Starting phenix.real_space_refine
on Wed Jul 30 20:31:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7a65_11666/07_2025/7a65_11666.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7a65_11666/07_2025/7a65_11666.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7a65_11666/07_2025/7a65_11666.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7a65_11666/07_2025/7a65_11666.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7a65_11666/07_2025/7a65_11666.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7a65_11666/07_2025/7a65_11666.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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      50      5.16       5
     C    8075      2.51       5
     N    2086      2.21       5
     O    2310      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12521
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1164, 9050
          Classifications: {'peptide': 1164}
          Link IDs: {'PTRANS': 27, 'TRANS': 1136}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1656
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'CYS%COO:oxt': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 1647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1647
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PRO%COO:oxt': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 168
          Unusual residues: {'CLR': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 7.70, per 1000 atoms: 0.61
  Number of scatterers: 12521
  At special positions: 0
  Unit cell: (102.48, 207.48, 99.96, 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      50     16.00
     O    2310      8.00
     N    2086      7.00
     C    8075      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=2.05
    Simple disulfide: pdb=" SG  CYS B 139 " - pdb=" SG  CYS B 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 220 " - pdb=" SG  CYS C 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 146 " - pdb=" SG  CYS C 201 " 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: 3.18
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2940

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 14 sheets defined
      53.9% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 40
      removed outlier: 3.705A  pdb=" N   PHE A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 82
      removed outlier: 4.504A  pdb=" N   LEU A  65 " --> pdb=" O   HIS A  61 " (cutoff:3.500A)
      Proline residue:  A  66  - end of helix
      removed outlier: 3.693A  pdb=" N   ASN A  81 " --> pdb=" O   ASP A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 158
      removed outlier: 3.642A  pdb=" N   TRP A 136 " --> pdb=" O   GLN A 132 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ARG A 157 " --> pdb=" O   HIS A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 166
    Processing helix  chain 'A' and resid 167 through 187
      removed outlier: 4.128A  pdb=" N   LEU A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   THR A 176 " --> pdb=" O   ASN A 172 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY A 185 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 211
      removed outlier: 4.292A  pdb=" N   GLY A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 221
      removed outlier: 3.708A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL A 217 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 237
    Processing helix  chain 'A' and resid 240 through 260
      removed outlier: 3.697A  pdb=" N   LEU A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   LYS A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   ALA A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 267
    Processing helix  chain 'A' and resid 269 through 323
      removed outlier: 3.544A  pdb=" N   LEU A 274 " --> pdb=" O   GLN A 270 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLU A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA A 284 " --> pdb=" O   ASN A 280 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER A 323 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 348
      removed outlier: 4.036A  pdb=" N   GLY A 346 " --> pdb=" O   ALA A 342 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLN A 347 " --> pdb=" O   PHE A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 371
      removed outlier: 3.680A  pdb=" N   ILE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   GLU A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 439
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.752A  pdb=" N   THR A 460 " --> pdb=" O   ASP A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 469
      removed outlier: 3.810A  pdb=" N   ILE A 469 " --> pdb=" O   PHE A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 488
    Processing helix  chain 'A' and resid 489 through 492
    Processing helix  chain 'A' and resid 496 through 508
    Processing helix  chain 'A' and resid 510 through 516
      removed outlier: 3.585A  pdb=" N   LEU A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 529
      removed outlier: 3.653A  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
    Processing helix  chain 'A' and resid 588 through 592
      removed outlier: 3.822A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 619
      removed outlier: 3.522A  pdb=" N   LYS A 619 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 630
    Processing helix  chain 'A' and resid 699 through 706
      removed outlier: 3.525A  pdb=" N   ASN A 704 " --> pdb=" O   ILE A 700 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   THR A 706 " --> pdb=" O   LYS A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 723
      removed outlier: 3.914A  pdb=" N   PHE A 711 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 741
      removed outlier: 3.627A  pdb=" N   ALA A 727 " --> pdb=" O   GLY A 723 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE A 739 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 799
    Processing helix  chain 'A' and resid 800 through 806
      removed outlier: 3.536A  pdb=" N   PHE A 804 " --> pdb=" O   ASP A 800 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ASP A 806 " --> pdb=" O   SER A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 810
      removed outlier: 3.573A  pdb=" N   THR A 810 " --> pdb=" O   PRO A 807 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 807 through 810'
    Processing helix  chain 'A' and resid 811 through 854
