Starting phenix.real_space_refine
on Wed Mar  4 10:56:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o9w_12765/03_2026/7o9w_12765.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o9w_12765/03_2026/7o9w_12765.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o9w_12765/03_2026/7o9w_12765.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o9w_12765/03_2026/7o9w_12765.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o9w_12765/03_2026/7o9w_12765.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o9w_12765/03_2026/7o9w_12765.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 526 atoms to isotropic.
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      52      5.16       5
     C    8101      2.51       5
     N    2118      2.21       5
     O    2347      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12618
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1169, 9089
          Classifications: {'peptide': 1169}
          Link IDs: {'PTRANS': 27, 'TRANS': 1141}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1710
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 207}
    Chain: "C"
      Number of atoms: 1717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1717
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211}
    Chain: "A"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 102
          Unusual residues: {'V5Q': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.38, per 1000 atoms: 0.19
  Number of scatterers: 12618
  At special positions: 0
  Unit cell: (147.84, 139.92, 162.36, 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      52     16.00
     O    2347      8.00
     N    2118      7.00
     C    8101      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 140 " - pdb=" SG  CYS B 200 " distance=2.47
    Simple disulfide: pdb=" SG  CYS B 220 " - pdb=" SG  CYS C 137 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 149 " - pdb=" SG  CYS C 204 " 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: 0.77
  Conformation dependent library (CDL) restraints added in 489.5 milliseconds
  

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2978

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 13 sheets defined
      52.5% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 40
      removed outlier: 3.802A  pdb=" N   MET A  39 " --> pdb=" O   SER A  35 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   PHE A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 35 through 40'
    Processing helix  chain 'A' and resid 44 through 89
      removed outlier: 3.508A  pdb=" N   LYS A  48 " --> pdb=" O   ASN A  44 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   LEU A  65 " --> pdb=" O   HIS A  61 " (cutoff:3.500A)
      Proline residue:  A  66  - end of helix
    Processing helix  chain 'A' and resid 105 through 157
      removed outlier: 4.147A  pdb=" N   GLU A 109 " --> pdb=" O   MET A 105 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   TYR A 116 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   TYR A 117 " --> pdb=" O   ARG A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 166
      removed outlier: 3.580A  pdb=" N   VAL A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   HIS A 166 " --> pdb=" O   TRP A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 187
      removed outlier: 3.833A  pdb=" N   LEU A 171 " --> pdb=" O   ASP A 167 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASN A 172 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 211
    Processing helix  chain 'A' and resid 211 through 238
      removed outlier: 3.609A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      Proline residue:  A 223  - end of helix
      removed outlier: 4.061A  pdb=" N   SER A 238 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 260
      removed outlier: 4.436A  pdb=" N   ALA A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA A 252 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   VAL A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 268
      removed outlier: 4.374A  pdb=" N   ALA A 266 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 323
    Processing helix  chain 'A' and resid 327 through 348
    Processing helix  chain 'A' and resid 348 through 371
      removed outlier: 4.215A  pdb=" N   ILE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   GLU A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ILE A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 441
      removed outlier: 3.687A  pdb=" N   GLN A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.874A  pdb=" N   THR A 460 " --> pdb=" O   ASP A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 469
      removed outlier: 3.835A  pdb=" N   ILE A 469 " --> pdb=" O   PHE A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 490
    Processing helix  chain 'A' and resid 496 through 508
    Processing helix  chain 'A' and resid 510 through 516
    Processing helix  chain 'A' and resid 525 through 529
      removed outlier: 3.735A  pdb=" N   GLY A 528 " --> pdb=" O   GLY A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 546
    Processing helix  chain 'A' and resid 562 through 576
      removed outlier: 3.526A  pdb=" N   GLU A 566 " --> pdb=" O   ASP A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 617
    Processing helix  chain 'A' and resid 620 through 630
    Processing helix  chain 'A' and resid 699 through 703
      removed outlier: 3.762A  pdb=" N   LYS A 702 " --> pdb=" O   ARG A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 706
      No H-bonds generated for 'chain 'A' and resid 704 through 706'
    Processing helix  chain 'A' and resid 707 through 741
      removed outlier: 4.778A  pdb=" N   GLN A 725 " --> pdb=" O   ASN A 721 " (cutoff:3.500A)
      Proline residue:  A 726  - end of helix
      removed outlier: 4.026A  pdb=" N   PHE A 739 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG A 741 " --> pdb=" O   GLY A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 798
    Processing helix  chain 'A' and resid 800 through 805
      removed outlier: 3.643A  pdb=" N   PHE A 804 " --> pdb=" O   ASP A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 854
      removed outlier: 3.999A  pdb=" N   ALA A 823 " --> pdb=" O   ALA A 819 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LYS A 826 " --> pdb=" O   ALA A 822 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   GLY A 827 " --> pdb=" O   ALA A 823 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   ARG A 832 " --> pdb=" O   ALA A 828 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   LEU A 833 " --> pdb=" O   ILE A 829 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   THR A 845 " --> pdb=" O   ALA A 841 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   GLY A 846 " --> pdb=" O   ASN A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 863
    Processing helix  chain 'A' and resid 864 through 880
      removed outlier: 3.785A  pdb=" N   SER A 880 " --> pdb=" O   MET A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 893
    Processing helix  chain 'A' and resid 894 through 903
      removed outlier: 3.506A  pdb=" N   THR A 898 " --> pdb=" O   GLY A 894 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 911
