Starting phenix.real_space_refine
on Wed Sep 17 07:31:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u3u_63827/09_2025/9u3u_63827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u3u_63827/09_2025/9u3u_63827.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u3u_63827/09_2025/9u3u_63827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u3u_63827/09_2025/9u3u_63827.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u3u_63827/09_2025/9u3u_63827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u3u_63827/09_2025/9u3u_63827.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.027
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      49      5.16       5
     C    4347      2.51       5
     N    1101      2.21       5
     O    1205      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6702
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 848, 6702
          Classifications: {'peptide': 848}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 825}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 1.75, per 1000 atoms: 0.26
  Number of scatterers: 6702
  At special positions: 0
  Unit cell: (64.64, 88.88, 150.49, 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      49     16.00
     O    1205      8.00
     N    1101      7.00
     C    4347      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 217 " - pdb=" SG  CYS A 268 " 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=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 335.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 6 sheets defined
      67.9% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 138
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 142 through 165
      removed outlier: 3.667A  pdb=" N   ALA A 147 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      Proline residue:  A 148  - end of helix
      removed outlier: 4.066A  pdb=" N   PHE A 164 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   THR A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 171
      removed outlier: 3.727A  pdb=" N   ALA A 169 " --> pdb=" O   THR A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 195
      removed outlier: 3.972A  pdb=" N   LEU A 195 " --> pdb=" O   GLN A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 237
      removed outlier: 3.745A  pdb=" N   SER A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 263
    Processing helix  chain 'A' and resid 279 through 336
      removed outlier: 3.989A  pdb=" N   LEU A 329 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 345
    Processing helix  chain 'A' and resid 402 through 408
    Processing helix  chain 'A' and resid 411 through 434
    Processing helix  chain 'A' and resid 457 through 481
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 3.548A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'A' and resid 549 through 555
    Processing helix  chain 'A' and resid 756 through 765
    Processing helix  chain 'A' and resid 765 through 774
    Processing helix  chain 'A' and resid 782 through 810
      removed outlier: 3.531A  pdb=" N   THR A 804 " --> pdb=" O   THR A 800 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   TYR A 809 " --> pdb=" O   CYS A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 844
    Processing helix  chain 'A' and resid 849 through 860
    Processing helix  chain 'A' and resid 861 through 882
      Proline residue:  A 876  - end of helix
      removed outlier: 3.568A  pdb=" N   ALA A 879 " --> pdb=" O   LEU A 875 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL A 880 " --> pdb=" O   PRO A 876 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   TYR A 881 " --> pdb=" O   ALA A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 909
      removed outlier: 3.777A  pdb=" N   ILE A 904 " --> pdb=" O   SER A 900 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TYR A 909 " --> pdb=" O   ALA A 905 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 928
    Processing helix  chain 'A' and resid 929 through 937
    Processing helix  chain 'A' and resid 978 through 1034
      removed outlier: 3.642A  pdb=" N   VAL A 983 " --> pdb=" O   GLY A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1047
      removed outlier: 3.564A  pdb=" N   ALA A1041 " --> pdb=" O   PRO A1037 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   GLU A1042 " --> pdb=" O   TYR A1038 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   GLN A1043 " --> pdb=" O   HIS A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1071
    Processing helix  chain 'A' and resid 1081 through 1098
      removed outlier: 3.835A  pdb=" N   LEU A1095 " --> pdb=" O   ASP A1091 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU A1096 " --> pdb=" O   PHE A1092 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER A1097 " --> pdb=" O   ASP A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1099 through 1102
      removed outlier: 3.723A  pdb=" N   SER A1102 " --> pdb=" O   PRO A1099 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1099 through 1102'
    Processing helix  chain 'A' and resid 1132 through 1144
    Processing helix  chain 'A' and resid 1144 through 1153
    Processing helix  chain 'A' and resid 1188 through 1200