      removed outlier: 3.647A  pdb=" N   LEU A 818 " --> pdb=" O   LEU A 814 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA A 819 " --> pdb=" O   THR A 815 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ALA A 822 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA A 823 " --> pdb=" O   ALA A 819 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLN A 824 " --> pdb=" O   ASN A 820 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LYS A 826 " --> pdb=" O   ALA A 822 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   GLY A 827 " --> pdb=" O   ALA A 823 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   SER A 831 " --> pdb=" O   GLY A 827 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   ARG A 832 " --> pdb=" O   ALA A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 863
      removed outlier: 3.638A  pdb=" N   THR A 858 " --> pdb=" O   GLY A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 881
      removed outlier: 3.600A  pdb=" N   ILE A 868 " --> pdb=" O   ILE A 864 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 903
      removed outlier: 3.540A  pdb=" N   ILE A 901 " --> pdb=" O   ALA A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 906
      No H-bonds generated for 'chain 'A' and resid 904 through 906'
    Processing helix  chain 'A' and resid 912 through 966
      removed outlier: 4.582A  pdb=" N   VAL A 926 " --> pdb=" O   GLN A 922 " (cutoff:3.500A)
      Proline residue:  A 927  - end of helix
      removed outlier: 4.457A  pdb=" N   TYR A 950 " --> pdb=" O   GLN A 946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 995
      removed outlier: 3.633A  pdb=" N   ALA A 995 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1014
      removed outlier: 3.625A  pdb=" N   ALA A1001 " --> pdb=" O   ASP A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1084
      removed outlier: 4.246A  pdb=" N   VAL A1080 " --> pdb=" O   LYS A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1105 through 1113
      removed outlier: 3.968A  pdb=" N   LEU A1109 " --> pdb=" O   ASN A1105 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ARG A1110 " --> pdb=" O   VAL A1106 " (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 1160
    Processing helix  chain 'A' and resid 1163 through 1167
      removed outlier: 3.996A  pdb=" N   THR A1167 " --> pdb=" O   LYS A1164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1174
      removed outlier: 3.728A  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: 3.902A  pdb=" N   LYS A1212 " --> pdb=" O   THR A1208 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL A1213 " --> pdb=" O   GLU A1209 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ALA A1217 " --> pdb=" O   VAL A1213 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A1218 " --> pdb=" O   VAL A1214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1239
      removed outlier: 4.205A  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
      removed outlier: 3.535A  pdb=" N   SER A1269 " --> pdb=" O   GLY A1265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 132
      removed outlier: 3.593A  pdb=" N   SER B 132 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 193
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.656A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 4.082A  pdb=" N   THR C  91 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 136
    Processing helix  chain 'C' and resid 162 through 164
      No H-bonds generated for 'chain 'C' and resid 162 through 164'
    Processing helix  chain 'C' and resid 206 through 209
    Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 394
    Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473
      removed outlier: 6.636A  pdb=" N   GLY A 471 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   ASP A 555 " --> pdb=" O   GLY A 471 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL A 473 " --> pdb=" O   ASP A 555 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   VAL A 423 " --> pdb=" O   VAL A 584 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   THR A 422 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   ALA A 599 " --> pdb=" O   THR A 422 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ALA A 424 " --> pdb=" O   ALA A 599 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   PHE A 601 " --> pdb=" O   ALA A 424 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   VAL A 426 " --> pdb=" O   PHE A 601 " (cutoff:3.500A)
      removed outlier: 6.509A  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: 5.167A  pdb=" N   LEU A1056 " --> pdb=" O   GLU A1039 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   VAL A1040 " --> pdb=" O   ALA A1091 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   ALA A1091 " --> pdb=" O   VAL A1040 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1114 through 1115
      removed outlier: 3.638A  pdb=" N   GLY A1114 " --> pdb=" O   ILE A1196 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU A1198 " --> pdb=" O   GLY A1114 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A1068 " --> pdb=" O   VAL A1229 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   VAL A1245 " --> pdb=" O   LYS A1252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 14
    Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 53
      removed outlier: 6.528A  pdb=" N   TRP B  40 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR B 102 " --> pdb=" O   GLN B  95 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 123
      removed outlier: 3.565A  pdb=" N   ASN B 142 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   TYR B 178 " --> pdb=" O   ASN B 143 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 161
      removed outlier: 4.257A  pdb=" N   TRP B 153 " --> pdb=" O   GLN B 161 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.812A  pdb=" N   MET C  34 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   THR C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 128 through 130
      removed outlier: 3.635A  pdb=" N   LEU C 130 " --> pdb=" O   GLY C 145 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   TYR C 181 " --> pdb=" O   GLY C 150 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 130
      removed outlier: 3.635A  pdb=" N   LEU C 130 " --> pdb=" O   GLY C 145 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   TYR C 181 " --> pdb=" O   GLY C 150 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 160

    731 hydrogen bonds defined for protein.
    2085 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: 4.70

  Time building geometry restraints manager: 3.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3974