      removed outlier: 3.723A  pdb=" N   VAL A 907 " --> pdb=" O   ASN A 903 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER A 909 " --> pdb=" O   ARG A 905 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR A 911 " --> pdb=" O   VAL A 907 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 966
      removed outlier: 3.523A  pdb=" N   PHE A 916 " --> pdb=" O   GLN A 912 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   VAL A 926 " --> pdb=" O   GLN A 922 " (cutoff:3.500A)
      Proline residue:  A 927  - end of helix
      removed outlier: 4.375A  pdb=" N   TYR A 953 " --> pdb=" O   MET A 949 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ALA A 954 " --> pdb=" O   TYR A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 995
      removed outlier: 4.311A  pdb=" N   PHE A 983 " --> pdb=" O   SER A 979 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY A 984 " --> pdb=" O   ALA A 980 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   PHE A 994 " --> pdb=" O   GLN A 990 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A 995 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1014
    Processing helix  chain 'A' and resid 1077 through 1084
    Processing helix  chain 'A' and resid 1105 through 1113
      removed outlier: 3.884A  pdb=" N   LEU A1109 " --> pdb=" O   ASN A1105 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ARG A1110 " --> pdb=" O   VAL A1106 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A1113 " --> pdb=" O   LEU A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1133
    Processing helix  chain 'A' and resid 1141 through 1152
    Processing helix  chain 'A' and resid 1154 through 1161
      removed outlier: 3.771A  pdb=" N   LEU A1161 " --> pdb=" O   PHE A1157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1174
      removed outlier: 3.896A  pdb=" N   GLY A1173 " --> pdb=" O   GLY A1170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1191
    Processing helix  chain 'A' and resid 1207 through 1222
      removed outlier: 3.945A  pdb=" N   LYS A1212 " --> pdb=" O   THR A1208 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A1213 " --> pdb=" O   GLU A1209 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ALA A1217 " --> pdb=" O   VAL A1213 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A1218 " --> pdb=" O   VAL A1214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1239
      removed outlier: 4.235A  pdb=" N   ASN A1239 " --> pdb=" O   SER A1235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1256 through 1263
    Processing helix  chain 'A' and resid 1265 through 1272
    Processing helix  chain 'B' and resid 127 through 133
    Processing helix  chain 'B' and resid 190 through 195
      removed outlier: 3.901A  pdb=" N   ARG B 194 " --> pdb=" O   ASP B 190 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   HIS B 195 " --> pdb=" O   GLU B 191 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 190 through 195'
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.574A  pdb=" N   ASP C  90 " --> pdb=" O   THR C  87 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER C  91 " --> pdb=" O   PHE C  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 87 through 91'
    Processing helix  chain 'C' and resid 163 through 167
    Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 417
      removed outlier: 3.743A  pdb=" N   ARG A 395 " --> pdb=" O   MET A 450 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   MET A 450 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   VAL A 397 " --> pdb=" O   GLU A 448 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   GLU A 448 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473
      removed outlier: 6.550A  pdb=" N   GLY A 471 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   ASP A 555 " --> pdb=" O   GLY A 471 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL A 473 " --> pdb=" O   ASP A 555 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   VAL A 423 " --> pdb=" O   VAL A 584 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   GLY A 600 " --> pdb=" O   VAL A 607 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1060
      removed outlier: 5.227A  pdb=" N   LEU A1056 " --> pdb=" O   GLU A1039 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   VAL A1040 " --> pdb=" O   ALA A1091 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   ALA A1091 " --> pdb=" O   VAL A1040 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1114 through 1116
      removed outlier: 4.021A  pdb=" N   LEU A1198 " --> pdb=" O   GLY A1114 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A1116 " --> pdb=" O   LEU A1198 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ASP A1200 " --> pdb=" O   VAL A1116 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A1068 " --> pdb=" O   VAL A1229 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ALA A1067 " --> pdb=" O   VAL A1244 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE A1246 " --> pdb=" O   ALA A1067 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   VAL A1069 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   VAL A1245 " --> pdb=" O   LYS A1252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6
      removed outlier: 3.969A  pdb=" N   ALA B  19 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE B  80 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.620A  pdb=" N   TRP B  40 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11
      removed outlier: 4.056A  pdb=" N   THR B 103 " --> pdb=" O   GLN B  95 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 123
      removed outlier: 3.536A  pdb=" N   ASN B 143 " --> pdb=" O   THR B 120 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER B 183 " --> pdb=" O   CYS B 140 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 160
    Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.621A  pdb=" N   GLU C  10 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   THR C 119 " --> pdb=" O   GLU C  10 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ILE C  34 " --> pdb=" O   PHE C  50 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   PHE C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   TRP C  36 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 131 through 132
      removed outlier: 3.507A  pdb=" N   CYS C 149 " --> pdb=" O   SER C 188 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   SER C 188 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL C 151 " --> pdb=" O   LEU C 186 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU C 186 " --> pdb=" O   VAL C 151 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   TYR C 184 " --> pdb=" O   GLY C 153 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU C 183 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LEU C 179 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   THR C 185 " --> pdb=" O   ALA C 177 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   ALA C 177 " --> pdb=" O   THR C 185 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   SER C 187 " --> pdb=" O   PHE C 175 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   PHE C 175 " --> pdb=" O   SER C 187 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 203 through 206

    693 hydrogen bonds defined for protein.
