8300  Z= 0.121
  Angle     :  0.491   7.652  11258  Z= 0.257
  Chirality :  0.039   0.212   1354
  Planarity :  0.004   0.049   1379
  Dihedral  :  9.661 175.338   1127
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 16.99 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.26), residues: 1015
  helix:  1.92 (0.19), residues: 731
  sheet:  1.20 (0.72), residues: 51
  loop :  0.12 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 643 
 HIS   0.003   0.001   HIS A 676 
 PHE   0.012   0.001   PHE A 972 
 TYR   0.008   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A1169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04050 (  578)
  hydrogen bonds       : angle       4.01684 ( 1704)
  covalent geometry    : bond        0.00264 ( 8300)
  covalent geometry    : angle       0.49113 (11258)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 220
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7274 (mt-10)
REVERT: A  155 ASP cc_start: 0.8342 (t0) cc_final: 0.8055 (t0)
REVERT: A  160 MET cc_start: 0.8087 (mmm) cc_final: 0.7774 (mmm)
REVERT: A  161 ARG cc_start: 0.7960 (mtm180) cc_final: 0.7726 (mtt180)
REVERT: A  187 ASN cc_start: 0.7886 (m-40) cc_final: 0.7519 (m-40)
REVERT: A  355 MET cc_start: 0.8449 (tmm) cc_final: 0.7903 (tmm)
REVERT: A  366 MET cc_start: 0.8292 (mtp) cc_final: 0.8009 (mtp)
REVERT: A  443 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7630 (tp30)
REVERT: A  474 ILE cc_start: 0.8387 (tp) cc_final: 0.8114 (tt)
REVERT: A  511 MET cc_start: 0.8129 (tmm) cc_final: 0.7763 (tmm)
REVERT: A  532 ILE cc_start: 0.8183 (mm) cc_final: 0.7944 (mt)
REVERT: A  588 LYS cc_start: 0.7972 (ttpp) cc_final: 0.7752 (ttpp)
REVERT: A  633 LYS cc_start: 0.8389 (mttt) cc_final: 0.8131 (mmtm)
REVERT: A  634 SER cc_start: 0.8107 (m) cc_final: 0.7733 (p)
REVERT: A  646 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7396 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7296 (mm) cc_final: 0.6891 (pt)
REVERT: A  697 MET cc_start: 0.5610 (tpp) cc_final: 0.5299 (tpp)
REVERT: A  847 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6982 (mm-30)
REVERT: A  931 GLU cc_start: 0.8125 (tt0) cc_final: 0.7752 (mt-10)
REVERT: A  974 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7983 (mtpp)
REVERT: A 1007 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7867 (tttt)
REVERT: A 1118 LYS cc_start: 0.5008 (tmtt) cc_final: 0.2693 (tppt)
REVERT: A 1122 GLU cc_start: 0.6971 (tt0) cc_final: 0.6003 (tt0)
REVERT: A 1143 GLU cc_start: 0.6995 (tt0) cc_final: 0.6756 (mt-10)
REVERT: A 1182 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6352 (mp0)
  outliers start: 34
  outliers final: 23
  residues processed: 234
  average time/residue: 0.2255
  time to fit residues: 69.2783
Evaluate side-chains
  239 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 215
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  649 GLU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  924 GLU
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1007 LYS
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 93 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.145005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.118533 restraints weight = 11721.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.79
r_work: 0.3298 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8300  Z= 0.158
  Angle     :  0.534   8.618  11258  Z= 0.276
  Chirality :  0.041   0.231   1354
  Planarity :  0.004   0.060   1379
  Dihedral  :  9.671 175.765   1127
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 17.33 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.26), residues: 1015
  helix:  1.88 (0.19), residues: 734
  sheet:  0.97 (0.72), residues: 53
  loop :  0.14 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 278 
 HIS   0.005   0.001   HIS A1172 
 PHE   0.014   0.001   PHE A1136 
 TYR   0.012   0.001   TYR A 309 
 ARG   0.003   0.000   ARG A1169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04262 (  578)
  hydrogen bonds       : angle       4.05587 ( 1704)
  covalent geometry    : bond        0.00360 ( 8300)
  covalent geometry    : angle       0.53387 (11258)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 221