    Processing helix  chain 'A' and resid 1209 through 1220
      removed outlier: 4.181A  pdb=" N   VAL A1215 " --> pdb=" O   GLU A1211 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   SER A1217 " --> pdb=" O   TYR A1213 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   LYS A1218 " --> pdb=" O   ARG A1214 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   MET A1219 " --> pdb=" O   VAL A1215 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLY A1220 " --> pdb=" O   LEU A1216 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388
      removed outlier: 3.839A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 401
      removed outlier: 3.891A  pdb=" N   VAL A 401 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE A 438 " --> pdb=" O   TYR A 446 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 401
      removed outlier: 3.891A  pdb=" N   VAL A 401 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   MET A 486 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   HIS A 530 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL A 488 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1104 through 1110
      removed outlier: 5.232A  pdb=" N   LYS A1106 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ALA A1117 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS A1108 " --> pdb=" O   MET A1115 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   SER A1051 " --> pdb=" O   VAL A1176 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   VAL A1176 " --> pdb=" O   SER A1051 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ASN A1053 " --> pdb=" O   ALA A1174 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   ALA A1174 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   ASP A1055 " --> pdb=" O   LEU A1172 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   LEU A1172 " --> pdb=" O   ASP A1055 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN A1168 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1104 through 1110
      removed outlier: 5.232A  pdb=" N   LYS A1106 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ALA A1117 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS A1108 " --> pdb=" O   MET A1115 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   SER A1051 " --> pdb=" O   VAL A1176 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   VAL A1176 " --> pdb=" O   SER A1051 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ASN A1053 " --> pdb=" O   ALA A1174 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   ALA A1174 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   ASP A1055 " --> pdb=" O   LEU A1172 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   LEU A1172 " --> pdb=" O   ASP A1055 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN A1168 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
      removed outlier: 8.829A  pdb=" N   GLN A1207 " --> pdb=" O   LEU A1163 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   VAL A1165 " --> pdb=" O   GLN A1207 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1224 through 1231
      removed outlier: 5.224A  pdb=" N   TYR A1225 " --> pdb=" O   LEU A1241 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   LEU A1241 " --> pdb=" O   TYR A1225 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY A1227 " --> pdb=" O   THR A1239 " (cutoff:3.500A)

    477 hydrogen bonds defined for protein.
    1401 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: 1.13

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2120
        1.34 -     1.46: 1697
        1.46 -     1.58: 2963
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 6852
  Sorted by residual:
  bond pdb=" CB  ASP A1015 "
       pdb=" CG  ASP A1015 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.46e+00
  bond pdb=" CA  ILE A 400 "
       pdb=" CB  ILE A 400 "
    ideal  model  delta    sigma   weight residual
    1.530  1.541 -0.011 1.05e-02 9.07e+03 1.01e+00
  bond pdb=" CB  ASP A 443 "
       pdb=" CG  ASP A 443 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.41e-01
  bond pdb=" CB  ASN A1168 "
       pdb=" CG  ASN A1168 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.36e-01
  bond pdb=" CD2 TYR A1213 "
       pdb=" CE2 TYR A1213 "
    ideal  model  delta    sigma   weight residual
    1.382  1.354  0.028 3.00e-02 1.11e+03 8.63e-01
  ... (remaining 6847 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 9173
        1.94 -     3.88: 88
        3.88 -     5.83: 18
        5.83 -     7.77: 3
        7.77 -     9.71: 1
  Bond angle restraints: 9283
  Sorted by residual:
  angle pdb=" CB  MET A 545 "
        pdb=" CG  MET A 545 "
        pdb=" SD  MET A 545 "
      ideal   model   delta    sigma   weight residual
     112.70  122.41   -9.71 3.00e+00 1.11e-01 1.05e+01
  angle pdb=" CA  MET A 849 "
        pdb=" CB  MET A 849 "
        pdb=" CG  MET A 849 "
      ideal   model   delta    sigma   weight residual
     114.10  118.99   -4.89 2.00e+00 2.50e-01 5.97e+00
  angle pdb=" N   MET A 138 "
        pdb=" CA  MET A 138 "
        pdb=" C   MET A 138 "
      ideal   model   delta    sigma   weight residual
     110.44  107.58    2.86 1.20e+00 6.94e-01 5.70e+00
  angle pdb=" CA  VAL A 237 "
        pdb=" CB  VAL A 237 "
        pdb=" CG2 VAL A 237 "
