Starting phenix.real_space_refine
on Thu Jun 12 01:33:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ekb_48117/06_2025/9ekb_48117.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ekb_48117/06_2025/9ekb_48117.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ekb_48117/06_2025/9ekb_48117.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ekb_48117/06_2025/9ekb_48117.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ekb_48117/06_2025/9ekb_48117.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ekb_48117/06_2025/9ekb_48117.cif"
  }
  resolution = 3.65
  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=   0.026
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: 6
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     Zn      1      6.06       5
     S      79      5.16       5
     C    8442      2.51       5
     N    2329      2.21       5
     O    2469      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13324
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 8206
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1041, 8202
          Classifications: {'peptide': 1041}
          Link IDs: {'PTRANS': 69, 'TRANS': 971}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 1041, 8202
          Classifications: {'peptide': 1041}
          Link IDs: {'PTRANS': 69, 'TRANS': 971}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 8370
    Chain: "B"
      Number of atoms: 3402
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3402
          Classifications: {'peptide': 442}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 407}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1125
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 2, 'TRANS': 139}
    Chain: "D"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 582
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 7, 'TRANS': 61}
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 9
          Unusual residues: {' ZN': 1, 'SF4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   7420  SG  CYS A1012      17.424  57.992  52.643  1.00174.63           S
  ATOM   7438  SG  CYS A1015      14.489  59.537  52.414  1.00181.12           S
  ATOM   7518  SG  CYS A1026      14.746  58.407  49.494  1.00180.80           S
  ATOM   7544  SG  CYS A1029      17.388  61.174  50.652  1.00175.46           S
  ATOM   7896  SG  CYS A1071      39.209  41.890  85.962  1.00122.69           S
  ATOM   7934  SG  CYS A1076      39.236  48.108  84.884  1.00148.70           S
  ATOM   7795  SG  CYS A1058      40.166  43.768  80.594  1.00128.76           S
  ATOM   7821  SG  CYS A1061      44.256  44.429  85.392  1.00132.37           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLY A1100 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A1100 " occ=0.50
  Time building chain proxies: 15.54, per 1000 atoms: 1.17
  Number of scatterers: 13324
  At special positions: 0
  Unit cell: (86.24, 113.12, 173.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Fe      4     26.01
     S      79     16.00
     O    2469      8.00
     N    2329      7.00
     C    8442      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.42
  Conformation dependent library (CDL) restraints added in 2.9 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A1202 "
        pdb="FE1  SF4 A1202 " - pdb=" SG  CYS A1071 "
        pdb="FE4  SF4 A1202 " - pdb=" SG  CYS A1061 "
        pdb="FE2  SF4 A1202 " - pdb=" SG  CYS A1076 "
        pdb="FE3  SF4 A1202 " - pdb=" SG  CYS A1058 "
      Number of angles added : 12
    Zn2+ tetrahedral coordination
      pdb="  ZN A1201 "
        pdb="ZN    ZN A1201 " - pdb=" SG  CYS A1015 "
        pdb="ZN    ZN A1201 " - pdb=" SG  CYS A1029 "
        pdb="ZN    ZN A1201 " - pdb=" SG  CYS A1012 "
        pdb="ZN    ZN A1201 " - pdb=" SG  CYS A1026 "
      Number of angles added : 6