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8126 (mm) cc_final: 0.7830 (mt)
REVERT: A  120 VAL cc_start: 0.8038 (t) cc_final: 0.7593 (p)
REVERT: A  124 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7320 (mt-10)
REVERT: A  155 ASP cc_start: 0.8355 (t0) cc_final: 0.8078 (t0)
REVERT: A  161 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7730 (mtt180)
REVERT: A  187 ASN cc_start: 0.7886 (m-40) cc_final: 0.7500 (m-40)
REVERT: A  256 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7787 (tm-30)
REVERT: A  355 MET cc_start: 0.8474 (tmm) cc_final: 0.7881 (tmm)
REVERT: A  366 MET cc_start: 0.8319 (mtp) cc_final: 0.8044 (mtp)
REVERT: A  383 MET cc_start: 0.8297 (mmm) cc_final: 0.8092 (mmm)
REVERT: A  443 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7748 (tp30)
REVERT: A  474 ILE cc_start: 0.8435 (tp) cc_final: 0.8168 (tt)
REVERT: A  511 MET cc_start: 0.8178 (tmm) cc_final: 0.7799 (tmm)
REVERT: A  532 ILE cc_start: 0.8155 (mm) cc_final: 0.7861 (mt)
REVERT: A  588 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7807 (ttpp)
REVERT: A  633 LYS cc_start: 0.8395 (mttt) cc_final: 0.8151 (mmtm)
REVERT: A  634 SER cc_start: 0.8025 (m) cc_final: 0.7784 (p)
REVERT: A  646 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7364 (ttp-170)
REVERT: A  678 MET cc_start: 0.5727 (mmm) cc_final: 0.5265 (mmm)
REVERT: A  684 ILE cc_start: 0.7355 (mm) cc_final: 0.6900 (pt)
REVERT: A  697 MET cc_start: 0.5634 (tpp) cc_final: 0.5298 (tpp)
REVERT: A  931 GLU cc_start: 0.8124 (tt0) cc_final: 0.7742 (mt-10)
REVERT: A  974 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8002 (mtpp)
REVERT: A 1007 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7926 (tttt)
REVERT: A 1118 LYS cc_start: 0.4857 (tmtt) cc_final: 0.2737 (mttm)
REVERT: A 1122 GLU cc_start: 0.7009 (tt0) cc_final: 0.5997 (tt0)
REVERT: A 1123 ARG cc_start: 0.7765 (mmt180) cc_final: 0.7002 (mmp-170)
REVERT: A 1143 GLU cc_start: 0.7016 (tt0) cc_final: 0.6774 (mt-10)
REVERT: A 1182 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6344 (mp0)
  outliers start: 33
  outliers final: 28
  residues processed: 233
  average time/residue: 0.2254
  time to fit residues: 68.9991
Evaluate side-chains
  243 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  924 GLU
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1007 LYS
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1062 THR
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0980
   chunk 19 optimal weight:    0.1980
   chunk 8 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 900 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.144690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.118094 restraints weight = 11793.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.80
r_work: 0.3309 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8300  Z= 0.130
  Angle     :  0.516   8.263  11258  Z= 0.266
  Chirality :  0.040   0.231   1354
  Planarity :  0.004   0.052   1379
  Dihedral  :  9.642 175.124   1127
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.78 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.26), residues: 1015
  helix:  1.95 (0.19), residues: 733
  sheet:  0.83 (0.71), residues: 53
  loop :  0.20 (0.42), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 278 
 HIS   0.003   0.001   HIS A 676 
 PHE   0.025   0.001   PHE A 163 
 TYR   0.009   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A1169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  578)
  hydrogen bonds       : angle       3.97847 ( 1704)
  covalent geometry    : bond        0.00292 ( 8300)
  covalent geometry    : angle       0.51584 (11258)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 216
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.8094 (mm) cc_final: 0.7801 (mt)
REVERT: A  120 VAL cc_start: 0.8024 (t) cc_final: 0.7552 (p)
REVERT: A  124 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7335 (mt-10)
REVERT: A  155 ASP cc_start: 0.8323 (t0) cc_final: 0.7991 (t0)
REVERT: A  161 ARG cc_start: 0.7952 (mtm180) cc_final: 0.7727 (mtt180)
REVERT: A  187 ASN cc_start: 0.7871 (m-40) cc_final: 0.7493 (m-40)
REVERT: A  229 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8201 (mt)
REVERT: A  256 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7720 (tm-30)