      ideal   model   delta    sigma   weight residual
     110.40  114.27   -3.87 1.70e+00 3.46e-01 5.19e+00
  angle pdb=" CA  TYR A1240 "
        pdb=" CB  TYR A1240 "
        pdb=" CG  TYR A1240 "
      ideal   model   delta    sigma   weight residual
     113.90  117.95   -4.05 1.80e+00 3.09e-01 5.05e+00
  ... (remaining 9278 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 3378
       17.73 -    35.47: 479
       35.47 -    53.20: 131
       53.20 -    70.93: 24
       70.93 -    88.66: 5
  Dihedral angle restraints: 4017
    sinusoidal: 1545
      harmonic: 2472
  Sorted by residual:
  dihedral pdb=" CA  TYR A 235 "
           pdb=" C   TYR A 235 "
           pdb=" N   THR A 236 "
           pdb=" CA  THR A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.10  -15.90     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CG  ARG A 264 "
           pdb=" CD  ARG A 264 "
           pdb=" NE  ARG A 264 "
           pdb=" CZ  ARG A 264 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.58  -43.42     2      1.50e+01 4.44e-03 1.01e+01
  dihedral pdb=" CA  THR A 236 "
           pdb=" C   THR A 236 "
           pdb=" N   VAL A 237 "
           pdb=" CA  VAL A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.43  -15.57     0      5.00e+00 4.00e-02 9.70e+00
  ... (remaining 4014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 980
       0.063 -    0.127: 83
       0.127 -    0.190: 0
       0.190 -    0.253: 0
       0.253 -    0.316: 1
  Chirality restraints: 1064
  Sorted by residual:
  chirality pdb=" CB  VAL A 237 "
            pdb=" CA  VAL A 237 "
            pdb=" CG1 VAL A 237 "
            pdb=" CG2 VAL A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" CA  ILE A1064 "
            pdb=" N   ILE A1064 "
            pdb=" C   ILE A1064 "
            pdb=" CB  ILE A1064 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  chirality pdb=" CA  ILE A1104 "
            pdb=" N   ILE A1104 "
            pdb=" C   ILE A1104 "
            pdb=" CB  ILE A1104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 1061 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 240 "   -0.033 5.00e-02 4.00e+02   4.98e-02 3.97e+00
        pdb=" N   PRO A 241 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 241 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 241 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 930 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A 931 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 931 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 931 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 761 "    0.081 9.50e-02 1.11e+02   3.66e-02 1.02e+00
        pdb=" NE  ARG A 761 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 761 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 761 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 761 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 445
        2.74 -     3.28: 7054
        3.28 -     3.82: 11335
        3.82 -     4.36: 13066
        4.36 -     4.90: 21973
  Nonbonded interactions: 53873
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 799 "
            pdb=" OG1 THR A 803 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   LYS A 434 "
            pdb=" NH2 ARG A 455 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OE1 GLU A 770 "
            pdb=" OG1 THR A 784 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" ND2 ASN A 748 "
            pdb=" OG  SER A 751 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   GLU A 331 "
            pdb=" ND1 HIS A 335 "
     model   vdw
     2.317 3.120
  ... (remaining 53868 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:             0.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.620
  Find NCS groups from input model:        0.020
  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:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
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      :  0.002   0.030   6853  Z= 0.104
  Angle     :  0.506   9.711   9285  Z= 0.258
  Chirality :  0.036   0.316   1064
  Planarity :  0.003   0.050   1159
  Dihedral  : 17.922  88.662   2416
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 32.23 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  0.92 (0.30), residues: 828
  helix:  1.19 (0.22), residues: 528
  sheet: -0.28 (0.71), residues: 59
  loop : -0.28 (0.43), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 761 
 TYR   0.009   0.001   TYR A1213 
 PHE   0.016   0.001   PHE A 785 
 TRP   0.003   0.000   TRP A1030 
 HIS   0.003   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 6852)
  covalent geometry    : angle       0.50590 ( 9283)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.18232 (    2)
  hydrogen bonds       : bond        0.25365 (  461)
  hydrogen bonds       : angle       7.91371 ( 1401)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 154
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A  798 PHE cc_start: 0.7553 (t80) cc_final: 0.7235 (t80)
REVERT: A 1156 MET cc_start: 0.7530 (tpp) cc_final: 0.7180 (mmm)
REVERT: A 1197 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6939 (mtt)
  outliers start: 3
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1062
  time to fit residues: 20.8603