  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3170

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 12 sheets defined
      42.1% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 57
      removed outlier: 3.626A  pdb=" N   GLU A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 175
      removed outlier: 3.786A  pdb=" N   MET A 161 " --> pdb=" O   GLY A 157 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   GLY A 162 " --> pdb=" O   PRO A 158 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ASP A 163 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   SER A 173 " --> pdb=" O   ASN A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 3.593A  pdb=" N   ALA A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLN A 229 " --> pdb=" O   ARG A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 259
    Processing helix  chain 'A' and resid 302 through 306
      removed outlier: 4.248A  pdb=" N   ARG A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 389
    Processing helix  chain 'A' and resid 401 through 414
      removed outlier: 3.640A  pdb=" N   TYR A 405 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 467
    Processing helix  chain 'A' and resid 473 through 483
    Processing helix  chain 'A' and resid 490 through 499
      removed outlier: 3.560A  pdb=" N   ASN A 499 " --> pdb=" O   THR A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 527
      Proline residue:  A 519  - end of helix
    Processing helix  chain 'A' and resid 527 through 539
    Processing helix  chain 'A' and resid 543 through 548
      removed outlier: 3.543A  pdb=" N   SER A 548 " --> pdb=" O   TYR A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.867A  pdb=" N   VAL A 555 " --> pdb=" O   GLN A 551 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS A 565 " --> pdb=" O   ARG A 561 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   GLU A 566 " --> pdb=" O   GLN A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 614
    Processing helix  chain 'A' and resid 626 through 631
    Processing helix  chain 'A' and resid 654 through 675
      removed outlier: 3.559A  pdb=" N   GLN A 658 " --> pdb=" O   GLY A 654 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA A 675 " --> pdb=" O   LYS A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 705
      removed outlier: 4.335A  pdb=" N   TYR A 701 " --> pdb=" O   ALA A 697 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY A 702 " --> pdb=" O   ASN A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 739
      removed outlier: 4.110A  pdb=" N   SER A 717 " --> pdb=" O   CYS A 713 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR A 739 " --> pdb=" O   VAL A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 744
    Processing helix  chain 'A' and resid 767 through 784
    Processing helix  chain 'A' and resid 837 through 853
      removed outlier: 3.960A  pdb=" N   ALA A 841 " --> pdb=" O   CYS A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 873
    Processing helix  chain 'A' and resid 877 through 882
      removed outlier: 3.736A  pdb=" N   VAL A 882 " --> pdb=" O   SER A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 894
    Processing helix  chain 'A' and resid 898 through 911
    Processing helix  chain 'A' and resid 934 through 937
    Processing helix  chain 'A' and resid 941 through 949
    Processing helix  chain 'A' and resid 953 through 962
      removed outlier: 3.724A  pdb=" N   TYR A 957 " --> pdb=" O   ASP A 953 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LEU A 962 " --> pdb=" O   LEU A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 962 through 975
      Proline residue:  A 972  - end of helix
    Processing helix  chain 'A' and resid 977 through 985
    Processing helix  chain 'A' and resid 1029 through 1031
      No H-bonds generated for 'chain 'A' and resid 1029 through 1031'
    Processing helix  chain 'A' and resid 1032 through 1063
      removed outlier: 3.739A  pdb=" N   SER A1042 " --> pdb=" O   GLN A1038 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   HIS A1043 " --> pdb=" O   LYS A1039 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ARG A1050 " --> pdb=" O   ALA A1046 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TRP A1055 " --> pdb=" O   PHE A1051 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   THR A1056 " --> pdb=" O   SER A1052 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   GLN A1057 " --> pdb=" O   ARG A1053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1097
      removed outlier: 4.039A  pdb=" N   TYR A1080 " --> pdb=" O   CYS A1076 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LYS A1083 " --> pdb=" O   PHE A1079 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 7
    Processing helix  chain 'B' and resid 36 through 40
    Processing helix  chain 'B' and resid 50 through 71
      removed outlier: 3.582A  pdb=" N   TYR B  54 " --> pdb=" O   TYR B  50 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ARG B  57 " --> pdb=" O   ILE B  53 " (cutoff:3.500A)
      Proline residue:  B  63  - end of helix
      removed outlier: 3.554A  pdb=" N   GLU B  66 " --> pdb=" O   ARG B  62 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ASN B  67 " --> pdb=" O   PRO B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 85
    Processing helix  chain 'B' and resid 106 through 112
    Processing helix  chain 'B' and resid 208 through 223
    Processing helix  chain 'B' and resid 228 through 236
    Processing helix  chain 'B' and resid 249 through 253
      removed outlier: 3.729A  pdb=" N   GLN B 253 " --> pdb=" O   HIS B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 288
      removed outlier: 4.017A  pdb=" N   ALA B 275 " --> pdb=" O   ALA B 271 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS B 277 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA B 288 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 316
    Processing helix  chain 'B' and resid 318 through 322
    Processing helix  chain 'B' and resid 346 through 355
    Processing helix  chain 'B' and resid 360 through 371
    Processing helix  chain 'B' and resid 430 through 435
    Processing helix  chain 'C' and resid 4 through 15
    Processing helix  chain 'C' and resid 22 through 31
      removed outlier: 3.758A  pdb=" N   LEU C  26 " --> pdb=" O   THR C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 52
      removed outlier: 3.794A  pdb=" N   ARG C  49 " --> pdb=" O   VAL C  45 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LYS C  50 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLU C  51 " --> pdb=" O   ARG C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 92
    Processing helix  chain 'C' and resid 111 through 125
    Processing helix  chain 'C' and resid 126 through 129
    Processing helix  chain 'D' and resid 40 through 55
    Processing helix  chain 'D' and resid 65 through 76
    Processing helix  chain 'D' and resid 81 through 91
      removed outlier: 3.949A  pdb=" N   TRP D  85 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 99
    Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 275
      removed outlier: 3.593A  pdb=" N   LEU A 286 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   HIS A 142 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   VAL A 122 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   VAL A 105 " --> pdb=" O   VAL A 122 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   VAL A 124 " --> pdb=" O   HIS A 103 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   HIS A 103 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ARG A 126 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ILE A 101 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   PHE A 128 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   TRP A 265 " --> pdb=" O   HIS A 298 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 151
      removed outlier: 7.979A  pdb=" N   LEU A 569 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   GLU A 196 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 371
      removed outlier: 3.669A  pdb=" N   GLN A 369 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TYR A 371 " --> pdb=" O   THR A 356 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ILE A 335 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   GLY A 395 " --> pdb=" O   MET A 457 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 431 through 438
    Processing sheet with id=AA5, first strand: chain 'A' and resid 592 through 594
      removed outlier: 6.987A  pdb=" N   ARG A 808 " --> pdb=" O   ILE A 804 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   THR A 600 " --> pdb=" O   GLU A 795 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   VAL A 797 " --> pdb=" O   ILE A 598 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   ILE A 598 " --> pdb=" O   VAL A 797 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   MET A 760 " --> pdb=" O   VAL A 752 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 592 through 594
      removed outlier: 6.987A  pdb=" N   ARG A 808 " --> pdb=" O   ILE A 804 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 639
    Processing sheet with id=AA8, first strand: chain 'A' and resid 883 through 886
    Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 25
      removed outlier: 6.808A  pdb=" N   PHE B  24 " --> pdb=" O   GLN C 136 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 32 through 34
      removed outlier: 6.726A  pdb=" N   ARG B 340 " --> pdb=" O   VAL B 401 " (cutoff:3.500A)
      removed outlier: 8.099A  pdb=" N   PHE B 403 " --> pdb=" O   ARG B 340 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU B 342 " --> pdb=" O   PHE B 403 " (cutoff:3.500A)
      removed outlier: 8.251A  pdb=" N   GLY B 405 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   THR B 344 " --> pdb=" O   GLY B 405 " (cutoff:3.500A)
      removed outlier: 9.168A  pdb=" N   THR B 407 " --> pdb=" O   THR B 344 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 91 through 100
      removed outlier: 5.248A  pdb=" N   LEU B 133 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   PHE B 162 " --> pdb=" O   GLU B 174 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   TYR B 176 " --> pdb=" O   ALA B 160 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   ALA B 160 " --> pdb=" O   TYR B 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 325 through 327
      removed outlier: 8.739A  pdb=" N   ASP B 293 " --> pdb=" O   SER B 239 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL B 241 " --> pdb=" O   ASP B 293 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   MET B 295 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   LEU B 243 " --> pdb=" O   MET B 295 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   PHE B 195 " --> pdb=" O   SER B 239 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   VAL B 241 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU B 197 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   LEU B 243 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   VAL B 199 " --> pdb=" O   LEU B 243 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   SER C  73 " --> pdb=" O   CYS B 447 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL C  79 " --> pdb=" O   SER B 453 " (cutoff:3.500A)
      removed outlier: 5.862A  pdb=" N   LEU C  62 " --> pdb=" O   VAL C 100 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   VAL C 100 " --> pdb=" O   LEU C  62 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   SER C  64 " --> pdb=" O   ILE C  98 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ILE C  98 " --> pdb=" O   SER C  64 " (cutoff:3.500A)
      removed outlier: 9.090A  pdb=" N   SER C  66 " --> pdb=" O   ALA C  96 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   ALA C  96 " --> pdb=" O   SER C  66 " (cutoff:3.500A)