    1983 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.27

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 2038
        1.31 -     1.44: 3511
        1.44 -     1.57: 7250
        1.57 -     1.70: 4
        1.70 -     1.83: 86
  Bond restraints: 12889
  Sorted by residual:
  bond pdb=" C09 V5Q A1402 "
       pdb=" N08 V5Q A1402 "
    ideal  model  delta    sigma   weight residual
    1.454  1.285  0.169 2.00e-02 2.50e+03 7.14e+01
  bond pdb=" C40 V5Q A1402 "
       pdb=" O41 V5Q A1402 "
    ideal  model  delta    sigma   weight residual
    1.352  1.520 -0.168 2.00e-02 2.50e+03 7.08e+01
  bond pdb=" C40 V5Q A1401 "
       pdb=" O41 V5Q A1401 "
    ideal  model  delta    sigma   weight residual
    1.352  1.520 -0.168 2.00e-02 2.50e+03 7.08e+01
  bond pdb=" C09 V5Q A1401 "
       pdb=" N08 V5Q A1401 "
    ideal  model  delta    sigma   weight residual
    1.454  1.291  0.163 2.00e-02 2.50e+03 6.61e+01
  bond pdb=" C20 V5Q A1402 "
       pdb=" C22 V5Q A1402 "
    ideal  model  delta    sigma   weight residual
    1.460  1.580 -0.120 2.00e-02 2.50e+03 3.63e+01
  ... (remaining 12884 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 17076
        2.46 -     4.92: 326
        4.92 -     7.39: 42
        7.39 -     9.85: 12
        9.85 -    12.31: 3
  Bond angle restraints: 17459
  Sorted by residual:
  angle pdb=" C   PRO B 100 "
        pdb=" N   PRO B 101 "
        pdb=" CA  PRO B 101 "
      ideal   model   delta    sigma   weight residual
     119.84  131.34  -11.50 1.25e+00 6.40e-01 8.47e+01
  angle pdb=" N   ILE B  99 "
        pdb=" CA  ILE B  99 "
        pdb=" C   ILE B  99 "
      ideal   model   delta    sigma   weight residual
     108.88  121.19  -12.31 2.16e+00 2.14e-01 3.25e+01
  angle pdb=" C   LYS B  55 "
        pdb=" CA  LYS B  55 "
        pdb=" CB  LYS B  55 "
      ideal   model   delta    sigma   weight residual
     116.63  110.19    6.44 1.16e+00 7.43e-01 3.08e+01
  angle pdb=" N   LYS B  55 "
        pdb=" CA  LYS B  55 "
        pdb=" C   LYS B  55 "
      ideal   model   delta    sigma   weight residual
     108.08  116.69   -8.61 1.69e+00 3.50e-01 2.59e+01
  angle pdb=" C   ILE B  99 "
        pdb=" N   PRO B 100 "
        pdb=" CA  PRO B 100 "
      ideal   model   delta    sigma   weight residual
     120.38  115.14    5.24 1.03e+00 9.43e-01 2.58e+01
  ... (remaining 17454 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.52: 7156
       27.52 -    55.04: 471
       55.04 -    82.57: 47
       82.57 -   110.09: 5
      110.09 -   137.61: 1
  Dihedral angle restraints: 7680
    sinusoidal: 3037
      harmonic: 4643
  Sorted by residual:
  dihedral pdb=" CB  CYS C 149 "
           pdb=" SG  CYS C 149 "
           pdb=" SG  CYS C 204 "
           pdb=" CB  CYS C 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   32.00   61.00     1      1.00e+01 1.00e-02 4.95e+01
  dihedral pdb=" CA  ASN A1163 "
           pdb=" C   ASN A1163 "
           pdb=" N   LYS A1164 "
           pdb=" CA  LYS A1164 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.69  -25.31     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  ASP A 997 "
           pdb=" C   ASP A 997 "
           pdb=" N   TYR A 998 "
           pdb=" CA  TYR A 998 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.89  -25.11     0      5.00e+00 4.00e-02 2.52e+01
  ... (remaining 7677 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.383: 1978
       0.383 -    0.767: 1
       0.767 -    1.150: 0
       1.150 -    1.533: 1
       1.533 -    1.917: 1
  Chirality restraints: 1981
  Sorted by residual:
  chirality pdb=" C35 V5Q A1401 "
            pdb=" C33 V5Q A1401 "
            pdb=" C36 V5Q A1401 "
            pdb=" O41 V5Q A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.39   -0.47   -1.92 2.00e-01 2.50e+01 9.18e+01
  chirality pdb=" C35 V5Q A1402 "
            pdb=" C33 V5Q A1402 "
            pdb=" C36 V5Q A1402 "
            pdb=" O41 V5Q A1402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.39   -1.09   -1.30 2.00e-01 2.50e+01 4.21e+01
  chirality pdb=" CB  VAL B  56 "
            pdb=" CA  VAL B  56 "
            pdb=" CG1 VAL B  56 "
            pdb=" CG2 VAL B  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.18   -0.45 2.00e-01 2.50e+01 5.11e+00
  ... (remaining 1978 not shown)

  Planarity restraints: 2202
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  97 "    0.018 2.00e-02 2.50e+03   3.53e-02 1.25e+01
        pdb=" C   THR B  97 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   THR B  97 "    0.023 2.00e-02 2.50e+03
        pdb=" N   HIS B  98 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 174 "    0.213 9.50e-02 1.11e+02   9.53e-02 5.57e+00
        pdb=" NE  ARG A 174 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 174 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 174 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 174 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C 109 "   -0.011 2.00e-02 2.50e+03   2.30e-02 5.29e+00
        pdb=" C   MET C 109 "    0.040 2.00e-02 2.50e+03
        pdb=" O   MET C 109 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASP C 110 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2199 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 398
        2.70 -     3.25: 12520
        3.25 -     3.80: 20005
        3.80 -     4.35: 25200
        4.35 -     4.90: 41561
  Nonbonded interactions: 99684
  Sorted by model distance:
  nonbonded pdb=" N   ASP C 110 "
            pdb=" OD1 ASP C 110 "
     model   vdw
     2.149 3.120
  nonbonded pdb=" O   GLN A 990 "
            pdb=" OG  SER A 993 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   GLY A 854 "
            pdb=" OG1 THR A 858 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   PRO B   8 "
            pdb=" OG1 THR B 108 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OE2 GLU A 707 "
            pdb=" NH2 ARG A 787 "
     model   vdw
     2.246 3.120
  ... (remaining 99679 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.420
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
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      :  0.008   0.441  12894  Z= 0.418
  Angle     :  0.885  15.402  17469  Z= 0.513
  Chirality :  0.072   1.917   1981
  Planarity :  0.005   0.095   2202
  Dihedral  : 16.948 137.612   4687
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 20.00
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.74 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 18.76 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.00 (0.18), residues: 1604
  helix: -1.45 (0.16), residues: 753
  sheet: -1.62 (0.31), residues: 263
  loop : -2.71 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1183 