        1.34 -     1.46: 2940
        1.46 -     1.58: 5788
        1.58 -     1.70: 0
        1.70 -     1.82: 83
  Bond restraints: 12785
  Sorted by residual:
  bond pdb=" C   TYR A1087 "
       pdb=" N   ASP A1088 "
    ideal  model  delta    sigma   weight residual
    1.333  1.300  0.033 1.61e-02 3.86e+03 4.24e+00
  bond pdb=" C   ALA B 116 "
       pdb=" N   ALA B 117 "
    ideal  model  delta    sigma   weight residual
    1.339  1.246  0.093 5.57e-02 3.22e+02 2.81e+00
  bond pdb=" C13 CLR A1303 "
       pdb=" C17 CLR A1303 "
    ideal  model  delta    sigma   weight residual
    1.550  1.517  0.033 2.00e-02 2.50e+03 2.69e+00
  bond pdb=" C10 CLR A1303 "
       pdb=" C9  CLR A1303 "
    ideal  model  delta    sigma   weight residual
    1.551  1.518  0.033 2.00e-02 2.50e+03 2.69e+00
  bond pdb=" CA  ALA A 260 "
       pdb=" CB  ALA A 260 "
    ideal  model  delta    sigma   weight residual
    1.527  1.488  0.040 2.48e-02 1.63e+03 2.56e+00
  ... (remaining 12780 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 16659
        1.77 -     3.54: 579
        3.54 -     5.31: 84
        5.31 -     7.08: 17
        7.08 -     8.85: 4
  Bond angle restraints: 17343
  Sorted by residual:
  angle pdb=" N   SER A1020 "
        pdb=" CA  SER A1020 "
        pdb=" C   SER A1020 "
      ideal   model   delta    sigma   weight residual
     113.97  109.29    4.68 1.28e+00 6.10e-01 1.34e+01
  angle pdb=" C   VAL A1273 "
        pdb=" CA  VAL A1273 "
        pdb=" CB  VAL A1273 "
      ideal   model   delta    sigma   weight residual
     111.71  108.72    2.99 8.50e-01 1.38e+00 1.24e+01
  angle pdb=" N   VAL A 592 "
        pdb=" CA  VAL A 592 "
        pdb=" C   VAL A 592 "
      ideal   model   delta    sigma   weight residual
     112.96  109.75    3.21 1.00e+00 1.00e+00 1.03e+01
  angle pdb=" C   TYR A1087 "
        pdb=" N   ASP A1088 "
        pdb=" CA  ASP A1088 "
      ideal   model   delta    sigma   weight residual
     121.83  116.94    4.89 1.56e+00 4.11e-01 9.83e+00
  angle pdb=" C   SER B  68 "
        pdb=" N   GLY B  69 "
        pdb=" CA  GLY B  69 "
      ideal   model   delta    sigma   weight residual
     122.73  119.95    2.78 9.30e-01 1.16e+00 8.91e+00
  ... (remaining 17338 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.20: 7188
       16.20 -    32.39: 536
       32.39 -    48.59: 134
       48.59 -    64.79: 34
       64.79 -    80.98: 6
  Dihedral angle restraints: 7898
    sinusoidal: 3312
      harmonic: 4586
  Sorted by residual:
  dihedral pdb=" CA  LYS B  55 "
           pdb=" C   LYS B  55 "
           pdb=" N   ILE B  56 "
           pdb=" CA  ILE B  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.58  -24.42     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  ASN B 216 "
           pdb=" C   ASN B 216 "
           pdb=" N   ARG B 217 "
           pdb=" CA  ARG B 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.78   22.22     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  ARG B 217 "
           pdb=" C   ARG B 217 "
           pdb=" N   ASN B 218 "
           pdb=" CA  ASN B 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.14   17.86     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 7895 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1656
       0.059 -    0.119: 299
       0.119 -    0.178: 39
       0.178 -    0.237: 6
       0.237 -    0.296: 6
  Chirality restraints: 2006
  Sorted by residual:
  chirality pdb=" C13 CLR A1300 "
            pdb=" C12 CLR A1300 "
            pdb=" C14 CLR A1300 "
            pdb=" C17 CLR A1300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.64   -0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" C13 CLR A1305 "
            pdb=" C12 CLR A1305 "
            pdb=" C14 CLR A1305 "
            pdb=" C17 CLR A1305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.66   -0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" C13 CLR A1303 "
            pdb=" C12 CLR A1303 "
            pdb=" C14 CLR A1303 "
            pdb=" C17 CLR A1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.66   -0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 2003 not shown)

  Planarity restraints: 2156
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  48 "    0.035 5.00e-02 4.00e+02   5.21e-02 4.34e+00
        pdb=" N   PRO B  49 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B  49 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B  49 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  99 "   -0.032 5.00e-02 4.00e+02   4.78e-02 3.66e+00
        pdb=" N   PRO B 100 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 100 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 100 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 173 "   -0.009 2.00e-02 2.50e+03   1.74e-02 3.02e+00
        pdb=" C   THR A 173 "    0.030 2.00e-02 2.50e+03
        pdb=" O   THR A 173 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG A 174 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 2153 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1468
        2.74 -     3.28: 12786
        3.28 -     3.82: 20171
        3.82 -     4.36: 23694
        4.36 -     4.90: 40420
  Nonbonded interactions: 98539
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 623 "
            pdb=" OG1 THR A 627 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   SER A1272 "
            pdb=" OG  SER A1272 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   PHE C  29 "
            pdb=" NH2 ARG C  72 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" O   ALA A 233 "
            pdb=" OG  SER A 237 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   SER A  43 "
            pdb=" NZ  LYS A  48 "
     model   vdw
     2.230 3.120
  ... (remaining 98534 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:             3.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     31.760
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
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      :  0.007   0.093  12790  Z= 0.334
  Angle     :  0.789   8.845  17353  Z= 0.432
  Chirality :  0.049   0.296   2006
  Planarity :  0.004   0.052   2156
  Dihedral  : 12.706  80.982   4943
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  7.72 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.19), residues: 1584
  helix: -1.10 (0.16), residues: 759
  sheet: -0.71 (0.29), residues: 283
  loop : -2.42 (0.23), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 160 
 HIS   0.004   0.001   HIS A 166 
