Starting phenix.real_space_refine
on Wed Mar  4 05:29:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s62_24847/03_2026/7s62_24847.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s62_24847/03_2026/7s62_24847.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s62_24847/03_2026/7s62_24847.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s62_24847/03_2026/7s62_24847.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s62_24847/03_2026/7s62_24847.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s62_24847/03_2026/7s62_24847.map"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    7000      2.51       5
     N    1768      2.21       5
     O    2191      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11013
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1382, 10775
          Classifications: {'peptide': 1382}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 61, 'TRANS': 1320}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 238
          Unusual residues: {'NAG': 17}
          Classifications: {'undetermined': 17}
          Link IDs: {None: 16}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 17
  Time building chain proxies: 2.39, per 1000 atoms: 0.22
  Number of scatterers: 11013
  At special positions: 0
  Unit cell: (126.42, 132.3, 107.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    2191      8.00
     N    1768      7.00
     C    7000      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  42 " - pdb=" SG  CYS A  80 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 122 " - pdb=" SG  CYS A 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 262 " - pdb=" SG  CYS A 283 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 467 " - pdb=" SG  CYS A 559 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 591 " - pdb=" SG  CYS A 758 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 809 " - pdb=" SG  CYS A 836 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1327 " - pdb=" SG  CYS A1441 " distance=2.03

  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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG A2101 " - " ASN A  64 "
      " NAG A2102 " - " ASN A  81 "
      " NAG A2103 " - " ASN A 242 "
      " NAG A2104 " - " ASN A 285 "
      " NAG A2105 " - " ASN A 415 "
      " NAG A2106 " - " ASN A 472 "
      " NAG A2107 " - " ASN A 526 "
      " NAG A2108 " - " ASN A 578 "
      " NAG A2109 " - " ASN A 721 "
      " NAG A2110 " - " ASN A 773 "
      " NAG A2111 " - " ASN A 918 "
      " NAG A2112 " - " ASN A 977 "
      " NAG A2113 " - " ASN A1096 "
      " NAG A2114 " - " ASN A1266 "
      " NAG A2115 " - " ASN A1286 "
      " NAG A2116 " - " ASN A1292 "
      " NAG A2117 " - " ASN A1348 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 543.7 milliseconds
  

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2582

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 26 sheets defined
      15.3% alpha, 30.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 612 through 617
    Processing helix  chain 'A' and resid 664 through 669
    Processing helix  chain 'A' and resid 942 through 946
      removed outlier: 3.579A  pdb=" N   LEU A 945 " --> pdb=" O   GLY A 942 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER A 946 " --> pdb=" O   LEU A 943 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 942 through 946'
    Processing helix  chain 'A' and resid 958 through 963
    Processing helix  chain 'A' and resid 968 through 979
    Processing helix  chain 'A' and resid 983 through 1002
    Processing helix  chain 'A' and resid 1003 through 1005
      No H-bonds generated for 'chain 'A' and resid 1003 through 1005'
    Processing helix  chain 'A' and resid 1022 through 1036
    Processing helix  chain 'A' and resid 1043 through 1057
      removed outlier: 3.654A  pdb=" N   GLN A1047 " --> pdb=" O   ASP A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1078
      No H-bonds generated for 'chain 'A' and resid 1076 through 1078'
    Processing helix  chain 'A' and resid 1079 through 1095
    Processing helix  chain 'A' and resid 1101 through 1113
      removed outlier: 3.851A  pdb=" N   ALA A1113 " --> pdb=" O   GLY A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1134
      removed outlier: 3.669A  pdb=" N   SER A1125 " --> pdb=" O   LEU A1121 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TYR A1126 " --> pdb=" O   TYR A1122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1138 through 1150
      removed outlier: 3.712A  pdb=" N   SER A1149 " --> pdb=" O   ASN A1145 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LYS A1150 " --> pdb=" O   GLU A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1180 through 1195
      removed outlier: 3.982A  pdb=" N   GLU A1184 " --> pdb=" O   PRO A1180 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE A1185 " --> pdb=" O   ALA A1181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1200 through 1217
      removed outlier: 3.894A  pdb=" N   THR A1205 " --> pdb=" O   HIS A1201 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   TYR A1206 " --> pdb=" O   ASP A1202 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   TRP A1213 " --> pdb=" O   GLN A1209 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A1214 " --> pdb=" O   ILE A1210 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLN A1217 " --> pdb=" O   TRP A1213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1226 through 1243
      removed outlier: 4.020A  pdb=" N   VAL A1232 " --> pdb=" O   GLN A1228 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU A1243 " --> pdb=" O   PHE A1239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1366 through 1376
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84
      removed outlier: 8.856A  pdb=" N   ARG A  40 " --> pdb=" O   PRO A  30 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE A  29 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34