Evaluate side-chains
  140 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1197 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 292 HIS
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.165953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.140966 restraints weight = 9882.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.145410 restraints weight = 5489.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.148545 restraints weight = 3739.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.150507 restraints weight = 2849.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.151753 restraints weight = 2365.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6551
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6853  Z= 0.175
  Angle     :  0.579   7.479   9285  Z= 0.313
  Chirality :  0.041   0.239   1064
  Planarity :  0.004   0.050   1159
  Dihedral  :  4.155  20.585    914
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 27.52 %
    Favored  : 66.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  1.61 (0.29), residues: 828
  helix:  1.93 (0.21), residues: 537
  sheet: -0.10 (0.62), residues: 71
  loop : -0.65 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1005 
 TYR   0.021   0.002   TYR A1240 
 PHE   0.013   0.001   PHE A 897 
 TRP   0.006   0.001   TRP A 994 
 HIS   0.004   0.001   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6852)
  covalent geometry    : angle       0.57909 ( 9283)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.10247 (    2)
  hydrogen bonds       : bond        0.05422 (  461)
  hydrogen bonds       : angle       5.06349 ( 1401)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5788 (pt)
REVERT: A  162 PHE cc_start: 0.6211 (t80) cc_final: 0.5990 (t80)
REVERT: A  240 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6736 (mt)
REVERT: A  301 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7946 (mmt)
REVERT: A  340 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5694 (mtm-85)
REVERT: A  406 MET cc_start: 0.4253 (OUTLIER) cc_final: 0.3962 (mtm)
REVERT: A  448 VAL cc_start: 0.7788 (m) cc_final: 0.7564 (t)
REVERT: A  787 SER cc_start: 0.8265 (t) cc_final: 0.7801 (m)
REVERT: A 1009 HIS cc_start: 0.8220 (t70) cc_final: 0.8017 (t-170)
REVERT: A 1025 ARG cc_start: 0.6473 (tpp80) cc_final: 0.6176 (tpp80)
REVERT: A 1106 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6385 (ttpt)
REVERT: A 1162 LYS cc_start: 0.7058 (pttt) cc_final: 0.6695 (pttt)
REVERT: A 1219 MET cc_start: 0.2192 (ttm) cc_final: 0.1974 (ttm)
  outliers start: 40
  outliers final: 17
  residues processed: 188
  average time/residue: 0.0930
  time to fit residues: 23.1003
Evaluate side-chains
  181 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  340 ARG
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1108 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 29 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 292 HIS
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.166337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.141150 restraints weight = 9786.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.145405 restraints weight = 5517.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.148474 restraints weight = 3844.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.150663 restraints weight = 2948.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.151774 restraints weight = 2438.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6552
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6853  Z= 0.145
  Angle     :  0.544   7.040   9285  Z= 0.287
  Chirality :  0.039   0.190   1064
  Planarity :  0.004   0.050   1159
  Dihedral  :  4.024  16.345    911
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 28.77 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  1.82 (0.29), residues: 828
  helix:  2.09 (0.21), residues: 531
  sheet: -0.15 (0.61), residues: 76
  loop : -0.43 (0.45), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 761 
 TYR   0.015   0.001   TYR A1240 
 PHE   0.012   0.001   PHE A1167 
 TRP   0.019   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6852)
  covalent geometry    : angle       0.54414 ( 9283)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.11778 (    2)
  hydrogen bonds       : bond        0.04857 (  461)
  hydrogen bonds       : angle       4.72011 ( 1401)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 ILE cc_start: 0.6009 (OUTLIER) cc_final: 0.5770 (pt)
REVERT: A  162 PHE cc_start: 0.6207 (t80) cc_final: 0.5952 (t80)
REVERT: A  301 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7873 (mmt)
REVERT: A  305 ARG cc_start: 0.7211 (mpt180) cc_final: 0.7009 (mtt90)
REVERT: A  396 LEU cc_start: 0.7936 (mt) cc_final: 0.7646 (tt)
REVERT: A  406 MET cc_start: 0.4197 (OUTLIER) cc_final: 0.3927 (mtm)
REVERT: A  448 VAL cc_start: 0.7887 (m) cc_final: 0.7521 (t)
REVERT: A  500 LEU cc_start: 0.8203 (mm) cc_final: 0.7788 (mp)
REVERT: A  787 SER cc_start: 0.8279 (t) cc_final: 0.7805 (m)
REVERT: A  798 PHE cc_start: 0.7849 (t80) cc_final: 0.7467 (t80)
REVERT: A  980 GLN cc_start: 0.6672 (tp40) cc_final: 0.6420 (tp40)
REVERT: A 1025 ARG cc_start: 0.6439 (tpp80) cc_final: 0.6213 (tpp80)
REVERT: A 1094 GLU cc_start: 0.6285 (tm-30) cc_final: 0.5907 (tm-30)