 PHE   0.020   0.002   PHE B  94 
 TYR   0.024   0.002   TYR C  95 
 ARG   0.004   0.001   ARG A 798 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17741 (  719)
  hydrogen bonds       : angle       7.19739 ( 2085)
  SS BOND              : bond        0.00773 (    5)
  SS BOND              : angle       1.62653 (   10)
  covalent geometry    : bond        0.00743 (12785)
  covalent geometry    : angle       0.78791 (17343)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 282
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 TRP cc_start: 0.7992 (t60) cc_final: 0.7673 (t60)
REVERT: A  499 GLU cc_start: 0.6276 (mt-10) cc_final: 0.6025 (mm-30)
REVERT: A  514 MET cc_start: 0.5423 (mtm) cc_final: 0.4637 (tmm)
REVERT: A  799 GLN cc_start: 0.7907 (mm110) cc_final: 0.7673 (mm-40)
REVERT: A  816 THR cc_start: 0.7941 (m) cc_final: 0.7392 (t)
REVERT: A 1183 ARG cc_start: 0.5891 (mtm180) cc_final: 0.5521 (mtp85)
REVERT: A 1270 MET cc_start: -0.0551 (OUTLIER) cc_final: -0.0877 (mtt)
REVERT: B  171 GLN cc_start: 0.8046 (tt0) cc_final: 0.6997 (tt0)
REVERT: C   25 SER cc_start: 0.8624 (p) cc_final: 0.8135 (t)
REVERT: C  121 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8177 (ptmm)
REVERT: C  173 PRO cc_start: 0.8225 (Cg_endo) cc_final: 0.7800 (Cg_exo)
  outliers start: 23
  outliers final: 7
  residues processed: 297
  average time/residue: 0.2967
  time to fit residues: 119.8995
Evaluate side-chains
  159 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 150
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  440 MET
Chi-restraints excluded: chain A residue  441 GLN
Chi-restraints excluded: chain A residue 1270 MET
Chi-restraints excluded: chain A residue 1271 VAL
Chi-restraints excluded: chain B residue   87 ASP
Chi-restraints excluded: chain B residue  113 ARG
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  121 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 133 optimal weight:    0.0670
   chunk 119 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 80 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 123 optimal weight:    0.6980
   chunk 47 optimal weight:    0.4980
   chunk 75 optimal weight:    0.7980
   chunk 92 optimal weight:    6.9990
   chunk 143 optimal weight:    1.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
A 398 HIS
A 438 GLN
A 462 ASN
A 475 GLN
A 612 HIS
A 704 ASN
A 750 GLN
A 799 GLN
A 912 GLN
A 914 GLN
A 946 GLN
A 966 HIS
A1054 GLN
A1105 ASN
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 HIS
A1182 GLN
A1248 ASN
B  18 GLN
B 129 GLN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.157001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.126211 restraints weight = 27492.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.123301 restraints weight = 40152.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.124218 restraints weight = 34475.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12790  Z= 0.139
  Angle     :  0.597   8.414  17353  Z= 0.309
  Chirality :  0.042   0.159   2006
  Planarity :  0.004   0.040   2156
  Dihedral  :  6.535  59.351   2131
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.38 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.20), residues: 1584
  helix:  0.65 (0.18), residues: 787
  sheet:  0.08 (0.31), residues: 276
  loop : -1.92 (0.24), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 698 
 HIS   0.004   0.001   HIS A 612 
 PHE   0.022   0.002   PHE A 200 
 TYR   0.016   0.001   TYR A1133 
 ARG   0.006   0.000   ARG A 538 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05847 (  719)
  hydrogen bonds       : angle       5.01628 ( 2085)
  SS BOND              : bond        0.00470 (    5)
  SS BOND              : angle       1.05093 (   10)
  covalent geometry    : bond        0.00282 (12785)
  covalent geometry    : angle       0.59689 (17343)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 192
  time to evaluate  : 1.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 MET cc_start: 0.7527 (mmm) cc_final: 0.7080 (tpp)
REVERT: A  232 TRP cc_start: 0.7726 (t60) cc_final: 0.7305 (t60)
REVERT: A  514 MET cc_start: 0.4776 (mtm) cc_final: 0.4280 (tmm)
REVERT: A  616 MET cc_start: 0.1386 (mmp) cc_final: 0.0813 (mmm)
REVERT: A  948 MET cc_start: 0.7479 (tpt) cc_final: 0.7269 (tpp)
REVERT: A  949 MET cc_start: 0.8145 (tmm) cc_final: 0.7622 (tpt)
REVERT: A  973 ASP cc_start: 0.8045 (t0) cc_final: 0.7672 (m-30)
REVERT: A 1270 MET cc_start: 0.0243 (tpt) cc_final: -0.0425 (mtt)
REVERT: C  173 PRO cc_start: 0.7697 (Cg_endo) cc_final: 0.7359 (Cg_exo)
  outliers start: 36
  outliers final: 13
  residues processed: 213
  average time/residue: 0.2312
  time to fit residues: 72.7512
Evaluate side-chains
  154 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  441 GLN
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  904 PHE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1136 ASN
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain C residue  138 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 133 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 127 optimal weight:    7.9990
   chunk 130 optimal weight:    0.2980
   chunk 63 optimal weight:    0.8980
   chunk 150 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 398 HIS
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1182 GLN
B  18 GLN
** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.153376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.121446 restraints weight = 28434.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.120287 restraints weight = 52603.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.121151 restraints weight = 39742.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12790  Z= 0.147
  Angle     :  0.576   7.983  17353  Z= 0.301
  Chirality :  0.042   0.144   2006
  Planarity :  0.004   0.042   2156
  Dihedral  :  5.977  59.885   2110
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.55 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.21), residues: 1584
  helix:  1.13 (0.18), residues: 785
  sheet:  0.47 (0.32), residues: 275
  loop : -1.62 (0.25), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 162 
 HIS   0.004   0.001   HIS C 170 
 PHE   0.024   0.002   PHE A 200 
 TYR   0.015   0.001   TYR B  54 
 ARG   0.004   0.000   ARG A 538 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05339 (  719)
  hydrogen bonds       : angle       4.72070 ( 2085)
  SS BOND              : bond        0.00546 (    5)
  SS BOND              : angle       1.17633 (   10)
  covalent geometry    : bond        0.00318 (12785)