      removed outlier: 6.684A  pdb=" N   LEU A  33 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE A  95 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 124
    Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 138
    Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 155
    Processing sheet with id=AA6, first strand: chain 'A' and resid 170 through 171
      removed outlier: 3.770A  pdb=" N   VAL A 158 " --> pdb=" O   TRP A 171 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 223 through 226
    Processing sheet with id=AA8, first strand: chain 'A' and resid 231 through 233
      removed outlier: 6.325A  pdb=" N   ILE A 232 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 238 through 239
    Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348
    Processing sheet with id=AB2, first strand: chain 'A' and resid 344 through 348
    Processing sheet with id=AB3, first strand: chain 'A' and resid 356 through 357
    Processing sheet with id=AB4, first strand: chain 'A' and resid 394 through 395
    Processing sheet with id=AB5, first strand: chain 'A' and resid 454 through 458
    Processing sheet with id=AB6, first strand: chain 'A' and resid 503 through 512
      removed outlier: 5.187A  pdb=" N   GLN A 505 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA A 497 " --> pdb=" O   GLN A 505 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   THR A 492 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 5.150A  pdb=" N   ILE A 542 " --> pdb=" O   THR A 492 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 572 through 573
    Processing sheet with id=AB8, first strand: chain 'A' and resid 578 through 583
    Processing sheet with id=AB9, first strand: chain 'A' and resid 590 through 596
    Processing sheet with id=AC1, first strand: chain 'A' and resid 647 through 648
    Processing sheet with id=AC2, first strand: chain 'A' and resid 780 through 785
      removed outlier: 3.659A  pdb=" N   SER A 785 " --> pdb=" O   LYS A 799 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   LYS A 799 " --> pdb=" O   SER A 785 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 802 " --> pdb=" O   SER A 841 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLY A 839 " --> pdb=" O   ASN A 804 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ASN A 846 " --> pdb=" O   ILE A 825 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 789 through 791
      removed outlier: 6.242A  pdb=" N   LEU A 790 " --> pdb=" O   GLN A 892 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR A 815 " --> pdb=" O   SER A 860 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'A' and resid 896 through 913
      removed outlier: 3.751A  pdb=" N   SER A1301 " --> pdb=" O   SER A 902 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   GLY A1293 " --> pdb=" O   ASP A 910 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   ASN A 912 " --> pdb=" O   ILE A1291 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ILE A1291 " --> pdb=" O   ASN A 912 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLY A1263 " --> pdb=" O   LEU A1255 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   SER A1257 " --> pdb=" O   ASP A1261 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   ASP A1261 " --> pdb=" O   SER A1257 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 896 through 913
      removed outlier: 3.751A  pdb=" N   SER A1301 " --> pdb=" O   SER A 902 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   GLY A1293 " --> pdb=" O   ASP A 910 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   ASN A 912 " --> pdb=" O   ILE A1291 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ILE A1291 " --> pdb=" O   ASN A 912 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A1298 " --> pdb=" O   VAL A 937 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   ALA A 932 " --> pdb=" O   LEU A1280 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'A' and resid 1152 through 1153
    Processing sheet with id=AC7, first strand: chain 'A' and resid 1317 through 1324
      removed outlier: 3.984A  pdb=" N   GLN A1364 " --> pdb=" O   LEU A1408 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'A' and resid 1381 through 1385
      removed outlier: 3.583A  pdb=" N   LYS A1381 " --> pdb=" O   TYR A1392 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   SER A1420 " --> pdb=" O   GLN A1358 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1059 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: 2.41

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3526
        1.34 -     1.46: 2633
        1.46 -     1.58: 5002
        1.58 -     1.70: 0
        1.70 -     1.82: 77
  Bond restraints: 11238
  Sorted by residual:
  bond pdb=" C1  NAG A2103 "
       pdb=" O5  NAG A2103 "
    ideal  model  delta    sigma   weight residual
    1.406  1.486 -0.080 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" C1  NAG A2109 "
       pdb=" O5  NAG A2109 "
    ideal  model  delta    sigma   weight residual
    1.406  1.484 -0.078 2.00e-02 2.50e+03 1.51e+01
  bond pdb=" N   PRO A  74 "
       pdb=" CA  PRO A  74 "
    ideal  model  delta    sigma   weight residual
    1.465  1.505 -0.040 2.03e-02 2.43e+03 3.88e+00
  bond pdb=" C1  NAG A2102 "
       pdb=" O5  NAG A2102 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.62e+00
  bond pdb=" CB  PRO A 893 "
       pdb=" CG  PRO A 893 "
    ideal  model  delta    sigma   weight residual
    1.492  1.581 -0.089 5.00e-02 4.00e+02 3.13e+00
  ... (remaining 11233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.62: 15254
        4.62 -     9.24: 28
        9.24 -    13.86: 1
       13.86 -    18.48: 0
       18.48 -    23.10: 1
  Bond angle restraints: 15284
  Sorted by residual:
  angle pdb=" C   GLN A  73 "