 TYR   0.016   0.002   TYR C  33 
 PHE   0.023   0.002   PHE C  50 
 TRP   0.011   0.001   TRP A 232 
 HIS   0.009   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00693 (12889)
  covalent geometry    : angle       0.87140 (17459)
  SS BOND              : bond        0.19732 (    5)
  SS BOND              : angle       6.52894 (   10)
  hydrogen bonds       : bond        0.14431 (  690)
  hydrogen bonds       : angle       6.34392 ( 1983)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 130
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7400 (tp)
REVERT: A  258 LEU cc_start: 0.6295 (mt) cc_final: 0.5911 (tt)
REVERT: A  332 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8072 (mp)
REVERT: A  440 MET cc_start: 0.2756 (tpt) cc_final: 0.2356 (mtt)
REVERT: A  514 MET cc_start: 0.3342 (mtm) cc_final: 0.2659 (ttm)
REVERT: A  616 MET cc_start: 0.2662 (mmp) cc_final: 0.0905 (mtp)
REVERT: A  703 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5829 (mp)
REVERT: A  824 GLN cc_start: 0.5937 (OUTLIER) cc_final: 0.5375 (tt0)
REVERT: A  875 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6808 (tm-30)
REVERT: A 1027 MET cc_start: 0.1858 (tpp) cc_final: 0.1400 (ttp)
REVERT: B   18 GLN cc_start: 0.6907 (mm110) cc_final: 0.4806 (pt0)
REVERT: B  146 TYR cc_start: 0.4866 (t80) cc_final: 0.4641 (t80)
  outliers start: 60
  outliers final: 39
  residues processed: 188
  average time/residue: 0.1048
  time to fit residues: 29.1136
Evaluate side-chains
  145 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 102
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  816 THR
Chi-restraints excluded: chain A residue  824 GLN
Chi-restraints excluded: chain A residue  855 TRP
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  876 MET
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  940 ILE
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue  981 VAL
Chi-restraints excluded: chain A residue 1273 VAL
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   23 CYS
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  162 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  44 ASN
A 143 GLN
A 145 HIS
A 158 GLN
A 347 GLN
A 387 ASN
A 398 HIS
A 438 GLN
A 518 HIS
A 537 GLN
A 725 GLN
A 750 GLN
A 820 ASN
A 946 GLN
A 966 HIS
A1054 GLN
A1105 ASN
A1153 ASN
A1232 HIS
** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1248 ASN
** B  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 HIS
B 167 ASN
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 ASN
B 216 ASN
C   5 GLN
C 102 GLN
C 105 ASN
C 164 ASN

Total number of N/Q/H flips: 28

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.230260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.190703 restraints weight = 16889.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.185733 restraints weight = 32716.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.180828 restraints weight = 27029.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.177636 restraints weight = 29445.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.174448 restraints weight = 30249.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6693
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12894  Z= 0.192
  Angle     :  0.641   9.243  17469  Z= 0.336
  Chirality :  0.045   0.346   1981
  Planarity :  0.005   0.045   2202
  Dihedral  : 11.239 133.164   1865
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 20.16 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.20), residues: 1604
  helix: -0.21 (0.17), residues: 780
  sheet: -1.05 (0.32), residues: 269
  loop : -2.23 (0.23), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 217 
 TYR   0.015   0.002   TYR C  33 
 PHE   0.022   0.002   PHE C  50 
 TRP   0.019   0.002   TRP A 232 
 HIS   0.008   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (12889)
  covalent geometry    : angle       0.64041 (17459)
  SS BOND              : bond        0.00551 (    5)
  SS BOND              : angle       1.28924 (   10)
  hydrogen bonds       : bond        0.06240 (  690)
  hydrogen bonds       : angle       4.96599 ( 1983)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 96
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A  144 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7823 (tp)
REVERT: A  258 LEU cc_start: 0.6527 (mt) cc_final: 0.6151 (tt)
REVERT: A  332 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8205 (mp)
REVERT: A  450 MET cc_start: 0.4611 (ttp) cc_final: 0.4106 (mtp)
REVERT: A  628 MET cc_start: 0.1315 (ptt) cc_final: -0.0566 (pmm)
REVERT: B   18 GLN cc_start: 0.6697 (mm110) cc_final: 0.5072 (pt0)
REVERT: B   99 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8051 (pp)
REVERT: B  146 TYR cc_start: 0.4758 (t80) cc_final: 0.4501 (t80)
  outliers start: 77
  outliers final: 49
  residues processed: 157
  average time/residue: 0.0903
  time to fit residues: 22.1992
Evaluate side-chains
  145 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 93
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  376 ASP
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  701 MET
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  824 GLN
Chi-restraints excluded: chain A residue  835 VAL
Chi-restraints excluded: chain A residue  855 TRP
Chi-restraints excluded: chain A residue  876 MET
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  117 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 123 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 119 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 112 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 799 GLN
** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.232333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.192620 restraints weight = 17088.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.186852 restraints weight = 32532.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.180484 restraints weight = 33401.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.177079 restraints weight = 33297.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.172961 restraints weight = 31726.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12894  Z= 0.131
  Angle     :  0.553   7.761  17469  Z= 0.290
  Chirality :  0.041   0.264   1981
  Planarity :  0.004   0.045   2202
  Dihedral  : 10.148 131.117   1843
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 22.22 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.21), residues: 1604
  helix:  0.64 (0.18), residues: 780
  sheet: -0.78 (0.33), residues: 267
  loop : -1.94 (0.24), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 217 
 TYR   0.015   0.001   TYR C  33 
 PHE   0.019   0.001   PHE B  92 