    603 hydrogen bonds defined for protein.
    1680 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: 9.81

  Time building geometry restraints manager: 4.29 seconds

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

  Histogram of bond lengths:
        1.23 -     1.44: 5690
        1.44 -     1.65: 7812
        1.65 -     1.86: 107
        1.86 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 13621
  Sorted by residual:
  bond pdb=" C   SER A 788 "
       pdb=" N   PRO A 789 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 2.34e-02 1.83e+03 1.20e+00
  bond pdb=" CA  VAL A 596 "
       pdb=" CB  VAL A 596 "
    ideal  model  delta    sigma   weight residual
    1.546  1.537  0.009 8.80e-03 1.29e+04 1.07e+00
  bond pdb=" C   ASN B 330 "
       pdb=" O   ASN B 330 "
    ideal  model  delta    sigma   weight residual
    1.244  1.236  0.008 9.10e-03 1.21e+04 8.08e-01
  bond pdb=" CA  PHE A 799 "
       pdb=" C   PHE A 799 "
    ideal  model  delta    sigma   weight residual
    1.521  1.531 -0.009 1.08e-02 8.57e+03 7.63e-01
  bond pdb=" N   ASN B 330 "
       pdb=" CA  ASN B 330 "
    ideal  model  delta    sigma   weight residual
    1.463  1.457  0.006 6.90e-03 2.10e+04 7.54e-01
  ... (remaining 13616 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 18047
        1.21 -     2.43: 324
        2.43 -     3.64: 103
        3.64 -     4.86: 11
        4.86 -     6.07: 8
  Bond angle restraints: 18493
  Sorted by residual:
  angle pdb=" N   PRO A 789 "
        pdb=" CA  PRO A 789 "
        pdb=" C   PRO A 789 "
      ideal   model   delta    sigma   weight residual
     112.47  118.35   -5.88 2.06e+00 2.36e-01 8.15e+00
  angle pdb=" N   LYS A 738 "
        pdb=" CA  LYS A 738 "
        pdb=" C   LYS A 738 "
      ideal   model   delta    sigma   weight residual
     111.03  113.66   -2.63 1.11e+00 8.12e-01 5.59e+00
  angle pdb=" C   TYR C 101 "
        pdb=" N   SER C 102 "
        pdb=" CA  SER C 102 "
      ideal   model   delta    sigma   weight residual
     122.37  118.59    3.78 1.72e+00 3.38e-01 4.83e+00
  angle pdb=" C   THR B 305 "
        pdb=" N   LEU B 306 "
        pdb=" CA  LEU B 306 "
      ideal   model   delta    sigma   weight residual
     121.80  116.56    5.24 2.44e+00 1.68e-01 4.61e+00
  angle pdb=" C   LEU B 327 "
        pdb=" N   VAL B 328 "
        pdb=" CA  VAL B 328 "
      ideal   model   delta    sigma   weight residual
     122.92  119.92    3.00 1.44e+00 4.82e-01 4.33e+00
  ... (remaining 18488 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.91: 7864
       15.91 -    31.82: 360
       31.82 -    47.74: 63
       47.74 -    63.65: 9
       63.65 -    79.56: 2
  Dihedral angle restraints: 8298
    sinusoidal: 3386
      harmonic: 4912
  Sorted by residual:
  dihedral pdb=" CA  ALA B 244 "
           pdb=" C   ALA B 244 "
           pdb=" N   GLY B 245 "
           pdb=" CA  GLY B 245 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.33   15.67     0      5.00e+00 4.00e-02 9.82e+00
  dihedral pdb=" N   GLU B 132 "
           pdb=" CA  GLU B 132 "
           pdb=" CB  GLU B 132 "
           pdb=" CG  GLU B 132 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.25  -59.75     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LYS A 574 "
           pdb=" CB  LYS A 574 "
           pdb=" CG  LYS A 574 "
           pdb=" CD  LYS A 574 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.24   59.24     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 8295 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1438
       0.036 -    0.072: 453
       0.072 -    0.108: 132
       0.108 -    0.144: 45
       0.144 -    0.180: 1
  Chirality restraints: 2069
  Sorted by residual:
  chirality pdb=" CA  PRO A 789 "
            pdb=" N   PRO A 789 "
            pdb=" C   PRO A 789 "
            pdb=" CB  PRO A 789 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 8.12e-01
  chirality pdb=" CA  ILE C 103 "
            pdb=" N   ILE C 103 "
            pdb=" C   ILE C 103 "
            pdb=" CB  ILE C 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.57e-01
  chirality pdb=" CA  VAL A 334 "
            pdb=" N   VAL A 334 "
            pdb=" C   VAL A 334 "
            pdb=" CB  VAL A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 2066 not shown)