REVERT: A  355 MET cc_start: 0.8456 (tmm) cc_final: 0.7911 (tmm)
REVERT: A  366 MET cc_start: 0.8316 (mtp) cc_final: 0.8047 (mtp)
REVERT: A  443 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7748 (tp30)
REVERT: A  474 ILE cc_start: 0.8392 (tp) cc_final: 0.8136 (tt)
REVERT: A  511 MET cc_start: 0.8144 (tmm) cc_final: 0.7765 (tmm)
REVERT: A  588 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7768 (ttpp)
REVERT: A  596 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8100 (ttmt)
REVERT: A  633 LYS cc_start: 0.8390 (mttt) cc_final: 0.8144 (mmtm)
REVERT: A  634 SER cc_start: 0.8058 (m) cc_final: 0.7789 (p)
REVERT: A  643 TRP cc_start: 0.7587 (t-100) cc_final: 0.7361 (t-100)
REVERT: A  646 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.7387 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7266 (mm) cc_final: 0.6855 (pt)
REVERT: A  697 MET cc_start: 0.5638 (tpp) cc_final: 0.5267 (tpp)
REVERT: A  841 LYS cc_start: 0.7959 (tptt) cc_final: 0.7563 (mptt)
REVERT: A  847 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7135 (mm-30)
REVERT: A  857 MET cc_start: 0.8147 (ptt) cc_final: 0.7927 (ppp)
REVERT: A  877 GLN cc_start: 0.8607 (tt0) cc_final: 0.8169 (tt0)
REVERT: A  931 GLU cc_start: 0.8092 (tt0) cc_final: 0.7688 (mt-10)
REVERT: A  974 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7989 (mtpp)
REVERT: A 1007 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7796 (tttt)
REVERT: A 1118 LYS cc_start: 0.4537 (tmtt) cc_final: 0.2547 (mttm)
REVERT: A 1122 GLU cc_start: 0.6933 (tt0) cc_final: 0.5899 (tt0)
REVERT: A 1123 ARG cc_start: 0.7775 (mmt180) cc_final: 0.7010 (mmp-170)
REVERT: A 1143 GLU cc_start: 0.6982 (tt0) cc_final: 0.6707 (mt-10)
REVERT: A 1182 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6342 (mp0)
  outliers start: 30
  outliers final: 25
  residues processed: 228
  average time/residue: 0.2237
  time to fit residues: 67.2320
Evaluate side-chains
  237 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 209
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  924 GLU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1007 LYS
Chi-restraints excluded: chain A residue 1062 THR
Chi-restraints excluded: chain A residue 1063 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0570
   chunk 73 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0040
   chunk 35 optimal weight:    0.4980
   chunk 75 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.3910

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.145338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.118698 restraints weight = 11883.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.83
r_work: 0.3325 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8300  Z= 0.116
  Angle     :  0.504   8.934  11258  Z= 0.262
  Chirality :  0.039   0.227   1354
  Planarity :  0.004   0.067   1379
  Dihedral  :  9.624 175.424   1127
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 18.01 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.26), residues: 1015
  helix:  2.03 (0.19), residues: 731
  sheet:  0.93 (0.72), residues: 53
  loop :  0.22 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 278 
 HIS   0.003   0.000   HIS A 676 
 PHE   0.011   0.001   PHE A 386 
 TYR   0.008   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A1169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03802 (  578)
  hydrogen bonds       : angle       3.92893 ( 1704)
  covalent geometry    : bond        0.00255 ( 8300)
  covalent geometry    : angle       0.50391 (11258)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 217
  time to evaluate  : 1.021 
Fit side-chains
REVERT: A  108 ILE cc_start: 0.8057 (mm) cc_final: 0.7777 (mt)
REVERT: A  120 VAL cc_start: 0.8028 (t) cc_final: 0.7413 (p)
REVERT: A  124 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7365 (mt-10)
REVERT: A  155 ASP cc_start: 0.8340 (t0) cc_final: 0.8047 (t0)
REVERT: A  161 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7647 (mtt180)
REVERT: A  187 ASN cc_start: 0.7842 (m-40) cc_final: 0.7478 (m-40)
REVERT: A  229 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8182 (mt)