 TRP   0.017   0.001   TRP A 232 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (12889)
  covalent geometry    : angle       0.55134 (17459)
  SS BOND              : bond        0.00700 (    5)
  SS BOND              : angle       2.09040 (   10)
  hydrogen bonds       : bond        0.05243 (  690)
  hydrogen bonds       : angle       4.52293 ( 1983)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 101
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8284 (mp)
REVERT: A  450 MET cc_start: 0.4784 (ttp) cc_final: 0.4092 (mtp)
REVERT: A  606 ILE cc_start: -0.0177 (OUTLIER) cc_final: -0.0688 (pt)
REVERT: A  628 MET cc_start: 0.1352 (ptt) cc_final: -0.0358 (pmm)
REVERT: A  770 PHE cc_start: 0.6005 (OUTLIER) cc_final: 0.5387 (t80)
REVERT: A  875 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7327 (tt0)
REVERT: A  917 GLU cc_start: 0.4139 (OUTLIER) cc_final: 0.3932 (tt0)
REVERT: B   18 GLN cc_start: 0.6611 (mm110) cc_final: 0.4853 (pt0)
REVERT: B   99 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.8008 (pp)
REVERT: B  146 TYR cc_start: 0.4855 (t80) cc_final: 0.4412 (t80)
  outliers start: 65
  outliers final: 41
  residues processed: 155
  average time/residue: 0.0968
  time to fit residues: 22.8235
Evaluate side-chains
  142 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 96
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 ASP
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  824 GLN
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  855 TRP
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  940 ILE
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  200 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 87 optimal weight:    0.7980
   chunk 102 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 77 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 152 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 71 optimal weight:    9.9990
   chunk 107 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0050
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 GLN
B   1 GLN
B  18 GLN
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.233688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.192069 restraints weight = 16962.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.188975 restraints weight = 33890.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.184420 restraints weight = 28759.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.182468 restraints weight = 30073.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.181026 restraints weight = 23878.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6548
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12894  Z= 0.114
  Angle     :  0.517   7.762  17469  Z= 0.268
  Chirality :  0.041   0.365   1981
  Planarity :  0.004   0.046   2202
  Dihedral  :  9.865 130.273   1829
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 22.59 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.21), residues: 1604
  helix:  1.19 (0.19), residues: 777
  sheet: -0.62 (0.33), residues: 270
  loop : -1.63 (0.25), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 217 
 TYR   0.014   0.001   TYR C  33 
 PHE   0.033   0.001   PHE A 983 
 TRP   0.017   0.001   TRP A 232 
 HIS   0.002   0.000   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (12889)
  covalent geometry    : angle       0.51627 (17459)
  SS BOND              : bond        0.00818 (    5)
  SS BOND              : angle       1.28036 (   10)
  hydrogen bonds       : bond        0.04711 (  690)
  hydrogen bonds       : angle       4.25469 ( 1983)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 106
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A  450 MET cc_start: 0.4777 (ttp) cc_final: 0.4122 (mtp)
REVERT: A  606 ILE cc_start: -0.0112 (OUTLIER) cc_final: -0.0562 (pt)
REVERT: A  628 MET cc_start: 0.1537 (ptt) cc_final: -0.0254 (pmm)
REVERT: A  770 PHE cc_start: 0.5745 (OUTLIER) cc_final: 0.5154 (t80)
REVERT: A  803 TRP cc_start: 0.6385 (t60) cc_final: 0.6118 (t60)
REVERT: A  875 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7322 (tt0)
REVERT: A  884 LEU cc_start: 0.4380 (OUTLIER) cc_final: 0.4120 (mp)
REVERT: B   18 GLN cc_start: 0.6622 (mm-40) cc_final: 0.4718 (pt0)
REVERT: B   99 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8082 (pp)
REVERT: B  146 TYR cc_start: 0.4624 (t80) cc_final: 0.4188 (t80)
  outliers start: 65
  outliers final: 43
  residues processed: 158
  average time/residue: 0.0910
  time to fit residues: 22.5428
Evaluate side-chains
  143 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 96
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  824 GLN
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  855 TRP
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  876 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  904 PHE
Chi-restraints excluded: chain A residue  940 ILE
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1203 THR
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  200 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 21 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 134 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0020
   chunk 154 optimal weight:    0.5980
   chunk 93 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
A 824 GLN
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 ASN
C 114 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.234321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.192365 restraints weight = 16970.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.186978 restraints weight = 31827.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.184131 restraints weight = 29572.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.182479 restraints weight = 24682.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.182703 restraints weight = 21434.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6509
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12894  Z= 0.107
  Angle     :  0.498   7.794  17469  Z= 0.259
  Chirality :  0.040   0.275   1981
  Planarity :  0.003   0.043   2202
  Dihedral  :  9.446 130.842   1824
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 23.03 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.22), residues: 1604
  helix:  1.46 (0.19), residues: 784
  sheet: -0.63 (0.33), residues: 290
  loop : -1.39 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 157 
 TYR   0.014   0.001   TYR C  33 
 PHE   0.025   0.001   PHE A 983 
 TRP   0.016   0.001   TRP A 232 
 HIS   0.002   0.000   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (12889)
  covalent geometry    : angle       0.49720 (17459)
  SS BOND              : bond        0.00517 (    5)
  SS BOND              : angle       1.15588 (   10)