  Planarity restraints: 2415
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 128 "   -0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO B 129 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 129 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 129 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 788 "    0.024 5.00e-02 4.00e+02   3.61e-02 2.08e+00
        pdb=" N   PRO A 789 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 789 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 789 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 112 "   -0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO C 113 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO C 113 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 113 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 2412 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1243
        2.74 -     3.28: 12554
        3.28 -     3.82: 20367
        3.82 -     4.36: 23043
        4.36 -     4.90: 41225
  Nonbonded interactions: 98432
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1073 "
            pdb=" OD1 ASP A1075 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OH  TYR A 593 "
            pdb=" O   LEU A 851 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OH  TYR A 798 "
            pdb=" OD2 ASP A 825 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG  SER A 815 "
            pdb=" OD2 ASP A 822 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG  SER B 200 "
            pdb=" OD1 ASN B 406 "
     model   vdw
     2.256 3.040
  ... (remaining 98427 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=0.50 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:             286.170
  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:             0.020
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.100
  Set scattering table:                    0.110
  Process input model:                     53.320
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.090
  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:             0.020
  Load rotamer database and sin/cos tables:3.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  343.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.341  13629  Z= 0.166
  Angle     :  1.018  52.960  18511  Z= 0.260
  Chirality :  0.041   0.180   2069
  Planarity :  0.004   0.037   2415
  Dihedral  :  9.437  79.561   5128
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.52 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  4.03 %
    Favored  : 94.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.21), residues: 1681
  helix:  1.89 (0.22), residues: 610
  sheet:  0.81 (0.33), residues: 253
  loop : -0.19 (0.23), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 344 
 HIS   0.002   0.001   HIS A 988 
 PHE   0.008   0.001   PHE A  96 
 TYR   0.013   0.001   TYR C  61 
 ARG   0.002   0.000   ARG A 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15160 (  596)
  hydrogen bonds       : angle       6.36490 ( 1680)
  metal coordination   : bond        0.16962 (    8)
  metal coordination   : angle      29.01403 (   18)
  covalent geometry    : bond        0.00255 (13621)
  covalent geometry    : angle       0.46770 (18493)