REVERT: A  256 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: A  355 MET cc_start: 0.8447 (tmm) cc_final: 0.7929 (tmm)
REVERT: A  366 MET cc_start: 0.8274 (mtp) cc_final: 0.7997 (mtp)
REVERT: A  443 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7720 (tp30)
REVERT: A  450 VAL cc_start: 0.8368 (m) cc_final: 0.8129 (p)
REVERT: A  474 ILE cc_start: 0.8406 (tp) cc_final: 0.8139 (tt)
REVERT: A  511 MET cc_start: 0.8141 (tmm) cc_final: 0.7775 (tmm)
REVERT: A  586 MET cc_start: 0.7633 (ttm) cc_final: 0.7415 (ttp)
REVERT: A  588 LYS cc_start: 0.7981 (ttpp) cc_final: 0.7761 (ttpp)
REVERT: A  596 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8099 (ttmt)
REVERT: A  633 LYS cc_start: 0.8362 (mttt) cc_final: 0.8129 (mmtm)
REVERT: A  634 SER cc_start: 0.8068 (m) cc_final: 0.7786 (p)
REVERT: A  646 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.7403 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7246 (mm) cc_final: 0.6848 (pt)
REVERT: A  697 MET cc_start: 0.5686 (tpp) cc_final: 0.5329 (tpp)
REVERT: A  841 LYS cc_start: 0.7950 (tptt) cc_final: 0.7546 (mptt)
REVERT: A  847 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7153 (mm-30)
REVERT: A  854 ILE cc_start: 0.7850 (pt) cc_final: 0.7554 (pt)
REVERT: A  857 MET cc_start: 0.8080 (ptt) cc_final: 0.7839 (ppp)
REVERT: A  931 GLU cc_start: 0.8112 (tt0) cc_final: 0.7718 (mt-10)
REVERT: A  974 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7965 (mtpp)
REVERT: A 1007 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7824 (tttt)
REVERT: A 1118 LYS cc_start: 0.4548 (tmtt) cc_final: 0.2556 (mttm)
REVERT: A 1122 GLU cc_start: 0.6908 (tt0) cc_final: 0.5878 (tt0)
REVERT: A 1123 ARG cc_start: 0.7810 (mmt180) cc_final: 0.6947 (mmp-170)
REVERT: A 1143 GLU cc_start: 0.6924 (tt0) cc_final: 0.6676 (mt-10)
REVERT: A 1182 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6325 (mp0)
  outliers start: 33
  outliers final: 28
  residues processed: 230
  average time/residue: 0.4024
  time to fit residues: 124.9274
Evaluate side-chains
  243 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 212
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  499 ARG
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1007 LYS
Chi-restraints excluded: chain A residue 1062 THR
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1097 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 42 optimal weight:    0.1980
   chunk 95 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
** A1133 HIS ** 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 = 0.3805 r_free = 0.3805 target = 0.144133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.117440 restraints weight = 12044.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.84
r_work: 0.3314 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8300  Z= 0.137
  Angle     :  0.515   9.275  11258  Z= 0.268
  Chirality :  0.040   0.234   1354
  Planarity :  0.004   0.062   1379
  Dihedral  :  9.621 175.345   1127
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 18.35 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.26), residues: 1015
  helix:  1.99 (0.19), residues: 734
  sheet:  0.97 (0.72), residues: 53
  loop :  0.26 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 643 
 HIS   0.003   0.001   HIS A 676 
 PHE   0.030   0.001   PHE A 163 
 TYR   0.010   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A1169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03943 (  578)
  hydrogen bonds       : angle       3.95484 ( 1704)
  covalent geometry    : bond        0.00312 ( 8300)
  covalent geometry    : angle       0.51526 (11258)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 213
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A  108 ILE cc_start: 0.8069 (mm) cc_final: 0.7799 (mt)
REVERT: A  120 VAL cc_start: 0.8034 (t) cc_final: 0.7500 (p)
REVERT: A  124 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7361 (mt-10)
REVERT: A  133 MET cc_start: 0.8651 (ptm) cc_final: 0.8186 (ttm)
REVERT: A  137 VAL cc_start: 0.8736 (t) cc_final: 0.8520 (m)
REVERT: A  140 GLN cc_start: 0.8235 (mp-120) cc_final: 0.7784 (mp10)
REVERT: A  155 ASP cc_start: 0.8342 (t0) cc_final: 0.8032 (t0)
REVERT: A  161 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7727 (mtt180)