        pdb=" N   PRO A  74 "
        pdb=" CD  PRO A  74 "
      ideal   model   delta    sigma   weight residual
     125.00  101.90   23.10 4.10e+00 5.95e-02 3.18e+01
  angle pdb=" CA  PRO A 893 "
        pdb=" N   PRO A 893 "
        pdb=" CD  PRO A 893 "
      ideal   model   delta    sigma   weight residual
     112.00  105.71    6.29 1.40e+00 5.10e-01 2.02e+01
  angle pdb=" N   PRO A  74 "
        pdb=" CA  PRO A  74 "
        pdb=" C   PRO A  74 "
      ideal   model   delta    sigma   weight residual
     110.70  116.08   -5.38 1.22e+00 6.72e-01 1.94e+01
  angle pdb=" N   GLY A 867 "
        pdb=" CA  GLY A 867 "
        pdb=" C   GLY A 867 "
      ideal   model   delta    sigma   weight residual
     112.73  117.33   -4.60 1.20e+00 6.94e-01 1.47e+01
  angle pdb=" CB  MET A1359 "
        pdb=" CG  MET A1359 "
        pdb=" SD  MET A1359 "
      ideal   model   delta    sigma   weight residual
     112.70  102.76    9.94 3.00e+00 1.11e-01 1.10e+01
  ... (remaining 15279 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.87: 6403
       23.87 -    47.75: 417
       47.75 -    71.62: 77
       71.62 -    95.49: 40
       95.49 -   119.36: 23
  Dihedral angle restraints: 6960
    sinusoidal: 2926
      harmonic: 4034
  Sorted by residual:
  dihedral pdb=" CB  CYS A1327 "
           pdb=" SG  CYS A1327 "
           pdb=" SG  CYS A1441 "
           pdb=" CB  CYS A1441 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.26   71.26     1      1.00e+01 1.00e-02 6.52e+01
  dihedral pdb=" CA  LEU A 590 "
           pdb=" C   LEU A 590 "
           pdb=" N   CYS A 591 "
           pdb=" CA  CYS A 591 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.31  -29.69     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CB  CYS A  42 "
           pdb=" SG  CYS A  42 "
           pdb=" SG  CYS A  80 "
           pdb=" CB  CYS A  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -45.51  -40.49     1      1.00e+01 1.00e-02 2.30e+01
  ... (remaining 6957 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1497
       0.065 -    0.131: 284
       0.131 -    0.196: 16
       0.196 -    0.262: 1
       0.262 -    0.327: 2
  Chirality restraints: 1800
  Sorted by residual:
  chirality pdb=" C1  NAG A2108 "
            pdb=" ND2 ASN A 578 "
            pdb=" C2  NAG A2108 "
            pdb=" O5  NAG A2108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.68e+00
  chirality pdb=" C1  NAG A2114 "
            pdb=" ND2 ASN A1266 "
            pdb=" C2  NAG A2114 "
            pdb=" O5  NAG A2114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" C1  NAG A2101 "
            pdb=" ND2 ASN A  64 "
            pdb=" C2  NAG A2101 "
            pdb=" O5  NAG A2101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1797 not shown)

  Planarity restraints: 1962
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A  73 "    0.118 5.00e-02 4.00e+02   1.82e-01 5.28e+01
        pdb=" N   PRO A  74 "   -0.314 5.00e-02 4.00e+02
        pdb=" CA  PRO A  74 "    0.110 5.00e-02 4.00e+02
        pdb=" CD  PRO A  74 "    0.085 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 892 "    0.084 5.00e-02 4.00e+02   1.24e-01 2.48e+01
        pdb=" N   PRO A 893 "   -0.215 5.00e-02 4.00e+02
        pdb=" CA  PRO A 893 "    0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO A 893 "    0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  73 "   -0.013 2.00e-02 2.50e+03   2.67e-02 7.13e+00
        pdb=" C   GLN A  73 "    0.046 2.00e-02 2.50e+03
        pdb=" O   GLN A  73 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PRO A  74 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1959 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.34: 19
        2.34 -     2.98: 5503
        2.98 -     3.62: 15351
        3.62 -     4.26: 22838
        4.26 -     4.90: 39111
  Nonbonded interactions: 82822
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A 958 "
            pdb=" CD  GLN A 961 "
     model   vdw
     1.694 3.630
  nonbonded pdb=" SG  CYS A 958 "
            pdb=" CG  GLN A 961 "
     model   vdw
     2.059 3.800
  nonbonded pdb=" ND2 ASN A1219 "
            pdb=" O   GLY A1223 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" O   GLY A 453 "
            pdb=" OG  SER A 480 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OE1 GLU A 324 "
            pdb=" OG1 THR A 327 "
     model   vdw
     2.200 3.040
  ... (remaining 82817 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.340
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089  11263  Z= 0.200
  Angle     :  0.751  23.104  15349  Z= 0.365
  Chirality :  0.049   0.327   1800
  Planarity :  0.006   0.182   1945
  Dihedral  : 19.021 119.364   4357
  Min Nonbonded Distance : 1.694

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.87 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.41 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.23), residues: 1376
  helix:  1.58 (0.37), residues: 194
  sheet: -0.45 (0.25), residues: 488
  loop : -2.05 (0.23), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 476 
 TYR   0.023   0.001   TYR A 449 
 PHE   0.021   0.002   PHE A 765 
 TRP   0.016   0.001   TRP A1160 
 HIS   0.005   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (11238)
  covalent geometry    : angle       0.71544 (15284)
  SS BOND              : bond        0.00324 (    7)
  SS BOND              : angle       1.99944 (   14)
  hydrogen bonds       : bond        0.14185 (  365)
  hydrogen bonds       : angle       6.42135 ( 1059)
  Misc. bond           : bond        0.00135 (    1)
  link_NAG-ASN         : bond        0.00690 (   17)
  link_NAG-ASN         : angle       3.88069 (   51)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A 1343 TYR cc_start: 0.8147 (t80) cc_final: 0.7920 (t80)
REVERT: A 1409 ILE cc_start: 0.8192 (tt) cc_final: 0.7931 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0807