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

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

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 223
  time to evaluate  : 1.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7469 (ttm) cc_final: 0.7239 (ttp)
REVERT: A   59 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.6269 (tm-30)
REVERT: A  448 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7476 (m)
REVERT: A  466 GLU cc_start: 0.6103 (mt-10) cc_final: 0.5851 (tt0)
REVERT: A  564 MET cc_start: 0.8410 (ttp) cc_final: 0.7901 (mmt)
REVERT: A  612 MET cc_start: 0.6459 (mtm) cc_final: 0.6203 (mtp)
REVERT: A  620 THR cc_start: 0.8430 (p) cc_final: 0.8180 (t)
REVERT: A  635 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7152 (t0)
REVERT: A  725 ARG cc_start: 0.5905 (mtm-85) cc_final: 0.5693 (mtt180)
REVERT: A  905 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8827 (mt-10)
REVERT: A  988 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7311 (p-80)
REVERT: B   61 MET cc_start: 0.8153 (mmm) cc_final: 0.7462 (mtt)
REVERT: B  304 TYR cc_start: 0.8791 (t80) cc_final: 0.8555 (t80)
REVERT: B  358 MET cc_start: 0.9219 (mtm) cc_final: 0.8954 (mtm)
REVERT: B  380 ASP cc_start: 0.8872 (t70) cc_final: 0.8529 (t0)
REVERT: C   46 GLU cc_start: 0.5583 (mm-30) cc_final: 0.5310 (mm-30)
REVERT: C   70 ASN cc_start: 0.8071 (m-40) cc_final: 0.7402 (p0)
REVERT: D   89 LYS cc_start: 0.8450 (tttt) cc_final: 0.8184 (ttmt)
REVERT: D   95 PRO cc_start: 0.8533 (Cg_endo) cc_final: 0.8126 (Cg_exo)
REVERT: D  101 LEU cc_start: 0.9062 (tp) cc_final: 0.8684 (tp)
  outliers start: 28
  outliers final: 7
  residues processed: 248
  average time/residue: 0.4139
  time to fit residues: 142.0941
Evaluate side-chains
  116 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 2.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLN
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain A residue  635 ASP
Chi-restraints excluded: chain A residue  790 ILE
Chi-restraints excluded: chain A residue  988 HIS
Chi-restraints excluded: chain A residue  992 LYS
Chi-restraints excluded: chain B residue   77 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    0.7980
   chunk 127 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 85 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 131 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 80 optimal weight:    8.9990
   chunk 98 optimal weight:    0.5980
   chunk 152 optimal weight:    4.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A  59 GLN
A 142 HIS
A 204 HIS
A 298 HIS
A 305 GLN
A 437 GLN
B 120 GLN
B 250 HIS
B 303 ASN
B 326 GLN
B 347 GLN
B 361 HIS
C  56 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.123183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.091680 restraints weight = 25324.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.093581 restraints weight = 15989.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.094220 restraints weight = 11174.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13629  Z= 0.157
  Angle     :  0.730  25.821  18511  Z= 0.302
  Chirality :  0.043   0.192   2069
  Planarity :  0.005   0.045   2415
  Dihedral  :  4.681  48.233   1878
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.75 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  :  8.82 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.21), residues: 1681
  helix:  2.28 (0.22), residues: 621
  sheet:  0.81 (0.33), residues: 254
  loop : -0.27 (0.23), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 102 
 HIS   0.003   0.001   HIS A 614 
 PHE   0.011   0.001   PHE A 814 
 TYR   0.014   0.001   TYR B 385 
 ARG   0.008   0.001   ARG A 849 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04645 (  596)
  hydrogen bonds       : angle       4.88898 ( 1680)
  metal coordination   : bond        0.00967 (    8)
  metal coordination   : angle      13.81328 (   18)
  covalent geometry    : bond        0.00368 (13621)
  covalent geometry    : angle       0.59024 (18493)

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

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

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 116
  time to evaluate  : 1.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8316 (mtp) cc_final: 0.7886 (mtt)
REVERT: A  245 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7891 (pt0)
REVERT: A  315 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8629 (p90)
REVERT: A  388 MET cc_start: 0.8165 (tmm) cc_final: 0.7552 (tmm)
REVERT: A  448 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7727 (m)
REVERT: A  466 GLU cc_start: 0.6181 (mt-10) cc_final: 0.5951 (tt0)
REVERT: A  564 MET cc_start: 0.8423 (ttp) cc_final: 0.7979 (mmt)
REVERT: A  620 THR cc_start: 0.8422 (p) cc_final: 0.8095 (t)
REVERT: A  725 ARG cc_start: 0.6191 (mtm-85) cc_final: 0.5891 (mtt180)
REVERT: A  827 LYS cc_start: 0.8298 (tppp) cc_final: 0.7884 (ttpt)
REVERT: A  905 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8878 (mt-10)
REVERT: A  940 GLU cc_start: 0.7907 (tp30) cc_final: 0.7499 (mm-30)
REVERT: A  988 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7443 (p-80)
REVERT: B  358 MET cc_start: 0.9180 (mtm) cc_final: 0.8970 (mtm)
REVERT: B  380 ASP cc_start: 0.8863 (t70) cc_final: 0.8476 (t0)
REVERT: C    3 ASP cc_start: 0.6008 (OUTLIER) cc_final: 0.5236 (t0)
REVERT: C   46 GLU cc_start: 0.5762 (mm-30) cc_final: 0.5504 (mm-30)
REVERT: C   70 ASN cc_start: 0.8023 (m-40) cc_final: 0.7459 (p0)
REVERT: C  128 ASN cc_start: 0.7906 (m-40) cc_final: 0.6581 (p0)
REVERT: D   89 LYS cc_start: 0.8639 (tttt) cc_final: 0.8414 (ttmt)
REVERT: D   95 PRO cc_start: 0.8268 (Cg_endo) cc_final: 0.8049 (Cg_exo)
  outliers start: 34
  outliers final: 18
  residues processed: 142
  average time/residue: 0.2907
  time to fit residues: 62.6814
Evaluate side-chains
  124 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain A residue  731 THR
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  988 HIS
Chi-restraints excluded: chain A residue  992 LYS
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue  120 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 84 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0060
   chunk 159 optimal weight:    1.9990
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
B 285 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.122719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.090250 restraints weight = 25613.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.094631 restraints weight = 15370.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.096459 restraints weight = 9177.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3379
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3379
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13629  Z= 0.124
  Angle     :  0.569  12.642  18511  Z= 0.272
  Chirality :  0.042   0.227   2069
  Planarity :  0.004   0.056   2415
  Dihedral  :  4.278  47.164   1869
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.28 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.43 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.21), residues: 1681
  helix:  2.41 (0.22), residues: 621
  sheet:  0.82 (0.34), residues: 250
  loop : -0.24 (0.23), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 102 
 HIS   0.010   0.001   HIS B 250 
 PHE   0.008   0.001   PHE A 148 
 TYR   0.013   0.001   TYR C   6 
 ARG   0.005   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  596)
  hydrogen bonds       : angle       4.57325 ( 1680)
  metal coordination   : bond        0.00696 (    8)
  metal coordination   : angle       6.15455 (   18)
  covalent geometry    : bond        0.00284 (13621)
  covalent geometry    : angle       0.53577 (18493)