REVERT: A  187 ASN cc_start: 0.7862 (m-40) cc_final: 0.7511 (m-40)
REVERT: A  229 ILE cc_start: 0.8446 (mm) cc_final: 0.8208 (mt)
REVERT: A  256 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7604 (tm-30)
REVERT: A  355 MET cc_start: 0.8454 (tmm) cc_final: 0.7909 (tmm)
REVERT: A  366 MET cc_start: 0.8310 (mtp) cc_final: 0.8048 (mtp)
REVERT: A  443 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7733 (tp30)
REVERT: A  450 VAL cc_start: 0.8382 (m) cc_final: 0.8141 (p)
REVERT: A  511 MET cc_start: 0.8189 (tmm) cc_final: 0.7804 (tmm)
REVERT: A  588 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7741 (ttpp)
REVERT: A  596 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8116 (ttmt)
REVERT: A  629 ASP cc_start: 0.7877 (p0) cc_final: 0.7657 (m-30)
REVERT: A  633 LYS cc_start: 0.8356 (mttt) cc_final: 0.8137 (mmtm)
REVERT: A  634 SER cc_start: 0.8068 (m) cc_final: 0.7794 (p)
REVERT: A  646 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.7427 (ttp-170)
REVERT: A  678 MET cc_start: 0.5607 (mmm) cc_final: 0.5161 (mmm)
REVERT: A  684 ILE cc_start: 0.7247 (mm) cc_final: 0.6851 (pt)
REVERT: A  697 MET cc_start: 0.5690 (tpp) cc_final: 0.5313 (tpp)
REVERT: A  812 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7713 (mtp-110)
REVERT: A  847 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7152 (mm-30)
REVERT: A  854 ILE cc_start: 0.7881 (pt) cc_final: 0.7603 (pt)
REVERT: A  857 MET cc_start: 0.8091 (ptt) cc_final: 0.7855 (ppp)
REVERT: A  931 GLU cc_start: 0.8069 (tt0) cc_final: 0.7669 (mt-10)
REVERT: A  974 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7966 (mtpp)
REVERT: A 1007 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7873 (tttt)
REVERT: A 1104 MET cc_start: 0.7759 (mmm) cc_final: 0.7513 (tpt)
REVERT: A 1118 LYS cc_start: 0.4561 (tmtt) cc_final: 0.2798 (mttm)
REVERT: A 1122 GLU cc_start: 0.6994 (tt0) cc_final: 0.6501 (mt-10)
REVERT: A 1123 ARG cc_start: 0.7867 (mmt180) cc_final: 0.6985 (mmp-170)
REVERT: A 1143 GLU cc_start: 0.6927 (tt0) cc_final: 0.6684 (mt-10)
REVERT: A 1182 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6322 (mp0)
  outliers start: 34
  outliers final: 31
  residues processed: 228
  average time/residue: 0.2255
  time to fit residues: 67.9058
Evaluate side-chains
  245 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 212
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  499 ARG
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  847 GLU
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1003 SER
Chi-restraints excluded: chain A residue 1007 LYS
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1062 THR
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1097 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 78 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 HIS ** 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 = 0.3804 r_free = 0.3804 target = 0.144729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.118057 restraints weight = 11745.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.80
r_work: 0.3312 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8300  Z= 0.152
  Angle     :  0.531   8.718  11258  Z= 0.274
  Chirality :  0.040   0.243   1354
  Planarity :  0.004   0.061   1379
  Dihedral  :  9.632 174.907   1127
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 18.57 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.26), residues: 1015
  helix:  1.94 (0.19), residues: 730
  sheet:  1.06 (0.72), residues: 53
  loop :  0.23 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 643 
 HIS   0.003   0.001   HIS A 458 
 PHE   0.016   0.002   PHE A 972 
 TYR   0.012   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A1169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04140 (  578)
  hydrogen bonds       : angle       4.01196 ( 1704)
  covalent geometry    : bond        0.00345 ( 8300)
  covalent geometry    : angle       0.53053 (11258)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 221
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A  108 ILE cc_start: 0.8075 (mm) cc_final: 0.7807 (mt)
REVERT: A  120 VAL cc_start: 0.8031 (t) cc_final: 0.7437 (p)
REVERT: A  124 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7405 (mt-10)