  time to fit residues: 20.8916
Evaluate side-chains
  137 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    0.4980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A1001 GLN
A1217 GLN
** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.164366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.139740 restraints weight = 15228.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.138861 restraints weight = 24335.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.140271 restraints weight = 23255.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.139806 restraints weight = 15374.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.140311 restraints weight = 16157.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.0930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  11263  Z= 0.141
  Angle     :  0.701  13.293  15349  Z= 0.332
  Chirality :  0.050   0.341   1800
  Planarity :  0.006   0.149   1945
  Dihedral  : 11.432 104.628   1853
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.70 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  9.32 %
    Favored  : 89.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.23), residues: 1376
  helix:  1.80 (0.38), residues: 193
  sheet: -0.30 (0.25), residues: 473
  loop : -2.01 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1304 
 TYR   0.014   0.001   TYR A 449 
 PHE   0.020   0.001   PHE A1245 
 TRP   0.007   0.001   TRP A 728 
 HIS   0.004   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (11238)
  covalent geometry    : angle       0.66738 (15284)
  SS BOND              : bond        0.00497 (    7)
  SS BOND              : angle       1.30552 (   14)
  hydrogen bonds       : bond        0.03355 (  365)
  hydrogen bonds       : angle       5.29819 ( 1059)
  Misc. bond           : bond        0.00075 (    1)
  link_NAG-ASN         : bond        0.00800 (   17)
  link_NAG-ASN         : angle       3.74980 (   51)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 159
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: A  201 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7325 (tm-30)
REVERT: A 1309 VAL cc_start: 0.8527 (t) cc_final: 0.8294 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 162
  average time/residue: 0.0871
  time to fit residues: 21.5475
Evaluate side-chains
  142 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 137
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1217 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 128 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 68 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 99 optimal weight:    0.6980
   chunk 133 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 426 HIS
A 512 HIS
A1217 GLN
A1218 GLN
** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.165086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.149874 restraints weight = 15366.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.146641 restraints weight = 25841.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.143805 restraints weight = 26970.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.144297 restraints weight = 25299.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.144552 restraints weight = 20212.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11263  Z= 0.143
  Angle     :  0.680  16.859  15349  Z= 0.323
  Chirality :  0.048   0.358   1800
  Planarity :  0.006   0.164   1945
  Dihedral  :  8.831 104.639   1853
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.36 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.00 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.23), residues: 1376
  helix:  1.89 (0.38), residues: 193
  sheet: -0.23 (0.25), residues: 478
  loop : -1.98 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 209 
 TYR   0.019   0.001   TYR A 449 
 PHE   0.020   0.001   PHE A1245 
 TRP   0.007   0.001   TRP A 728 
 HIS   0.004   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (11238)
  covalent geometry    : angle       0.64376 (15284)
  SS BOND              : bond        0.00352 (    7)
  SS BOND              : angle       1.04592 (   14)
  hydrogen bonds       : bond        0.03345 (  365)
  hydrogen bonds       : angle       5.11849 ( 1059)
  Misc. bond           : bond        0.00086 (    1)
  link_NAG-ASN         : bond        0.00763 (   17)
  link_NAG-ASN         : angle       3.81854 (   51)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7442 (tm-30)
REVERT: A  222 PHE cc_start: 0.7842 (m-80) cc_final: 0.7503 (m-80)
REVERT: A  430 TYR cc_start: 0.7090 (m-80) cc_final: 0.6749 (m-10)
REVERT: A  484 MET cc_start: 0.5856 (ppp) cc_final: 0.4932 (ppp)
REVERT: A 1309 VAL cc_start: 0.8652 (t) cc_final: 0.8435 (m)
REVERT: A 1343 TYR cc_start: 0.7905 (t80) cc_final: 0.7606 (t80)
  outliers start: 17
  outliers final: 9
  residues processed: 159
  average time/residue: 0.0749
  time to fit residues: 18.4609
Evaluate side-chains
  144 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 135
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  591 CYS
Chi-restraints excluded: chain A residue 1073 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 136 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  76 HIS
A 210 GLN
A1217 GLN
A1218 GLN
** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.159415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.134211 restraints weight = 15568.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.132545 restraints weight = 23358.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.133894 restraints weight = 25824.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.134460 restraints weight = 15316.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.134920 restraints weight = 13719.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  11263  Z= 0.189
  Angle     :  0.700  18.618  15349  Z= 0.339