  hydrogen bonds       : bond        0.04489 (  690)
  hydrogen bonds       : angle       4.08382 ( 1983)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 106
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  450 MET cc_start: 0.4804 (ttp) cc_final: 0.4159 (mtp)
REVERT: A  606 ILE cc_start: -0.0155 (OUTLIER) cc_final: -0.0504 (pt)
REVERT: A  628 MET cc_start: 0.1587 (ptt) cc_final: -0.0245 (pmm)
REVERT: A  770 PHE cc_start: 0.5731 (OUTLIER) cc_final: 0.5172 (t80)
REVERT: A  824 GLN cc_start: 0.5866 (OUTLIER) cc_final: 0.5168 (tt0)
REVERT: A  875 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7279 (tt0)
REVERT: A  884 LEU cc_start: 0.4279 (OUTLIER) cc_final: 0.4048 (mp)
REVERT: A  917 GLU cc_start: 0.3938 (OUTLIER) cc_final: 0.3732 (tt0)
REVERT: B   18 GLN cc_start: 0.6699 (mm-40) cc_final: 0.4746 (pt0)
REVERT: B   99 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7983 (pp)
  outliers start: 63
  outliers final: 46
  residues processed: 154
  average time/residue: 0.0916
  time to fit residues: 22.2048
Evaluate side-chains
  150 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 98
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 ASP
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  510 TYR
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  824 GLN
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  855 TRP
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  876 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  917 GLU
Chi-restraints excluded: chain A residue  940 ILE
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1203 THR
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  200 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 158 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 38 optimal weight:   20.0000
   chunk 17 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 121 optimal weight:    2.9990
   chunk 149 optimal weight:    0.7980
   chunk 89 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1034 ASN
** A1112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 ASN
C 114 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.228006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.188500 restraints weight = 16788.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.182417 restraints weight = 33760.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.178260 restraints weight = 29560.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.175562 restraints weight = 32514.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.172784 restraints weight = 26288.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12894  Z= 0.230
  Angle     :  0.660   8.686  17469  Z= 0.348
  Chirality :  0.046   0.489   1981
  Planarity :  0.005   0.073   2202
  Dihedral  : 10.521 136.610   1823
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 23.69 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.21), residues: 1604
  helix:  0.80 (0.18), residues: 783
  sheet: -0.52 (0.33), residues: 276
  loop : -1.62 (0.25), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 798 
 TYR   0.016   0.002   TYR B  41 
 PHE   0.029   0.002   PHE A 983 
 TRP   0.034   0.002   TRP A 803 
 HIS   0.016   0.002   HIS A1112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (12889)
  covalent geometry    : angle       0.65922 (17459)
  SS BOND              : bond        0.00900 (    5)
  SS BOND              : angle       1.50816 (   10)
  hydrogen bonds       : bond        0.06449 (  690)
  hydrogen bonds       : angle       4.64232 ( 1983)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 95
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A  440 MET cc_start: 0.3135 (mtt) cc_final: 0.2871 (mtp)
REVERT: A  450 MET cc_start: 0.4811 (ttp) cc_final: 0.4014 (mtp)
REVERT: A  606 ILE cc_start: -0.0016 (OUTLIER) cc_final: -0.0446 (pt)
REVERT: A  628 MET cc_start: 0.1671 (ptt) cc_final: -0.0137 (pmm)
REVERT: A  770 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.5607 (t80)
REVERT: A  777 PHE cc_start: 0.6686 (m-80) cc_final: 0.6375 (m-80)
REVERT: A  875 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7187 (tt0)
REVERT: A  884 LEU cc_start: 0.4361 (OUTLIER) cc_final: 0.4117 (mp)
REVERT: B   18 GLN cc_start: 0.7271 (mm-40) cc_final: 0.5432 (pt0)
REVERT: B   99 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8077 (pp)
REVERT: B  116 ASP cc_start: 0.3691 (OUTLIER) cc_final: 0.2966 (t0)
  outliers start: 70
  outliers final: 53
  residues processed: 154
  average time/residue: 0.0863
  time to fit residues: 21.2279
Evaluate side-chains
  147 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 89
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 ASP
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  855 TRP
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  876 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  904 PHE
Chi-restraints excluded: chain A residue  940 ILE
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1203 THR
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  162 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 149 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 119 optimal weight:    0.0670
   chunk 82 optimal weight:    0.9990
   chunk 45 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   overall best weight:    0.7722

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 ASN
C 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.232647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.193155 restraints weight = 16756.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.188060 restraints weight = 33300.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.184395 restraints weight = 29719.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.182743 restraints weight = 30285.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.180511 restraints weight = 26294.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6567
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12894  Z= 0.115
  Angle     :  0.516   9.840  17469  Z= 0.270
  Chirality :  0.040   0.263   1981
  Planarity :  0.004   0.071   2202
  Dihedral  :  9.265 130.574   1820
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 25.09 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.22), residues: 1604
  helix:  1.39 (0.19), residues: 786
  sheet: -0.51 (0.33), residues: 287
  loop : -1.36 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 276 
 TYR   0.026   0.001   TYR A 510 
 PHE   0.029   0.001   PHE A 983 
 TRP   0.020   0.001   TRP A 803 
 HIS   0.012   0.001   HIS A1112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (12889)
  covalent geometry    : angle       0.51584 (17459)