REVERT: A  137 VAL cc_start: 0.8652 (t) cc_final: 0.8452 (m)
REVERT: A  140 GLN cc_start: 0.8277 (mp-120) cc_final: 0.7906 (mp10)
REVERT: A  155 ASP cc_start: 0.8326 (t0) cc_final: 0.7972 (t0)
REVERT: A  161 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7705 (mtt180)
REVERT: A  187 ASN cc_start: 0.7868 (m-40) cc_final: 0.7506 (m-40)
REVERT: A  229 ILE cc_start: 0.8432 (mm) cc_final: 0.8216 (mt)
REVERT: A  256 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7605 (tm-30)
REVERT: A  355 MET cc_start: 0.8459 (tmm) cc_final: 0.7901 (tmm)
REVERT: A  366 MET cc_start: 0.8349 (mtp) cc_final: 0.8109 (mtp)
REVERT: A  443 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7723 (tp30)
REVERT: A  450 VAL cc_start: 0.8379 (m) cc_final: 0.8128 (p)
REVERT: A  474 ILE cc_start: 0.8416 (tp) cc_final: 0.8171 (tt)
REVERT: A  511 MET cc_start: 0.8188 (tmm) cc_final: 0.7806 (tmm)
REVERT: A  588 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7740 (ttpp)
REVERT: A  596 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8086 (ttmt)
REVERT: A  629 ASP cc_start: 0.7886 (p0) cc_final: 0.7657 (m-30)
REVERT: A  633 LYS cc_start: 0.8363 (mttt) cc_final: 0.8136 (mmtm)
REVERT: A  634 SER cc_start: 0.8115 (m) cc_final: 0.7814 (p)
REVERT: A  646 ARG cc_start: 0.7701 (ttp-170) cc_final: 0.7418 (ttp-170)
REVERT: A  684 ILE cc_start: 0.7266 (mm) cc_final: 0.6879 (pt)
REVERT: A  697 MET cc_start: 0.5725 (tpp) cc_final: 0.5326 (tpp)
REVERT: A  812 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7347 (ttm110)
REVERT: A  854 ILE cc_start: 0.7869 (pt) cc_final: 0.7583 (pt)
REVERT: A  857 MET cc_start: 0.8092 (ptt) cc_final: 0.7871 (ppp)
REVERT: A  931 GLU cc_start: 0.8054 (tt0) cc_final: 0.7651 (mt-10)
REVERT: A  974 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7965 (mtpp)
REVERT: A  996 ASP cc_start: 0.7617 (m-30) cc_final: 0.7414 (m-30)
REVERT: A 1118 LYS cc_start: 0.4229 (tmtt) cc_final: 0.2340 (mttm)
REVERT: A 1122 GLU cc_start: 0.7342 (tt0) cc_final: 0.6678 (tt0)
REVERT: A 1123 ARG cc_start: 0.7879 (mmt180) cc_final: 0.6903 (mmt180)
REVERT: A 1143 GLU cc_start: 0.6926 (tt0) cc_final: 0.6691 (mt-10)
REVERT: A 1182 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6318 (mp0)
  outliers start: 32
  outliers final: 29
  residues processed: 233
  average time/residue: 0.2195
  time to fit residues: 67.4551
Evaluate side-chains
  248 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 219
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  499 ARG
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  946 SER
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1002 VAL
Chi-restraints excluded: chain A residue 1047 VAL
Chi-restraints excluded: chain A residue 1062 THR
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1097 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0370
   chunk 30 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 101 optimal weight:    0.0980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
** A1133 HIS ** 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 = 0.3809 r_free = 0.3809 target = 0.144873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.118141 restraints weight = 11940.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.81
r_work: 0.3298 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8300  Z= 0.127
  Angle     :  0.512   8.146  11258  Z= 0.266
  Chirality :  0.040   0.238   1354
  Planarity :  0.004   0.059   1379
  Dihedral  :  9.620 174.603   1127
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 19.03 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.26), residues: 1015
  helix:  1.98 (0.19), residues: 730
  sheet:  1.02 (0.72), residues: 53
  loop :  0.27 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 643 
 HIS   0.002   0.001   HIS A 676 
 PHE   0.011   0.001   PHE A 972 
 TYR   0.009   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A1169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 (  578)
  hydrogen bonds       : angle       3.95320 ( 1704)
  covalent geometry    : bond        0.00286 ( 8300)
  covalent geometry    : angle       0.51162 (11258)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5110.35 seconds
wall clock time: 88 minutes 46.31 seconds (5326.31 seconds total)