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

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

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 1.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8273 (mtp) cc_final: 0.7855 (mtt)
REVERT: A  315 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8552 (p90)
REVERT: A  388 MET cc_start: 0.8065 (tmm) cc_final: 0.7249 (tmm)
REVERT: A  466 GLU cc_start: 0.6181 (mt-10) cc_final: 0.5931 (tt0)
REVERT: A  564 MET cc_start: 0.8389 (ttp) cc_final: 0.7905 (mmt)
REVERT: A  620 THR cc_start: 0.8376 (p) cc_final: 0.8059 (t)
REVERT: A  725 ARG cc_start: 0.6039 (mtm-85) cc_final: 0.5754 (mtt180)
REVERT: A  827 LYS cc_start: 0.8247 (tppp) cc_final: 0.7701 (ttpt)
REVERT: A  905 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8865 (mt-10)
REVERT: A  937 MET cc_start: 0.8220 (tpp) cc_final: 0.7677 (tpp)
REVERT: B  312 HIS cc_start: 0.7807 (t-90) cc_final: 0.7425 (t-90)
REVERT: B  358 MET cc_start: 0.9157 (mtm) cc_final: 0.8942 (mtm)
REVERT: B  380 ASP cc_start: 0.8888 (t70) cc_final: 0.8488 (t0)
REVERT: C    3 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.4970 (t0)
REVERT: C   46 GLU cc_start: 0.5629 (mm-30) cc_final: 0.5361 (mm-30)
REVERT: C   70 ASN cc_start: 0.8018 (m-40) cc_final: 0.7419 (p0)
REVERT: C  128 ASN cc_start: 0.7867 (m-40) cc_final: 0.6502 (p0)
REVERT: D   89 LYS cc_start: 0.8563 (tttt) cc_final: 0.8288 (ttmt)
  outliers start: 31
  outliers final: 19
  residues processed: 130
  average time/residue: 0.2588
  time to fit residues: 50.4480
Evaluate side-chains
  123 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1021 HIS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   86 GLU
Chi-restraints excluded: chain C residue  120 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 166 optimal weight:    0.9980
   chunk 162 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 98 optimal weight:    0.5980
   chunk 125 optimal weight:    0.8980
   chunk 129 optimal weight:    7.9990
   chunk 150 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 114 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 399 GLN
B 250 HIS
** C  52 ASN ** 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 = 0.3760 r_free = 0.3760 target = 0.123228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.091273 restraints weight = 25207.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.095134 restraints weight = 14866.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.096803 restraints weight = 9379.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3382
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3382
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13629  Z= 0.117
  Angle     :  0.525   8.502  18511  Z= 0.259
  Chirality :  0.041   0.214   2069
  Planarity :  0.004   0.057   2415
  Dihedral  :  4.053  46.053   1862
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.16 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  9.57 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.22), residues: 1681
  helix:  2.46 (0.22), residues: 623
  sheet:  0.79 (0.33), residues: 252
  loop : -0.22 (0.23), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 102 
 HIS   0.004   0.001   HIS B 250 
 PHE   0.017   0.001   PHE A 350 
 TYR   0.014   0.001   TYR A 511 
 ARG   0.004   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03762 (  596)
  hydrogen bonds       : angle       4.42500 ( 1680)
  metal coordination   : bond        0.00544 (    8)
  metal coordination   : angle       3.61598 (   18)
  covalent geometry    : bond        0.00270 (13621)
  covalent geometry    : angle       0.51345 (18493)