  covalent geometry    : angle       0.57507 (17343)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 161
  time to evaluate  : 1.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 TRP cc_start: 0.7864 (t60) cc_final: 0.7553 (t60)
REVERT: A  514 MET cc_start: 0.4656 (mtm) cc_final: 0.4254 (tmm)
REVERT: A  570 GLN cc_start: 0.5940 (tp-100) cc_final: 0.4817 (pt0)
REVERT: A  891 GLU cc_start: 0.7365 (tt0) cc_final: 0.6674 (pp20)
REVERT: A  948 MET cc_start: 0.7591 (tpt) cc_final: 0.7345 (tpp)
REVERT: A  949 MET cc_start: 0.8192 (tmm) cc_final: 0.7556 (tpt)
REVERT: A 1119 GLU cc_start: 0.3080 (OUTLIER) cc_final: 0.2209 (pp20)
REVERT: A 1270 MET cc_start: 0.0168 (tpt) cc_final: -0.0536 (mtt)
REVERT: B  110 GLU cc_start: 0.7633 (tp30) cc_final: 0.7423 (tp30)
REVERT: B  171 GLN cc_start: 0.7492 (tt0) cc_final: 0.6953 (tt0)
REVERT: C  102 TYR cc_start: 0.7400 (m-80) cc_final: 0.7180 (m-10)
REVERT: C  103 GLU cc_start: 0.7305 (mp0) cc_final: 0.6966 (mp0)
  outliers start: 42
  outliers final: 22
  residues processed: 196
  average time/residue: 0.2752
  time to fit residues: 80.0906
Evaluate side-chains
  159 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  904 PHE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1119 GLU
Chi-restraints excluded: chain A residue 1136 ASN
Chi-restraints excluded: chain A residue 1182 GLN
Chi-restraints excluded: chain A residue 1271 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  142 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 130 optimal weight:    0.0670
   chunk 107 optimal weight:    4.9990
   chunk 142 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 118 optimal weight:    7.9990
   chunk 106 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 136 optimal weight:    8.9990
   chunk 157 optimal weight:    7.9990
   overall best weight:    1.1522

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

Flipped N/Q/H residues before XYZ refinement:
A 280 ASN
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.152388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.121164 restraints weight = 27603.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.117177 restraints weight = 39109.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.118899 restraints weight = 33047.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12790  Z= 0.139
  Angle     :  0.558   9.080  17353  Z= 0.290
  Chirality :  0.041   0.167   2006
  Planarity :  0.004   0.048   2156
  Dihedral  :  5.637  54.862   2107
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.53 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.21), residues: 1584
  helix:  1.31 (0.18), residues: 785
  sheet:  0.57 (0.32), residues: 273
  loop : -1.51 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 803 
 HIS   0.004   0.001   HIS A 612 
 PHE   0.021   0.002   PHE A 200 
 TYR   0.023   0.002   TYR A 998 
 ARG   0.003   0.000   ARG A1183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05051 (  719)
  hydrogen bonds       : angle       4.53838 ( 2085)
  SS BOND              : bond        0.01478 (    5)
  SS BOND              : angle       1.61844 (   10)
  covalent geometry    : bond        0.00297 (12785)
  covalent geometry    : angle       0.55671 (17343)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 157
  time to evaluate  : 1.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8670 (tt)
REVERT: A  232 TRP cc_start: 0.7926 (t60) cc_final: 0.7232 (t60)
REVERT: A  277 TYR cc_start: 0.7669 (t80) cc_final: 0.7436 (t80)
REVERT: A  514 MET cc_start: 0.5136 (mtm) cc_final: 0.4642 (tmm)
REVERT: A  570 GLN cc_start: 0.6202 (tp-100) cc_final: 0.4938 (pt0)
REVERT: A  796 MET cc_start: 0.7840 (mtt) cc_final: 0.7536 (mtt)
REVERT: A  891 GLU cc_start: 0.7478 (tt0) cc_final: 0.6676 (pp20)
REVERT: A  948 MET cc_start: 0.7540 (tpt) cc_final: 0.7266 (tpp)
REVERT: A  949 MET cc_start: 0.8134 (tmm) cc_final: 0.7738 (tpt)
REVERT: A 1119 GLU cc_start: 0.3199 (OUTLIER) cc_final: 0.2398 (pp20)
REVERT: A 1270 MET cc_start: -0.0044 (tpt) cc_final: -0.0673 (mtt)
REVERT: B  110 GLU cc_start: 0.7471 (tp30) cc_final: 0.7266 (tp30)
REVERT: B  153 TRP cc_start: 0.3897 (m100) cc_final: 0.2659 (m100)
REVERT: B  171 GLN cc_start: 0.7651 (tt0) cc_final: 0.7412 (tt0)
REVERT: C  102 TYR cc_start: 0.7433 (m-80) cc_final: 0.7055 (m-80)
REVERT: C  103 GLU cc_start: 0.7343 (mp0) cc_final: 0.7006 (mp0)
  outliers start: 42
  outliers final: 26
  residues processed: 191
  average time/residue: 0.3425
  time to fit residues: 98.4452
Evaluate side-chains
  164 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1119 GLU
Chi-restraints excluded: chain A residue 1136 ASN
Chi-restraints excluded: chain A residue 1182 GLN
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  142 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 131 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 95 optimal weight:    7.9990
   chunk 88 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 117 optimal weight:    7.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 912 GLN
A1182 GLN
** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.147045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.116987 restraints weight = 27715.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.116179 restraints weight = 57614.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.116890 restraints weight = 42744.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.4418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12790  Z= 0.195
  Angle     :  0.644  11.983  17353  Z= 0.333
  Chirality :  0.043   0.140   2006
  Planarity :  0.004   0.048   2156
  Dihedral  :  5.683  53.198   2107
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 18.05 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.21), residues: 1584
  helix:  1.14 (0.18), residues: 780
  sheet:  0.53 (0.32), residues: 277
  loop : -1.62 (0.25), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 232 
 HIS   0.007   0.001   HIS A 612 
 PHE   0.019   0.002   PHE A 200 
 TYR   0.018   0.002   TYR C  95 
 ARG   0.011   0.001   ARG B 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05615 (  719)
  hydrogen bonds       : angle       4.76698 ( 2085)
  SS BOND              : bond        0.01001 (    5)
  SS BOND              : angle       1.80620 (   10)
  covalent geometry    : bond        0.00442 (12785)
  covalent geometry    : angle       0.64238 (17343)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 131
  time to evaluate  : 1.316 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it.