REVERT: A 1114 TYR cc_start: 0.8216 (t80) cc_final: 0.6827 (t80)
REVERT: A 1162 LYS cc_start: 0.7048 (pttt) cc_final: 0.6509 (pttt)
  outliers start: 28
  outliers final: 18
  residues processed: 184
  average time/residue: 0.0959
  time to fit residues: 22.9707
Evaluate side-chains
  178 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.165271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.139670 restraints weight = 9946.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.144243 restraints weight = 5586.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.147397 restraints weight = 3815.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.149493 restraints weight = 2924.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.150717 restraints weight = 2422.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6853  Z= 0.164
  Angle     :  0.546   8.370   9285  Z= 0.288
  Chirality :  0.039   0.173   1064
  Planarity :  0.004   0.053   1159
  Dihedral  :  4.108  15.062    911
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 28.49 %
    Favored  : 66.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  1.73 (0.30), residues: 828
  helix:  2.02 (0.22), residues: 537
  sheet: -0.42 (0.59), residues: 78
  loop : -0.44 (0.46), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 761 
 TYR   0.020   0.002   TYR A1240 
 PHE   0.022   0.001   PHE A1223 
 TRP   0.015   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6852)
  covalent geometry    : angle       0.54609 ( 9283)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       0.12206 (    2)
  hydrogen bonds       : bond        0.04603 (  461)
  hydrogen bonds       : angle       4.61254 ( 1401)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 162
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 ILE cc_start: 0.6175 (OUTLIER) cc_final: 0.5929 (pt)
REVERT: A  240 LEU cc_start: 0.7503 (mm) cc_final: 0.7214 (mt)
REVERT: A  305 ARG cc_start: 0.7274 (mpt180) cc_final: 0.7055 (mtt90)
REVERT: A  396 LEU cc_start: 0.7967 (mt) cc_final: 0.7653 (tt)
REVERT: A  406 MET cc_start: 0.4187 (OUTLIER) cc_final: 0.3901 (mtm)
REVERT: A  448 VAL cc_start: 0.7805 (m) cc_final: 0.7537 (t)
REVERT: A  464 GLU cc_start: 0.6193 (tm-30) cc_final: 0.5984 (tm-30)
REVERT: A  500 LEU cc_start: 0.8193 (mm) cc_final: 0.7819 (mp)
REVERT: A  787 SER cc_start: 0.8281 (t) cc_final: 0.7785 (m)
REVERT: A  980 GLN cc_start: 0.6584 (tp40) cc_final: 0.6286 (tp40)
REVERT: A 1094 GLU cc_start: 0.6390 (tm-30) cc_final: 0.6055 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6446 (ptmm)
REVERT: A 1162 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6443 (pttt)
  outliers start: 36
  outliers final: 22
  residues processed: 183
  average time/residue: 0.0920
  time to fit residues: 22.0278
Evaluate side-chains
  178 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  388 GLN
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0070
   chunk 65 optimal weight:    0.0270
   chunk 75 optimal weight:    0.2980
   chunk 70 optimal weight:    0.5980
   chunk 9 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0670
   chunk 69 optimal weight:    4.9990
   overall best weight:    0.1994

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.167611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.142375 restraints weight = 9919.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.146879 restraints weight = 5548.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.150077 restraints weight = 3815.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.151879 restraints weight = 2901.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.153405 restraints weight = 2436.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6516
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6853  Z= 0.115
  Angle     :  0.530  10.416   9285  Z= 0.274
  Chirality :  0.038   0.209   1064
  Planarity :  0.003   0.051   1159
  Dihedral  :  3.966  15.082    911
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 30.29 %
    Favored  : 65.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  1.84 (0.30), residues: 828
  helix:  2.14 (0.22), residues: 537
  sheet: -0.44 (0.64), residues: 73
  loop : -0.47 (0.45), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 761 
 TYR   0.018   0.001   TYR A1240 
 PHE   0.019   0.001   PHE A 798 
 TRP   0.012   0.001   TRP A 510 
 HIS   0.003   0.000   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6852)
  covalent geometry    : angle       0.52984 ( 9283)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.11514 (    2)
  hydrogen bonds       : bond        0.04146 (  461)
  hydrogen bonds       : angle       4.39043 ( 1401)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  143 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5834 (pt)
REVERT: A  396 LEU cc_start: 0.7974 (mt) cc_final: 0.7672 (tt)
REVERT: A  406 MET cc_start: 0.3836 (OUTLIER) cc_final: 0.3542 (mtm)
REVERT: A  433 THR cc_start: 0.5702 (m) cc_final: 0.4020 (t)
REVERT: A  464 GLU cc_start: 0.6303 (tm-30) cc_final: 0.5947 (tm-30)
REVERT: A  500 LEU cc_start: 0.8120 (mm) cc_final: 0.7833 (mp)
REVERT: A  980 GLN cc_start: 0.6461 (tp40) cc_final: 0.6113 (tp40)