  SS BOND              : bond        0.00472 (    5)
  SS BOND              : angle       1.09745 (   10)
  hydrogen bonds       : bond        0.04817 (  690)
  hydrogen bonds       : angle       4.15799 ( 1983)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 101
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  440 MET cc_start: 0.3098 (mtt) cc_final: 0.2829 (mtp)
REVERT: A  450 MET cc_start: 0.4824 (ttp) cc_final: 0.4055 (mtp)
REVERT: A  606 ILE cc_start: 0.0086 (OUTLIER) cc_final: -0.0272 (pt)
REVERT: A  628 MET cc_start: 0.1702 (ptt) cc_final: 0.0385 (pmm)
REVERT: A  770 PHE cc_start: 0.5864 (OUTLIER) cc_final: 0.5451 (t80)
REVERT: A  777 PHE cc_start: 0.6596 (m-80) cc_final: 0.6304 (m-80)
REVERT: A  875 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7260 (tt0)
REVERT: A  884 LEU cc_start: 0.4211 (OUTLIER) cc_final: 0.3977 (mp)
REVERT: B   18 GLN cc_start: 0.6714 (mm-40) cc_final: 0.4795 (pt0)
REVERT: B   99 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8066 (pp)
  outliers start: 56
  outliers final: 39
  residues processed: 147
  average time/residue: 0.0890
  time to fit residues: 20.2786
Evaluate side-chains
  139 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 96
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 ASP
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  876 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  904 PHE
Chi-restraints excluded: chain A residue  940 ILE
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1203 THR
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  162 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 120 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 131 optimal weight:    5.9990
   chunk 95 optimal weight:   20.0000
   chunk 101 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.227540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.185738 restraints weight = 16744.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.182886 restraints weight = 31807.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.178481 restraints weight = 31863.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.175766 restraints weight = 30470.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.174147 restraints weight = 26228.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082  12894  Z= 0.214
  Angle     :  0.644   8.365  17469  Z= 0.340
  Chirality :  0.045   0.423   1981
  Planarity :  0.005   0.066   2202
  Dihedral  : 10.230 137.921   1818
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 24.65 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.21), residues: 1604
  helix:  0.91 (0.18), residues: 778
  sheet: -0.66 (0.33), residues: 281
  loop : -1.48 (0.25), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1188 
 TYR   0.017   0.002   TYR A 510 
 PHE   0.027   0.002   PHE A 983 
 TRP   0.031   0.002   TRP A 803 
 HIS   0.010   0.001   HIS A1112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 (12889)
  covalent geometry    : angle       0.64297 (17459)
  SS BOND              : bond        0.00812 (    5)
  SS BOND              : angle       1.44575 (   10)
  hydrogen bonds       : bond        0.06262 (  690)
  hydrogen bonds       : angle       4.60514 ( 1983)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 89
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A  440 MET cc_start: 0.3184 (mtt) cc_final: 0.2894 (mtp)
REVERT: A  450 MET cc_start: 0.4892 (ttp) cc_final: 0.4056 (mtp)
REVERT: A  475 GLN cc_start: 0.2796 (OUTLIER) cc_final: 0.1977 (mt0)
REVERT: A  514 MET cc_start: 0.2319 (mpp) cc_final: 0.2079 (mmm)
REVERT: A  628 MET cc_start: 0.1828 (ptt) cc_final: -0.0093 (pmm)
REVERT: A  770 PHE cc_start: 0.5869 (OUTLIER) cc_final: 0.5598 (t80)
REVERT: A  875 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7293 (tt0)
REVERT: A  884 LEU cc_start: 0.4280 (OUTLIER) cc_final: 0.4055 (mp)
REVERT: B   18 GLN cc_start: 0.7284 (mm-40) cc_final: 0.5465 (pt0)
REVERT: B   99 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8137 (pp)
  outliers start: 66
  outliers final: 53
  residues processed: 143
  average time/residue: 0.0913
  time to fit residues: 20.6707
Evaluate side-chains
  143 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 86
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 ASP
Chi-restraints excluded: chain A residue  475 GLN
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  876 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  904 PHE
Chi-restraints excluded: chain A residue  940 ILE
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1203 THR
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  162 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 54 optimal weight:   30.0000
   chunk 97 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 148 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.229501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.186987 restraints weight = 16785.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.181775 restraints weight = 31788.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.178354 restraints weight = 27839.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.176430 restraints weight = 29188.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.175908 restraints weight = 25797.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6666
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12894  Z= 0.151
  Angle     :  0.568   9.418  17469  Z= 0.296
  Chirality :  0.042   0.289   1981
  Planarity :  0.004   0.057   2202
  Dihedral  :  9.591 134.875   1818
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 25.39 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.21), residues: 1604
  helix:  1.14 (0.18), residues: 778
  sheet: -0.54 (0.34), residues: 273
  loop : -1.44 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 276 
 TYR   0.014   0.002   TYR A 510 
 PHE   0.028   0.002   PHE A 983 
 TRP   0.023   0.001   TRP A 803 
 HIS   0.010   0.001   HIS A1112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (12889)
  covalent geometry    : angle       0.56718 (17459)
  SS BOND              : bond        0.00591 (    5)
  SS BOND              : angle       1.42971 (   10)
  hydrogen bonds       : bond        0.05431 (  690)
  hydrogen bonds       : angle       4.37673 ( 1983)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 93
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  244 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.4965 (tt)
REVERT: A  440 MET cc_start: 0.3161 (mtt) cc_final: 0.2855 (mtp)
REVERT: A  450 MET cc_start: 0.4902 (ttp) cc_final: 0.4060 (mtp)
REVERT: A  628 MET cc_start: 0.1975 (ptt) cc_final: 0.0366 (pmm)
REVERT: A  758 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8279 (mp)