REVERT: A  514 MET cc_start: 0.4744 (mtm) cc_final: 0.4514 (tmm)
REVERT: A  570 GLN cc_start: 0.6414 (tp-100) cc_final: 0.6173 (mm-40)
REVERT: A  796 MET cc_start: 0.7827 (mtt) cc_final: 0.7320 (mtm)
REVERT: A  814 LEU cc_start: 0.8469 (mt) cc_final: 0.8042 (mt)
REVERT: A  891 GLU cc_start: 0.7304 (tt0) cc_final: 0.6425 (pp20)
REVERT: A  948 MET cc_start: 0.7758 (tpt) cc_final: 0.7496 (tpp)
REVERT: A 1119 GLU cc_start: 0.3249 (OUTLIER) cc_final: 0.2443 (pp20)
REVERT: A 1270 MET cc_start: 0.0359 (tpt) cc_final: -0.0299 (mtp)
REVERT: B  171 GLN cc_start: 0.7602 (tt0) cc_final: 0.7268 (tt0)
  outliers start: 56
  outliers final: 36
  residues processed: 178
  average time/residue: 0.2190
  time to fit residues: 58.6528
Evaluate side-chains
  146 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 109
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  801 VAL
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  904 PHE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1104 LEU
Chi-restraints excluded: chain A residue 1115 ILE
Chi-restraints excluded: chain A residue 1119 GLU
Chi-restraints excluded: chain A residue 1136 ASN
Chi-restraints excluded: chain A residue 1271 VAL
Chi-restraints excluded: chain B residue   22 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain B residue  220 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 151 optimal weight:    2.9990
   chunk 103 optimal weight:    0.3980
   chunk 35 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 136 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 462 ASN
B 162 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.148896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.119366 restraints weight = 28113.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.115906 restraints weight = 46371.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.117360 restraints weight = 41374.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.4753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12790  Z= 0.128
  Angle     :  0.570   9.849  17353  Z= 0.293
  Chirality :  0.041   0.203   2006
  Planarity :  0.003   0.044   2156
  Dihedral  :  5.331  46.505   2107
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 20.52 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.21), residues: 1584
  helix:  1.42 (0.18), residues: 785
  sheet:  0.80 (0.33), residues: 263
  loop : -1.51 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 803 
 HIS   0.002   0.001   HIS A 936 
 PHE   0.024   0.001   PHE A 200 
 TYR   0.014   0.001   TYR C  95 
 ARG   0.004   0.000   ARG A 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04886 (  719)
  hydrogen bonds       : angle       4.49548 ( 2085)
  SS BOND              : bond        0.00791 (    5)
  SS BOND              : angle       2.51984 (   10)
  covalent geometry    : bond        0.00270 (12785)
  covalent geometry    : angle       0.56738 (17343)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 123
  time to evaluate  : 1.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8725 (tt)
REVERT: A  514 MET cc_start: 0.5120 (mtm) cc_final: 0.4708 (tmm)
REVERT: A  616 MET cc_start: 0.3280 (mpp) cc_final: 0.2868 (mpp)
REVERT: A  814 LEU cc_start: 0.8521 (mt) cc_final: 0.8082 (mt)
REVERT: A  891 GLU cc_start: 0.7303 (tt0) cc_final: 0.6483 (pp20)
REVERT: A  948 MET cc_start: 0.7510 (tpt) cc_final: 0.7168 (tpp)
REVERT: A 1270 MET cc_start: 0.0435 (tpt) cc_final: -0.0214 (mtt)
REVERT: B  110 GLU cc_start: 0.7729 (tp30) cc_final: 0.7450 (tp30)
REVERT: B  171 GLN cc_start: 0.7403 (tt0) cc_final: 0.7089 (tt0)
  outliers start: 38
  outliers final: 28
  residues processed: 153
  average time/residue: 0.2428
  time to fit residues: 56.4440
Evaluate side-chains
  143 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 1.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  441 GLN
Chi-restraints excluded: chain A residue  462 ASN
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1119 GLU
Chi-restraints excluded: chain A residue 1271 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  138 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 152 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9980
   chunk 121 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 156 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 117 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 144 optimal weight:    6.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 462 ASN
A 570 GLN
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.148529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.118688 restraints weight = 27647.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.118226 restraints weight = 53163.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.119350 restraints weight = 39671.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.5009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12790  Z= 0.126
  Angle     :  0.559  11.756  17353  Z= 0.284
  Chirality :  0.040   0.141   2006
  Planarity :  0.003   0.040   2156
  Dihedral  :  5.117  44.679   2107
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.78 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.21), residues: 1584
  helix:  1.58 (0.18), residues: 787
  sheet:  0.78 (0.33), residues: 265
  loop : -1.44 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 803 
 HIS   0.002   0.001   HIS A 936 
 PHE   0.022   0.001   PHE A 200 
 TYR   0.014   0.001   TYR B  54 
 ARG   0.004   0.000   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04706 (  719)
  hydrogen bonds       : angle       4.38393 ( 2085)
  SS BOND              : bond        0.00782 (    5)
  SS BOND              : angle       1.75981 (   10)
  covalent geometry    : bond        0.00267 (12785)
  covalent geometry    : angle       0.55793 (17343)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 125