REVERT: A 1094 GLU cc_start: 0.6351 (tm-30) cc_final: 0.5954 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6552 (ttpt)
REVERT: A 1114 TYR cc_start: 0.8194 (t80) cc_final: 0.5794 (t80)
REVERT: A 1162 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6385 (pttt)
REVERT: A 1219 MET cc_start: 0.1583 (ttm) cc_final: 0.1189 (ttm)
  outliers start: 29
  outliers final: 17
  residues processed: 178
  average time/residue: 0.0966
  time to fit residues: 22.3232
Evaluate side-chains
  177 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 68 optimal weight:    0.3980
   chunk 38 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.164544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.139030 restraints weight = 9846.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.143506 restraints weight = 5551.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.146613 restraints weight = 3794.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.148673 restraints weight = 2908.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.149979 restraints weight = 2418.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6612
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6853  Z= 0.207
  Angle     :  0.594  10.654   9285  Z= 0.308
  Chirality :  0.042   0.186   1064
  Planarity :  0.004   0.052   1159
  Dihedral  :  4.193  15.518    911
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 30.29 %
    Favored  : 65.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  1.67 (0.30), residues: 828
  helix:  1.98 (0.22), residues: 537
  sheet: -0.40 (0.59), residues: 78
  loop : -0.51 (0.46), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 761 
 TYR   0.019   0.002   TYR A 909 
 PHE   0.018   0.002   PHE A 798 
 TRP   0.013   0.001   TRP A 510 
 HIS   0.004   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 6852)
  covalent geometry    : angle       0.59365 ( 9283)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       0.11386 (    2)
  hydrogen bonds       : bond        0.04690 (  461)
  hydrogen bonds       : angle       4.62052 ( 1401)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 160
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  137 HIS cc_start: 0.6759 (m90) cc_final: 0.6525 (m170)
REVERT: A  143 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.6056 (pt)
REVERT: A  152 PHE cc_start: 0.5746 (t80) cc_final: 0.5421 (t80)
REVERT: A  240 LEU cc_start: 0.7702 (mm) cc_final: 0.7466 (mt)
REVERT: A  340 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.5768 (mtm-85)
REVERT: A  406 MET cc_start: 0.4189 (OUTLIER) cc_final: 0.3912 (mtm)
REVERT: A  448 VAL cc_start: 0.7880 (t) cc_final: 0.7657 (p)
REVERT: A  465 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.5551 (tpt)
REVERT: A  500 LEU cc_start: 0.8271 (mm) cc_final: 0.7958 (mp)
REVERT: A  980 GLN cc_start: 0.6524 (tp40) cc_final: 0.6117 (tp40)
REVERT: A 1021 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7739 (mm)
REVERT: A 1094 GLU cc_start: 0.6385 (tm-30) cc_final: 0.6040 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6492 (ptmm)
REVERT: A 1162 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6436 (pttt)
REVERT: A 1213 TYR cc_start: 0.4459 (m-80) cc_final: 0.4131 (m-80)
  outliers start: 32
  outliers final: 21
  residues processed: 177
  average time/residue: 0.0935
  time to fit residues: 21.6258
Evaluate side-chains
  184 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  340 ARG
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1021 ILE
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.165264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.139951 restraints weight = 9776.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.144526 restraints weight = 5475.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.147620 restraints weight = 3736.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.149626 restraints weight = 2868.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.150906 restraints weight = 2380.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6853  Z= 0.151
  Angle     :  0.571  11.197   9285  Z= 0.292
  Chirality :  0.040   0.170   1064
  Planarity :  0.003   0.050   1159
  Dihedral  :  4.139  15.599    911
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 31.40 %
    Favored  : 64.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  1.75 (0.30), residues: 828
  helix:  2.09 (0.22), residues: 532
  sheet: -0.36 (0.60), residues: 78
  loop : -0.57 (0.45), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 761 
 TYR   0.013   0.001   TYR A1114 
 PHE   0.015   0.001   PHE A 798 
 TRP   0.013   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6852)
  covalent geometry    : angle       0.57146 ( 9283)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.11602 (    2)
  hydrogen bonds       : bond        0.04356 (  461)
  hydrogen bonds       : angle       4.49524 ( 1401)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  137 HIS cc_start: 0.6730 (m90) cc_final: 0.6496 (m170)
REVERT: A  143 ILE cc_start: 0.6309 (OUTLIER) cc_final: 0.6081 (pt)
REVERT: A  152 PHE cc_start: 0.5697 (t80) cc_final: 0.5403 (t80)
REVERT: A  240 LEU cc_start: 0.7709 (mm) cc_final: 0.7471 (mt)
REVERT: A  406 MET cc_start: 0.3957 (OUTLIER) cc_final: 0.3664 (mtm)