REVERT: A  770 PHE cc_start: 0.5848 (OUTLIER) cc_final: 0.5456 (t80)
REVERT: A  777 PHE cc_start: 0.6621 (m-80) cc_final: 0.6355 (m-80)
REVERT: A  875 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7251 (tt0)
REVERT: A  884 LEU cc_start: 0.4138 (OUTLIER) cc_final: 0.3917 (mp)
REVERT: A 1027 MET cc_start: 0.4266 (ttp) cc_final: 0.3490 (tpp)
REVERT: B   18 GLN cc_start: 0.7029 (mm-40) cc_final: 0.5164 (pt0)
REVERT: B   99 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8037 (pp)
  outliers start: 55
  outliers final: 44
  residues processed: 139
  average time/residue: 0.0952
  time to fit residues: 20.5629
Evaluate side-chains
  137 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 88
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 ASP
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  824 GLN
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  876 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  904 PHE
Chi-restraints excluded: chain A residue  940 ILE
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1203 THR
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  162 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 131 optimal weight:    1.9990
   chunk 146 optimal weight:    0.9990
   chunk 115 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:   20.0000
   chunk 88 optimal weight:    0.7980
   chunk 54 optimal weight:    0.2980
   chunk 37 optimal weight:    7.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.231518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.190988 restraints weight = 16809.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.186843 restraints weight = 32277.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.180457 restraints weight = 29747.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.177743 restraints weight = 30627.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.176168 restraints weight = 22661.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6660
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12894  Z= 0.122
  Angle     :  0.533   8.345  17469  Z= 0.276
  Chirality :  0.041   0.253   1981
  Planarity :  0.004   0.073   2202
  Dihedral  :  9.197 133.223   1818
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 25.90 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.22), residues: 1604
  helix:  1.48 (0.19), residues: 777
  sheet: -0.49 (0.34), residues: 278
  loop : -1.42 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 157 
 TYR   0.014   0.001   TYR C  33 
 PHE   0.024   0.001   PHE A 983 
 TRP   0.019   0.001   TRP A 232 
 HIS   0.009   0.001   HIS A1112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (12889)
  covalent geometry    : angle       0.53159 (17459)
  SS BOND              : bond        0.00514 (    5)
  SS BOND              : angle       1.44357 (   10)
  hydrogen bonds       : bond        0.04808 (  690)
  hydrogen bonds       : angle       4.16484 ( 1983)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 95
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A  244 LEU cc_start: 0.5699 (OUTLIER) cc_final: 0.5036 (tt)
REVERT: A  440 MET cc_start: 0.3374 (mtt) cc_final: 0.3013 (mtp)
REVERT: A  450 MET cc_start: 0.5025 (ttp) cc_final: 0.4126 (mtp)
REVERT: A  628 MET cc_start: 0.1940 (ptt) cc_final: 0.0443 (pmm)
REVERT: A  770 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.5423 (t80)
REVERT: A  777 PHE cc_start: 0.6543 (m-80) cc_final: 0.6304 (m-80)
REVERT: A  803 TRP cc_start: 0.5893 (t60) cc_final: 0.5319 (t60)
REVERT: A  824 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.5981 (mm110)
REVERT: A  875 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7228 (tt0)
REVERT: A 1027 MET cc_start: 0.4423 (ttp) cc_final: 0.3691 (tpp)
REVERT: B   18 GLN cc_start: 0.6803 (mm-40) cc_final: 0.4923 (pt0)
REVERT: B   99 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7971 (pp)
  outliers start: 48
  outliers final: 42
  residues processed: 135
  average time/residue: 0.0895
  time to fit residues: 18.8866
Evaluate side-chains
  138 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 92
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 ASP
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  698 TRP
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  824 GLN
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  876 MET
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  904 PHE
Chi-restraints excluded: chain A residue  940 ILE
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1203 THR
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   14 THR
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  162 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0370
   chunk 77 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 127 optimal weight:    6.9990
   chunk 103 optimal weight:   20.0000
   chunk 123 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.9460

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

Flipped N/Q/H residues before XYZ refinement:
B  98 HIS
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.231819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.191342 restraints weight = 16813.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.187706 restraints weight = 32650.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.183355 restraints weight = 31349.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.180550 restraints weight = 30539.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.176651 restraints weight = 29100.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6638
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12894  Z= 0.118
  Angle     :  0.523   7.964  17469  Z= 0.270
  Chirality :  0.040   0.253   1981
  Planarity :  0.004   0.068   2202
  Dihedral  :  9.151 133.995   1818
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.68 %
    Favored  : 70.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.22), residues: 1604
  helix:  1.61 (0.19), residues: 777
  sheet: -0.35 (0.34), residues: 273
  loop : -1.41 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 157 
 TYR   0.014   0.001   TYR C  33 
 PHE   0.024   0.001   PHE A 983 
 TRP   0.020   0.001   TRP A 803 
 HIS   0.009   0.001   HIS A1112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (12889)
  covalent geometry    : angle       0.52228 (17459)
  SS BOND              : bond        0.00482 (    5)
  SS BOND              : angle       1.45375 (   10)
  hydrogen bonds       : bond        0.04716 (  690)
  hydrogen bonds       : angle       4.09196 ( 1983)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2297.33 seconds
wall clock time: 40 minutes 21.01 seconds (2421.01 seconds total)