  time to evaluate  : 2.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8650 (tt)
REVERT: A  273 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7119 (mm-30)
REVERT: A  514 MET cc_start: 0.4967 (mtm) cc_final: 0.4639 (tmm)
REVERT: A  814 LEU cc_start: 0.8422 (mt) cc_final: 0.7955 (mt)
REVERT: A  891 GLU cc_start: 0.7168 (tt0) cc_final: 0.6443 (pp20)
REVERT: A 1270 MET cc_start: 0.0448 (tpt) cc_final: -0.0216 (mtt)
REVERT: B  171 GLN cc_start: 0.7460 (tt0) cc_final: 0.7032 (tt0)
REVERT: C   34 MET cc_start: 0.8953 (mmm) cc_final: 0.8732 (mmt)
  outliers start: 44
  outliers final: 36
  residues processed: 162
  average time/residue: 0.2251
  time to fit residues: 57.7920
Evaluate side-chains
  151 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 114
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  462 ASN
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  976 LEU
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1115 ILE
Chi-restraints excluded: chain A residue 1119 GLU
Chi-restraints excluded: chain A residue 1271 VAL
Chi-restraints excluded: chain B residue   22 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  212 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 140 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0570
   chunk 142 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 131 optimal weight:   10.0000
   overall best weight:    1.3502

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 462 ASN
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1195 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.146983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.116914 restraints weight = 27795.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.116549 restraints weight = 53983.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.117717 restraints weight = 39605.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.5219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12790  Z= 0.144
  Angle     :  0.578   9.511  17353  Z= 0.296
  Chirality :  0.042   0.193   2006
  Planarity :  0.003   0.039   2156
  Dihedral  :  5.107  45.987   2107
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 19.55 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.21), residues: 1584
  helix:  1.59 (0.18), residues: 785
  sheet:  0.74 (0.33), residues: 265
  loop : -1.44 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 708 
 HIS   0.003   0.001   HIS A 936 
 PHE   0.021   0.002   PHE A 200 
 TYR   0.015   0.002   TYR C  95 
 ARG   0.008   0.000   ARG A 464 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04838 (  719)
  hydrogen bonds       : angle       4.43399 ( 2085)
  SS BOND              : bond        0.00838 (    5)
  SS BOND              : angle       1.63973 (   10)
  covalent geometry    : bond        0.00318 (12785)
  covalent geometry    : angle       0.57637 (17343)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 119
  time to evaluate  : 1.279 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7098 (mm-30)
REVERT: A  514 MET cc_start: 0.4997 (mtm) cc_final: 0.4680 (tmm)
REVERT: A  891 GLU cc_start: 0.7259 (tt0) cc_final: 0.6528 (pp20)
REVERT: A  920 TYR cc_start: 0.7755 (t80) cc_final: 0.7279 (t80)
REVERT: A 1087 TYR cc_start: 0.5755 (m-80) cc_final: 0.5554 (m-80)
REVERT: A 1088 ASP cc_start: 0.6887 (m-30) cc_final: 0.6603 (t0)
REVERT: A 1270 MET cc_start: 0.0480 (tpt) cc_final: -0.0227 (mtt)
REVERT: C   34 MET cc_start: 0.8894 (mmm) cc_final: 0.8693 (mmt)
  outliers start: 49
  outliers final: 39
  residues processed: 160
  average time/residue: 0.2158
  time to fit residues: 53.3564
Evaluate side-chains
  153 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 114
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  462 ASN
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  976 LEU
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1115 ILE
Chi-restraints excluded: chain A residue 1119 GLU
Chi-restraints excluded: chain A residue 1271 VAL
Chi-restraints excluded: chain B residue   22 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  212 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 130 optimal weight:    0.0770
   chunk 33 optimal weight:   10.0000
   chunk 146 optimal weight:    0.7980
   chunk 102 optimal weight:    1.9990
   chunk 126 optimal weight:    0.9980
   overall best weight:    0.9742

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 903 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.147303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.117144 restraints weight = 27500.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.116074 restraints weight = 52145.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.117421 restraints weight = 38773.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.5485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  12790  Z= 0.127
  Angle     :  0.570  11.572  17353  Z= 0.291
  Chirality :  0.041   0.162   2006
  Planarity :  0.003   0.038   2156
  Dihedral  :  4.934  48.127   2107
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.45 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.21), residues: 1584
  helix:  1.73 (0.18), residues: 789
  sheet:  0.77 (0.33), residues: 265
  loop : -1.35 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 708 
 HIS   0.002   0.001   HIS A 612 
 PHE   0.025   0.001   PHE A 200 
 TYR   0.014   0.001   TYR C  95 
 ARG   0.005   0.000   ARG A 699 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04564 (  719)
  hydrogen bonds       : angle       4.34788 ( 2085)
  SS BOND              : bond        0.00783 (    5)
  SS BOND              : angle       1.45772 (   10)
  covalent geometry    : bond        0.00280 (12785)
  covalent geometry    : angle       0.56867 (17343)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 130
  time to evaluate  : 1.447 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7056 (mm-30)