REVERT: A  464 GLU cc_start: 0.6230 (tm-30) cc_final: 0.5991 (tm-30)
REVERT: A  500 LEU cc_start: 0.8146 (mm) cc_final: 0.7780 (mp)
REVERT: A  980 GLN cc_start: 0.6445 (tp40) cc_final: 0.6025 (tp40)
REVERT: A 1005 ARG cc_start: 0.7226 (mtp85) cc_final: 0.7012 (mtp85)
REVERT: A 1094 GLU cc_start: 0.6365 (tm-30) cc_final: 0.5978 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6414 (ptmm)
REVERT: A 1162 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6409 (pttt)
REVERT: A 1213 TYR cc_start: 0.4453 (m-80) cc_final: 0.4169 (m-80)
  outliers start: 29
  outliers final: 23
  residues processed: 176
  average time/residue: 0.0940
  time to fit residues: 21.6031
Evaluate side-chains
  181 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  388 GLN
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1197 MET
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0980
   chunk 41 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   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 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.165353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.140147 restraints weight = 9842.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.144626 restraints weight = 5469.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.147730 restraints weight = 3737.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.149871 restraints weight = 2856.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.151155 restraints weight = 2346.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6853  Z= 0.145
  Angle     :  0.579  11.897   9285  Z= 0.293
  Chirality :  0.039   0.154   1064
  Planarity :  0.003   0.050   1159
  Dihedral  :  4.130  15.810    911
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 30.71 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  1.79 (0.30), residues: 828
  helix:  2.14 (0.22), residues: 531
  sheet: -0.35 (0.62), residues: 73
  loop : -0.59 (0.44), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 761 
 TYR   0.013   0.001   TYR A1114 
 PHE   0.015   0.001   PHE A 798 
 TRP   0.011   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A1134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6852)
  covalent geometry    : angle       0.57924 ( 9283)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.09869 (    2)
  hydrogen bonds       : bond        0.04261 (  461)
  hydrogen bonds       : angle       4.44435 ( 1401)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  137 HIS cc_start: 0.6745 (m90) cc_final: 0.6534 (m170)
REVERT: A  143 ILE cc_start: 0.6381 (OUTLIER) cc_final: 0.6150 (pt)
REVERT: A  152 PHE cc_start: 0.5703 (t80) cc_final: 0.5391 (t80)
REVERT: A  240 LEU cc_start: 0.7768 (mm) cc_final: 0.7528 (mt)
REVERT: A  406 MET cc_start: 0.3917 (OUTLIER) cc_final: 0.3622 (mtm)
REVERT: A  464 GLU cc_start: 0.6290 (tm-30) cc_final: 0.6086 (tm-30)
REVERT: A  980 GLN cc_start: 0.6404 (tp40) cc_final: 0.5967 (tp40)
REVERT: A 1094 GLU cc_start: 0.6327 (tm-30) cc_final: 0.5947 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6430 (ptmm)
REVERT: A 1162 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6413 (pttt)
  outliers start: 31
  outliers final: 22
  residues processed: 173
  average time/residue: 0.0949
  time to fit residues: 21.5526
Evaluate side-chains
  173 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  388 GLN
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.165214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.139930 restraints weight = 9886.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.144467 restraints weight = 5475.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.147527 restraints weight = 3723.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.149701 restraints weight = 2842.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.150965 restraints weight = 2331.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6585
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6853  Z= 0.157
  Angle     :  0.590  12.198   9285  Z= 0.299
  Chirality :  0.040   0.161   1064
  Planarity :  0.004   0.050   1159
  Dihedral  :  4.150  16.001    911
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 31.26 %
    Favored  : 64.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  1.73 (0.30), residues: 828
  helix:  2.04 (0.22), residues: 538
  sheet: -0.53 (0.59), residues: 78
  loop : -0.48 (0.45), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 761 
 TYR   0.016   0.002   TYR A 909 
 PHE   0.015   0.001   PHE A 897 
 TRP   0.020   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6852)
  covalent geometry    : angle       0.59018 ( 9283)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       0.08619 (    2)
  hydrogen bonds       : bond        0.04303 (  461)
  hydrogen bonds       : angle       4.44567 ( 1401)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 HIS cc_start: 0.6750 (m90) cc_final: 0.6547 (m170)
REVERT: A  143 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.6186 (pt)
REVERT: A  152 PHE cc_start: 0.5704 (t80) cc_final: 0.5397 (t80)
REVERT: A  240 LEU cc_start: 0.7849 (mm) cc_final: 0.7614 (mt)
REVERT: A  406 MET cc_start: 0.3968 (OUTLIER) cc_final: 0.3680 (mtm)
REVERT: A  464 GLU cc_start: 0.6285 (tm-30) cc_final: 0.6040 (tm-30)