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

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

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 105
  time to evaluate  : 1.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8254 (mtp) cc_final: 0.7832 (mtt)
REVERT: A  315 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8536 (p90)
REVERT: A  466 GLU cc_start: 0.6213 (mt-10) cc_final: 0.5970 (tt0)
REVERT: A  487 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7141 (mm-30)
REVERT: A  514 LYS cc_start: 0.5522 (mmtt) cc_final: 0.5038 (mptt)
REVERT: A  564 MET cc_start: 0.8379 (ttp) cc_final: 0.7872 (mmt)
REVERT: A  620 THR cc_start: 0.8392 (p) cc_final: 0.8064 (t)
REVERT: A  725 ARG cc_start: 0.6080 (mtm-85) cc_final: 0.5781 (mtt180)
REVERT: A  905 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8840 (mt-10)
REVERT: A  937 MET cc_start: 0.8061 (tpp) cc_final: 0.7570 (tpp)
REVERT: B  312 HIS cc_start: 0.7853 (t-90) cc_final: 0.7498 (t-90)
REVERT: B  380 ASP cc_start: 0.8838 (t70) cc_final: 0.8455 (t0)
REVERT: C    3 ASP cc_start: 0.5824 (OUTLIER) cc_final: 0.4963 (t0)
REVERT: C   46 GLU cc_start: 0.5738 (mm-30) cc_final: 0.5458 (mm-30)
REVERT: C  128 ASN cc_start: 0.7893 (m-40) cc_final: 0.6580 (p0)
REVERT: D   89 LYS cc_start: 0.8689 (tttt) cc_final: 0.8447 (ttmt)
  outliers start: 37
  outliers final: 27
  residues processed: 129
  average time/residue: 0.2784
  time to fit residues: 55.6162
Evaluate side-chains
  125 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 2.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain A residue  731 THR
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1021 HIS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   86 GLU
Chi-restraints excluded: chain C residue  120 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 127 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 123 optimal weight:    0.1980
   chunk 105 optimal weight:    0.0970
   chunk 58 optimal weight:    3.9990
   chunk 157 optimal weight:    0.6980
   chunk 137 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.124392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.092171 restraints weight = 25430.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.096729 restraints weight = 14880.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.098326 restraints weight = 9273.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3397
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13629  Z= 0.095
  Angle     :  0.504   7.548  18511  Z= 0.247
  Chirality :  0.041   0.202   2069
  Planarity :  0.004   0.061   2415
  Dihedral  :  3.922  45.471   1862
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.04 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.39 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.22), residues: 1681
  helix:  2.55 (0.22), residues: 625
  sheet:  0.93 (0.34), residues: 241
  loop : -0.14 (0.23), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 102 
 HIS   0.014   0.001   HIS A 988 
 PHE   0.017   0.001   PHE A 350 
 TYR   0.011   0.001   TYR C  61 
 ARG   0.004   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03369 (  596)
  hydrogen bonds       : angle       4.29523 ( 1680)
  metal coordination   : bond        0.00437 (    8)
  metal coordination   : angle       3.36171 (   18)
  covalent geometry    : bond        0.00208 (13621)
  covalent geometry    : angle       0.49297 (18493)

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

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

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 1.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.6590 (ttm) cc_final: 0.6053 (tmm)
REVERT: A   44 MET cc_start: 0.8159 (mtp) cc_final: 0.7708 (mtt)
REVERT: A  315 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8487 (p90)
REVERT: A  388 MET cc_start: 0.8075 (tmm) cc_final: 0.7471 (tmm)
REVERT: A  466 GLU cc_start: 0.6189 (mt-10) cc_final: 0.5925 (tt0)
REVERT: A  487 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6989 (mm-30)
REVERT: A  514 LYS cc_start: 0.5364 (mmtt) cc_final: 0.4936 (mptt)
REVERT: A  564 MET cc_start: 0.8357 (ttp) cc_final: 0.7820 (mmt)
REVERT: A  620 THR cc_start: 0.8328 (p) cc_final: 0.8027 (t)
REVERT: A  725 ARG cc_start: 0.6012 (mtm-85) cc_final: 0.5707 (mtt180)
REVERT: A  905 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8823 (mt-10)
REVERT: A  937 MET cc_start: 0.8077 (tpp) cc_final: 0.7591 (tpp)
REVERT: B  312 HIS cc_start: 0.7749 (t-90) cc_final: 0.7396 (t-90)
REVERT: B  380 ASP cc_start: 0.8857 (t70) cc_final: 0.8455 (t0)
REVERT: C    3 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.4939 (t0)
REVERT: C   46 GLU cc_start: 0.5663 (mm-30) cc_final: 0.5347 (mm-30)
REVERT: C  128 ASN cc_start: 0.7761 (m-40) cc_final: 0.6408 (p0)
REVERT: D   89 LYS cc_start: 0.8375 (tttt) cc_final: 0.8062 (ttmt)
  outliers start: 29
  outliers final: 24
  residues processed: 118
  average time/residue: 0.2957
  time to fit residues: 53.7045
Evaluate side-chains
  119 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 1.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  824 MET
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1021 HIS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   86 GLU
Chi-restraints excluded: chain C residue  120 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 111 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 98 optimal weight:    0.5980
   chunk 164 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 126 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.123660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.091993 restraints weight = 25226.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.096235 restraints weight = 14442.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.097747 restraints weight = 8804.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3393
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3393
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13629  Z= 0.116
  Angle     :  0.513   6.993  18511  Z= 0.253
  Chirality :  0.041   0.202   2069
  Planarity :  0.004   0.061   2415
  Dihedral  :  3.927  44.701   1862
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.16 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  :  9.91 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.22), residues: 1681
  helix:  2.53 (0.22), residues: 625
  sheet:  0.86 (0.34), residues: 243
  loop : -0.10 (0.23), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 102 
 HIS   0.009   0.001   HIS A 988 
 PHE   0.018   0.001   PHE A 350 
 TYR   0.017   0.001   TYR A 149 
 ARG   0.004   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  596)
  hydrogen bonds       : angle       4.31258 ( 1680)
  metal coordination   : bond        0.00477 (    8)
  metal coordination   : angle       3.18470 (   18)
  covalent geometry    : bond        0.00271 (13621)
  covalent geometry    : angle       0.50337 (18493)