REVERT: A  514 MET cc_start: 0.4982 (mtm) cc_final: 0.4725 (tmm)
REVERT: A  786 LYS cc_start: 0.7795 (tmtt) cc_final: 0.7419 (tmtt)
REVERT: A  891 GLU cc_start: 0.7135 (tt0) cc_final: 0.6500 (pp20)
REVERT: A  920 TYR cc_start: 0.7679 (t80) cc_final: 0.7234 (t80)
REVERT: A 1088 ASP cc_start: 0.6924 (m-30) cc_final: 0.6690 (t0)
REVERT: A 1270 MET cc_start: 0.0612 (tpt) cc_final: -0.0239 (mtt)
  outliers start: 35
  outliers final: 32
  residues processed: 160
  average time/residue: 0.2661
  time to fit residues: 63.7654
Evaluate side-chains
  145 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  976 LEU
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1115 ILE
Chi-restraints excluded: chain A residue 1119 GLU
Chi-restraints excluded: chain A residue 1271 VAL
Chi-restraints excluded: chain B residue   22 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  212 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 109 optimal weight:    0.0060
   chunk 121 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 127 optimal weight:   20.0000
   chunk 64 optimal weight:    4.9990
   chunk 143 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    1.5200

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 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 = 0.4061 r_free = 0.4061 target = 0.145311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.115159 restraints weight = 27435.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.114325 restraints weight = 53038.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.115923 restraints weight = 38008.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.5686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  12790  Z= 0.153
  Angle     :  0.605  10.596  17353  Z= 0.309
  Chirality :  0.042   0.165   2006
  Planarity :  0.004   0.040   2156
  Dihedral  :  5.086  49.329   2107
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.15 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.21), residues: 1584
  helix:  1.63 (0.18), residues: 789
  sheet:  0.67 (0.33), residues: 265
  loop : -1.35 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP B 153 
 HIS   0.003   0.001   HIS A 936 
 PHE   0.024   0.002   PHE A 200 
 TYR   0.017   0.002   TYR B  54 
 ARG   0.008   0.000   ARG B 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04870 (  719)
  hydrogen bonds       : angle       4.46298 ( 2085)
  SS BOND              : bond        0.00897 (    5)
  SS BOND              : angle       1.64124 (   10)
  covalent geometry    : bond        0.00344 (12785)
  covalent geometry    : angle       0.60403 (17343)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 117
  time to evaluate  : 1.394 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6956 (mm-30)
REVERT: A  514 MET cc_start: 0.4950 (mtm) cc_final: 0.4673 (tmm)
REVERT: A  891 GLU cc_start: 0.7187 (tt0) cc_final: 0.6554 (pp20)
REVERT: A  920 TYR cc_start: 0.7749 (t80) cc_final: 0.7263 (t80)
REVERT: A  949 MET cc_start: 0.8128 (tmm) cc_final: 0.7748 (tpt)
REVERT: A  953 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6542 (t80)
REVERT: A 1088 ASP cc_start: 0.7042 (m-30) cc_final: 0.6802 (t0)
REVERT: A 1270 MET cc_start: 0.0542 (tpt) cc_final: -0.0310 (mtt)
REVERT: C   34 MET cc_start: 0.8997 (mmm) cc_final: 0.8769 (mmm)
  outliers start: 40
  outliers final: 37
  residues processed: 151
  average time/residue: 0.2472
  time to fit residues: 57.7110
Evaluate side-chains
  148 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 110
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  494 ASN
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  953 TYR
Chi-restraints excluded: chain A residue  976 LEU
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1115 ILE
Chi-restraints excluded: chain A residue 1119 GLU
Chi-restraints excluded: chain A residue 1271 VAL
Chi-restraints excluded: chain B residue   22 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  189 ASP
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  212 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 92 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 152 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 148 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 145 optimal weight:    0.0470
   chunk 98 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.9280

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 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 = 0.4071 r_free = 0.4071 target = 0.146177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.116200 restraints weight = 27474.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.115258 restraints weight = 49953.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.116803 restraints weight = 37733.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.5850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  12790  Z= 0.128
  Angle     :  0.584  10.421  17353  Z= 0.297
  Chirality :  0.041   0.152   2006
  Planarity :  0.004   0.082   2156
  Dihedral  :  4.939  50.685   2107
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.45 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.22), residues: 1584
  helix:  1.71 (0.18), residues: 789
  sheet:  0.66 (0.33), residues: 265
  loop : -1.28 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.002   TRP B 153 
 HIS   0.002   0.001   HIS A1007 
 PHE   0.027   0.001   PHE A 200 
 TYR   0.015   0.001   TYR A 490 
 ARG   0.007   0.000   ARG B 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04617 (  719)
  hydrogen bonds       : angle       4.35398 ( 2085)
  SS BOND              : bond        0.00791 (    5)
  SS BOND              : angle       1.46342 (   10)
  covalent geometry    : bond        0.00278 (12785)
  covalent geometry    : angle       0.58359 (17343)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5859.16 seconds
wall clock time: 106 minutes 51.39 seconds (6411.39 seconds total)