  Chirality :  0.049   0.329   1800
  Planarity :  0.006   0.166   1945
  Dihedral  :  8.531 103.938   1853
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.43 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.65 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.23), residues: 1376
  helix:  1.67 (0.38), residues: 195
  sheet: -0.35 (0.24), residues: 497
  loop : -2.07 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 652 
 TYR   0.022   0.002   TYR A 449 
 PHE   0.026   0.002   PHE A 765 
 TRP   0.009   0.001   TRP A1015 
 HIS   0.004   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (11238)
  covalent geometry    : angle       0.66516 (15284)
  SS BOND              : bond        0.00371 (    7)
  SS BOND              : angle       1.19224 (   14)
  hydrogen bonds       : bond        0.03535 (  365)
  hydrogen bonds       : angle       5.17052 ( 1059)
  Misc. bond           : bond        0.00132 (    1)
  link_NAG-ASN         : bond        0.00768 (   17)
  link_NAG-ASN         : angle       3.82779 (   51)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7412 (tm-30)
REVERT: A  222 PHE cc_start: 0.7870 (m-80) cc_final: 0.7328 (m-80)
REVERT: A 1188 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8319 (m-10)
REVERT: A 1217 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7434 (mp-120)
REVERT: A 1278 LEU cc_start: 0.8405 (tt) cc_final: 0.8173 (mp)
REVERT: A 1426 TYR cc_start: 0.8438 (t80) cc_final: 0.7783 (t80)
  outliers start: 27
  outliers final: 19
  residues processed: 165
  average time/residue: 0.0805
  time to fit residues: 20.4294
Evaluate side-chains
  161 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  591 CYS
Chi-restraints excluded: chain A residue  748 THR
Chi-restraints excluded: chain A residue  758 CYS
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1188 TYR
Chi-restraints excluded: chain A residue 1217 GLN
Chi-restraints excluded: chain A residue 1307 ILE
Chi-restraints excluded: chain A residue 1425 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 126 optimal weight:    1.9990
   chunk 121 optimal weight:    7.9990
   chunk 95 optimal weight:    0.3980
   chunk 2 optimal weight:    0.5980
   chunk 11 optimal weight:    0.4980
   chunk 119 optimal weight:   10.0000
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 426 HIS
A1217 GLN
** A1378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.164881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.148094 restraints weight = 15236.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.146659 restraints weight = 26875.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.146179 restraints weight = 28168.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.145487 restraints weight = 23143.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.145755 restraints weight = 20689.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11263  Z= 0.130
  Angle     :  0.653  19.735  15349  Z= 0.314
  Chirality :  0.047   0.328   1800
  Planarity :  0.006   0.172   1945
  Dihedral  :  8.105 103.590   1853
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.14 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.64 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.23), residues: 1376
  helix:  1.84 (0.38), residues: 196
  sheet: -0.19 (0.25), residues: 485
  loop : -2.05 (0.23), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 897 
 TYR   0.021   0.001   TYR A 449 
 PHE   0.021   0.001   PHE A1245 
 TRP   0.007   0.001   TRP A 728 
 HIS   0.004   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11238)
  covalent geometry    : angle       0.62093 (15284)
  SS BOND              : bond        0.00307 (    7)
  SS BOND              : angle       1.03156 (   14)
  hydrogen bonds       : bond        0.03208 (  365)
  hydrogen bonds       : angle       4.95278 ( 1059)
  Misc. bond           : bond        0.00106 (    1)
  link_NAG-ASN         : bond        0.00729 (   17)
  link_NAG-ASN         : angle       3.53772 (   51)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.7791 (m-80) cc_final: 0.7298 (m-80)
REVERT: A  484 MET cc_start: 0.6089 (ppp) cc_final: 0.5066 (ppp)
REVERT: A  667 GLN cc_start: 0.7863 (mp10) cc_final: 0.7469 (mp10)
REVERT: A  897 ARG cc_start: 0.7003 (mmm-85) cc_final: 0.6562 (ttm-80)
REVERT: A 1188 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8501 (m-10)
REVERT: A 1217 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7173 (mt0)
REVERT: A 1343 TYR cc_start: 0.7912 (t80) cc_final: 0.7586 (t80)
  outliers start: 30
  outliers final: 21
  residues processed: 173
  average time/residue: 0.0796
  time to fit residues: 21.3264
Evaluate side-chains
  161 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  591 CYS
Chi-restraints excluded: chain A residue  758 CYS
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1064 CYS
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1188 TYR
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1217 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 126 optimal weight:    7.9990
   chunk 91 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 81 optimal weight:    6.9990
   chunk 119 optimal weight:   20.0000
   chunk 5 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 135 optimal weight:    2.9990
   chunk 124 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 426 HIS
A1217 GLN
** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.166891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.149069 restraints weight = 15355.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.147197 restraints weight = 25713.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.147130 restraints weight = 27474.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.146012 restraints weight = 24592.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.146549 restraints weight = 21640.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11263  Z= 0.131
  Angle     :  0.653  21.276  15349  Z= 0.313