REVERT: A  980 GLN cc_start: 0.6402 (tp40) cc_final: 0.5966 (tp40)
REVERT: A 1094 GLU cc_start: 0.6353 (tm-30) cc_final: 0.5904 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6526 (ttpt)
REVERT: A 1162 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6414 (pttt)
REVERT: A 1181 LYS cc_start: 0.7421 (mtpp) cc_final: 0.7216 (mtmm)
  outliers start: 29
  outliers final: 24
  residues processed: 172
  average time/residue: 0.0974
  time to fit residues: 21.9712
Evaluate side-chains
  180 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  388 GLN
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Chi-restraints excluded: chain A residue 1215 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 69 optimal weight:    0.1980
   chunk 64 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.165831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.140479 restraints weight = 9753.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.145174 restraints weight = 5408.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.148283 restraints weight = 3641.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.150354 restraints weight = 2782.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.151648 restraints weight = 2296.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.3541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6853  Z= 0.144
  Angle     :  0.594  12.561   9285  Z= 0.299
  Chirality :  0.040   0.155   1064
  Planarity :  0.004   0.050   1159
  Dihedral  :  4.133  15.993    911
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 30.98 %
    Favored  : 64.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  1.74 (0.30), residues: 828
  helix:  2.06 (0.22), residues: 539
  sheet: -0.52 (0.59), residues: 78
  loop : -0.50 (0.46), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 761 
 TYR   0.026   0.002   TYR A1213 
 PHE   0.018   0.001   PHE A1223 
 TRP   0.019   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6852)
  covalent geometry    : angle       0.59422 ( 9283)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.08739 (    2)
  hydrogen bonds       : bond        0.04230 (  461)
  hydrogen bonds       : angle       4.42084 ( 1401)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 158
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 HIS cc_start: 0.6722 (m90) cc_final: 0.6512 (m170)
REVERT: A  143 ILE cc_start: 0.6442 (OUTLIER) cc_final: 0.6209 (pt)
REVERT: A  152 PHE cc_start: 0.5699 (t80) cc_final: 0.5389 (t80)
REVERT: A  240 LEU cc_start: 0.7870 (mm) cc_final: 0.7632 (mt)
REVERT: A  406 MET cc_start: 0.3993 (OUTLIER) cc_final: 0.3703 (mtm)
REVERT: A  464 GLU cc_start: 0.6311 (tm-30) cc_final: 0.6104 (tm-30)
REVERT: A  980 GLN cc_start: 0.6383 (tp40) cc_final: 0.5937 (tp40)
REVERT: A 1043 GLN cc_start: 0.6970 (tm-30) cc_final: 0.6708 (tp-100)
REVERT: A 1094 GLU cc_start: 0.6274 (tm-30) cc_final: 0.5900 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6412 (ptmm)
REVERT: A 1107 ILE cc_start: 0.7650 (mm) cc_final: 0.7435 (mm)
REVERT: A 1162 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6409 (pttt)
REVERT: A 1181 LYS cc_start: 0.7395 (mtpp) cc_final: 0.7195 (mtmm)
  outliers start: 30
  outliers final: 26
  residues processed: 175
  average time/residue: 0.0960
  time to fit residues: 21.9534
Evaluate side-chains
  184 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 154
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  388 GLN
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1197 MET
Chi-restraints excluded: chain A residue 1202 VAL
Chi-restraints excluded: chain A residue 1215 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 65 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.165909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.140803 restraints weight = 9831.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.145416 restraints weight = 5468.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.148529 restraints weight = 3686.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.150460 restraints weight = 2816.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.151921 restraints weight = 2343.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6570
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6853  Z= 0.147
  Angle     :  0.598  12.752   9285  Z= 0.300
  Chirality :  0.040   0.155   1064
  Planarity :  0.004   0.049   1159
  Dihedral  :  4.094  16.179    911
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 30.57 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  1.73 (0.30), residues: 828
  helix:  2.05 (0.22), residues: 540
  sheet: -0.51 (0.58), residues: 78
  loop : -0.53 (0.46), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 761 
 TYR   0.023   0.002   TYR A1213 
 PHE   0.018   0.001   PHE A1223 
 TRP   0.019   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6852)
  covalent geometry    : angle       0.59852 ( 9283)
  SS BOND              : bond        0.00018 (    1)
  SS BOND              : angle       0.06013 (    2)
  hydrogen bonds       : bond        0.04213 (  461)
  hydrogen bonds       : angle       4.42276 ( 1401)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1345.61 seconds
wall clock time: 24 minutes 3.01 seconds (1443.01 seconds total)