  Chirality :  0.047   0.326   1800
  Planarity :  0.006   0.176   1945
  Dihedral  :  7.959 103.208   1853
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.99 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.97 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.23), residues: 1376
  helix:  1.85 (0.37), residues: 196
  sheet: -0.21 (0.25), residues: 481
  loop : -2.02 (0.23), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 897 
 TYR   0.017   0.001   TYR A 449 
 PHE   0.021   0.001   PHE A1245 
 TRP   0.007   0.001   TRP A 728 
 HIS   0.004   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (11238)
  covalent geometry    : angle       0.62271 (15284)
  SS BOND              : bond        0.00429 (    7)
  SS BOND              : angle       1.18068 (   14)
  hydrogen bonds       : bond        0.03153 (  365)
  hydrogen bonds       : angle       4.89048 ( 1059)
  Misc. bond           : bond        0.00101 (    1)
  link_NAG-ASN         : bond        0.00719 (   17)
  link_NAG-ASN         : angle       3.43435 (   51)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 144
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 PRO cc_start: 0.5178 (OUTLIER) cc_final: 0.4958 (Cg_exo)
REVERT: A  222 PHE cc_start: 0.7819 (m-80) cc_final: 0.7338 (m-80)
REVERT: A  479 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7246 (mp)
REVERT: A  484 MET cc_start: 0.6013 (ppp) cc_final: 0.4983 (ppp)
REVERT: A  667 GLN cc_start: 0.7942 (mp10) cc_final: 0.7447 (mp10)
REVERT: A 1158 LEU cc_start: 0.8142 (mt) cc_final: 0.7825 (mt)
REVERT: A 1188 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8563 (m-10)
REVERT: A 1217 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7254 (mt0)
  outliers start: 36
  outliers final: 24
  residues processed: 173
  average time/residue: 0.0793
  time to fit residues: 21.1964
Evaluate side-chains
  166 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   74 PRO
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  591 CYS
Chi-restraints excluded: chain A residue  758 CYS
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1052 LEU
Chi-restraints excluded: chain A residue 1064 CYS
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1188 TYR
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1217 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 121 optimal weight:    7.9990
   chunk 69 optimal weight:    0.6980
   chunk 114 optimal weight:    0.0040
   chunk 43 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A1217 GLN
A1242 GLN
** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.166713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.148274 restraints weight = 15155.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.146394 restraints weight = 25619.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.147019 restraints weight = 25442.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.146832 restraints weight = 18298.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.147097 restraints weight = 18358.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11263  Z= 0.130
  Angle     :  0.654  20.410  15349  Z= 0.314
  Chirality :  0.047   0.327   1800
  Planarity :  0.006   0.173   1945
  Dihedral  :  7.847 102.552   1853
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.36 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 18.38 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.23), residues: 1376
  helix:  1.82 (0.38), residues: 197
  sheet: -0.21 (0.25), residues: 480
  loop : -1.97 (0.23), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1304 
 TYR   0.025   0.001   TYR A 449 
 PHE   0.022   0.001   PHE A1245 
 TRP   0.009   0.001   TRP A 845 
 HIS   0.004   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11238)
  covalent geometry    : angle       0.62549 (15284)
  SS BOND              : bond        0.00310 (    7)
  SS BOND              : angle       1.06926 (   14)
  hydrogen bonds       : bond        0.03141 (  365)
  hydrogen bonds       : angle       4.85323 ( 1059)
  Misc. bond           : bond        0.00101 (    1)
  link_NAG-ASN         : bond        0.00708 (   17)
  link_NAG-ASN         : angle       3.35110 (   51)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 150
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 PRO cc_start: 0.4972 (OUTLIER) cc_final: 0.4732 (Cg_exo)
REVERT: A  124 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7569 (mm)
REVERT: A  222 PHE cc_start: 0.7824 (m-80) cc_final: 0.7357 (m-80)
REVERT: A  235 LEU cc_start: 0.7646 (pt) cc_final: 0.7265 (pp)
REVERT: A  479 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7262 (mp)
REVERT: A  484 MET cc_start: 0.6123 (ppp) cc_final: 0.5051 (ppp)
REVERT: A  667 GLN cc_start: 0.7830 (mp10) cc_final: 0.7345 (mp10)
REVERT: A 1158 LEU cc_start: 0.8400 (mt) cc_final: 0.8179 (mt)
REVERT: A 1188 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8570 (m-10)
  outliers start: 39
  outliers final: 30
  residues processed: 182
  average time/residue: 0.0729
  time to fit residues: 20.9868
Evaluate side-chains
  177 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 143
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   74 PRO
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  591 CYS
Chi-restraints excluded: chain A residue  758 CYS
Chi-restraints excluded: chain A residue  824 VAL
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1064 CYS
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1188 TYR
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1217 GLN
Chi-restraints excluded: chain A residue 1331 VAL
Chi-restraints excluded: chain A residue 1354 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 135 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 426 HIS
A1217 GLN
A1300 GLN
** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.159647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.135333 restraints weight = 15397.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.134381 restraints weight = 25243.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.135927 restraints weight = 24716.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.135848 restraints weight = 16126.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.136291 restraints weight = 17575.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11263  Z= 0.185
  Angle     :  0.700  19.948  15349  Z= 0.338
  Chirality :  0.048   0.333   1800
  Planarity :  0.006   0.171   1945
  Dihedral  :  7.998 102.105   1853
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.94 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.55 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.23), residues: 1376
  helix:  1.68 (0.38), residues: 198
  sheet: -0.36 (0.25), residues: 488
  loop : -2.06 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 652 
 TYR   0.021   0.002   TYR A 449 
 PHE   0.022   0.002   PHE A1245 
 TRP   0.010   0.001   TRP A 845 
 HIS   0.004   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (11238)
  covalent geometry    : angle       0.67234 (15284)
  SS BOND              : bond        0.00208 (    7)
  SS BOND              : angle       1.31005 (   14)
  hydrogen bonds       : bond        0.03418 (  365)
  hydrogen bonds       : angle       5.02503 ( 1059)
  Misc. bond           : bond        0.00131 (    1)
  link_NAG-ASN         : bond        0.00694 (   17)
  link_NAG-ASN         : angle       3.38004 (   51)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 146
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7619 (mm)
REVERT: A  222 PHE cc_start: 0.7830 (m-80) cc_final: 0.7361 (m-80)
REVERT: A  235 LEU cc_start: 0.7766 (pt) cc_final: 0.7380 (pp)
REVERT: A  479 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7251 (mp)
REVERT: A  667 GLN cc_start: 0.7849 (mp10) cc_final: 0.7310 (mp10)
REVERT: A 1158 LEU cc_start: 0.8649 (mt) cc_final: 0.8426 (mt)
REVERT: A 1188 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8494 (m-10)
REVERT: A 1217 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.5833 (mp-120)
  outliers start: 41
  outliers final: 31
  residues processed: 177
  average time/residue: 0.0757
  time to fit residues: 20.9989
Evaluate side-chains
  180 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 145
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  591 CYS
Chi-restraints excluded: chain A residue  748 THR
Chi-restraints excluded: chain A residue  758 CYS
Chi-restraints excluded: chain A residue  765 PHE
Chi-restraints excluded: chain A residue  824 VAL
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1064 CYS
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1188 TYR
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1217 GLN
Chi-restraints excluded: chain A residue 1331 VAL
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1425 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0030
   chunk 110 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A1217 GLN
A1300 GLN
** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.166558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.148296 restraints weight = 15069.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.147052 restraints weight = 26820.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.147300 restraints weight = 25258.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.146746 restraints weight = 20085.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.147000 restraints weight = 19846.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11263  Z= 0.136
  Angle     :  0.711  26.410  15349  Z= 0.331
  Chirality :  0.049   0.585   1800
  Planarity :  0.006   0.192   1945
  Dihedral  :  7.997 101.808   1853
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.85 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.13 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.23), residues: 1376
  helix:  1.83 (0.38), residues: 197
  sheet: -0.22 (0.25), residues: 481
  loop : -2.01 (0.23), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 652 
 TYR   0.027   0.001   TYR A 449 
 PHE   0.021   0.002   PHE A1245 
 TRP   0.007   0.001   TRP A 845 
 HIS   0.005   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (11238)
  covalent geometry    : angle       0.67039 (15284)
  SS BOND              : bond        0.00387 (    7)
  SS BOND              : angle       1.17019 (   14)
  hydrogen bonds       : bond        0.03217 (  365)
  hydrogen bonds       : angle       4.89277 ( 1059)
  Misc. bond           : bond        0.00107 (    1)
  link_NAG-ASN         : bond        0.00640 (   17)
  link_NAG-ASN         : angle       4.11391 (   51)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 147
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7551 (mm)
REVERT: A  222 PHE cc_start: 0.7932 (m-80) cc_final: 0.7483 (m-80)
REVERT: A  235 LEU cc_start: 0.7760 (pt) cc_final: 0.7341 (pp)
REVERT: A  479 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7289 (mp)
REVERT: A  484 MET cc_start: 0.6191 (ppp) cc_final: 0.5080 (ppp)
REVERT: A  667 GLN cc_start: 0.7927 (mp10) cc_final: 0.7399 (mp10)
REVERT: A 1158 LEU cc_start: 0.8462 (mt) cc_final: 0.8256 (mt)
REVERT: A 1188 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8580 (m-10)
REVERT: A 1217 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6988 (mt0)
REVERT: A 1244 LEU cc_start: 0.7912 (mt) cc_final: 0.7523 (pp)
  outliers start: 36
  outliers final: 31
  residues processed: 176
  average time/residue: 0.0716
  time to fit residues: 19.8179
Evaluate side-chains
  175 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  591 CYS
Chi-restraints excluded: chain A residue  758 CYS
Chi-restraints excluded: chain A residue  765 PHE
Chi-restraints excluded: chain A residue  824 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1064 CYS
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1188 TYR
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1217 GLN
Chi-restraints excluded: chain A residue 1331 VAL
Chi-restraints excluded: chain A residue 1354 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0670
   chunk 64 optimal weight:    2.9990
   chunk 132 optimal weight:    0.8980
   chunk 111 optimal weight:    0.3980
   chunk 3 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0670
   chunk 133 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 63 optimal weight:    0.3980
   chunk 107 optimal weight:    2.9990
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
A 375 ASN
A 426 HIS
A1217 GLN
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1387 ASN
A1388 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.170231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.153376 restraints weight = 15128.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.151828 restraints weight = 24454.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.151715 restraints weight = 24699.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.150852 restraints weight = 21851.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.151255 restraints weight = 20500.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11263  Z= 0.120
  Angle     :  0.679  22.361  15349  Z= 0.323
  Chirality :  0.048   0.447   1800
  Planarity :  0.006   0.173   1945
  Dihedral  :  7.642 101.052   1853
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.70 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 19.70 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.23), residues: 1376
  helix:  1.96 (0.38), residues: 196
  sheet: -0.13 (0.25), residues: 481
  loop : -1.96 (0.23), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1304 
 TYR   0.026   0.001   TYR A 449 
 PHE   0.021   0.001   PHE A1245 
 TRP   0.009   0.001   TRP A1213 
 HIS   0.005   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (11238)
  covalent geometry    : angle       0.64963 (15284)
  SS BOND              : bond        0.00353 (    7)
  SS BOND              : angle       1.08739 (   14)
  hydrogen bonds       : bond        0.03033 (  365)
  hydrogen bonds       : angle       4.79022 ( 1059)
  Misc. bond           : bond        0.00081 (    1)
  link_NAG-ASN         : bond        0.00602 (   17)
  link_NAG-ASN         : angle       3.47587 (   51)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7490 (mm)
REVERT: A  222 PHE cc_start: 0.7953 (m-80) cc_final: 0.7484 (m-80)
REVERT: A  235 LEU cc_start: 0.7696 (pt) cc_final: 0.7304 (pp)
REVERT: A  479 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7316 (mp)
REVERT: A  667 GLN cc_start: 0.7813 (mp10) cc_final: 0.7330 (mp10)
REVERT: A 1188 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8576 (m-10)
REVERT: A 1244 LEU cc_start: 0.7752 (mt) cc_final: 0.7443 (pp)
  outliers start: 33
  outliers final: 25
  residues processed: 169
  average time/residue: 0.0756
  time to fit residues: 20.1207
Evaluate side-chains
  166 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  591 CYS
Chi-restraints excluded: chain A residue  758 CYS
Chi-restraints excluded: chain A residue  765 PHE
Chi-restraints excluded: chain A residue  824 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  913 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1064 CYS
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1188 TYR
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1354 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 112 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 126 optimal weight:    0.0970
   chunk 72 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 133 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A 375 ASN
A1217 GLN
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.167760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.150667 restraints weight = 15215.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.148892 restraints weight = 24866.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.149104 restraints weight = 25463.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.148479 restraints weight = 19286.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.148763 restraints weight = 18921.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11263  Z= 0.127
  Angle     :  0.662  20.135  15349  Z= 0.318
  Chirality :  0.047   0.331   1800
  Planarity :  0.005   0.165   1945
  Dihedral  :  7.692 103.569   1853
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.85 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.29 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.23), residues: 1376
  helix:  2.06 (0.38), residues: 193
  sheet: -0.08 (0.25), residues: 479
  loop : -1.94 (0.23), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1304 
 TYR   0.025   0.001   TYR A 449 
 PHE   0.020   0.001   PHE A1245 
 TRP   0.009   0.001   TRP A 728 
 HIS   0.005   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (11238)
  covalent geometry    : angle       0.63528 (15284)
  SS BOND              : bond        0.00357 (    7)
  SS BOND              : angle       1.11434 (   14)
  hydrogen bonds       : bond        0.03075 (  365)
  hydrogen bonds       : angle       4.79133 ( 1059)
  Misc. bond           : bond        0.00092 (    1)
  link_NAG-ASN         : bond        0.00590 (   17)
  link_NAG-ASN         : angle       3.28398 (   51)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1658.46 seconds
wall clock time: 29 minutes 29.78 seconds (1769.78 seconds total)