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

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

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 94
  time to evaluate  : 1.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8162 (mtp) cc_final: 0.7730 (mtt)
REVERT: A  315 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8507 (p90)
REVERT: A  388 MET cc_start: 0.8067 (tmm) cc_final: 0.7408 (tmm)
REVERT: A  466 GLU cc_start: 0.6213 (mt-10) cc_final: 0.5934 (tt0)
REVERT: A  564 MET cc_start: 0.8365 (ttp) cc_final: 0.7862 (mmt)
REVERT: A  620 THR cc_start: 0.8320 (p) cc_final: 0.8030 (t)
REVERT: A  725 ARG cc_start: 0.6027 (mtm-85) cc_final: 0.5712 (mtt180)
REVERT: A  905 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8836 (mt-10)
REVERT: A  937 MET cc_start: 0.8116 (tpp) cc_final: 0.7605 (tpp)
REVERT: B  312 HIS cc_start: 0.7791 (t-90) cc_final: 0.7388 (t-90)
REVERT: B  380 ASP cc_start: 0.8875 (t70) cc_final: 0.8476 (t0)
REVERT: C    3 ASP cc_start: 0.5919 (OUTLIER) cc_final: 0.5009 (t0)
REVERT: C   46 GLU cc_start: 0.5695 (mm-30) cc_final: 0.5400 (mm-30)
REVERT: D   89 LYS cc_start: 0.8461 (tttt) cc_final: 0.8171 (ttmt)
  outliers start: 38
  outliers final: 27
  residues processed: 119
  average time/residue: 0.2487
  time to fit residues: 45.1168
Evaluate side-chains
  119 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 1.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain A residue  731 THR
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  790 ILE
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  824 MET
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   86 GLU
Chi-restraints excluded: chain C residue  120 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0970
   chunk 130 optimal weight:    0.6980
   chunk 148 optimal weight:    0.6980
   chunk 78 optimal weight:    0.2980
   chunk 4 optimal weight:    0.5980
   chunk 75 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 124 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.125240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.093303 restraints weight = 25677.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.097114 restraints weight = 14868.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.098670 restraints weight = 9437.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3406
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3406
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13629  Z= 0.091
  Angle     :  0.494   7.306  18511  Z= 0.241
  Chirality :  0.041   0.195   2069
  Planarity :  0.004   0.062   2415
  Dihedral  :  3.812  44.564   1862
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.86 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.66 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.22), residues: 1681
  helix:  2.63 (0.21), residues: 625
  sheet:  0.85 (0.34), residues: 243
  loop : -0.03 (0.23), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 102 
 HIS   0.008   0.001   HIS A 988 
 PHE   0.016   0.001   PHE A 350 
 TYR   0.011   0.001   TYR C  61 
 ARG   0.004   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03123 (  596)
  hydrogen bonds       : angle       4.17751 ( 1680)
  metal coordination   : bond        0.00356 (    8)
  metal coordination   : angle       3.11492 (   18)
  covalent geometry    : bond        0.00201 (13621)
  covalent geometry    : angle       0.48494 (18493)

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

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

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 1.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8208 (mtp) cc_final: 0.7783 (mtt)
REVERT: A  315 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8520 (p90)
REVERT: A  388 MET cc_start: 0.8067 (tmm) cc_final: 0.7386 (tmm)
REVERT: A  466 GLU cc_start: 0.6187 (mt-10) cc_final: 0.5909 (tt0)
REVERT: A  487 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7030 (mm-30)
REVERT: A  564 MET cc_start: 0.8323 (ttp) cc_final: 0.7836 (mmt)
REVERT: A  620 THR cc_start: 0.8311 (p) cc_final: 0.8007 (t)
REVERT: A  877 ASP cc_start: 0.7704 (t0) cc_final: 0.7277 (t0)
REVERT: A  905 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8828 (mt-10)
REVERT: A  937 MET cc_start: 0.8183 (tpp) cc_final: 0.7687 (tpp)
REVERT: B  312 HIS cc_start: 0.7722 (t-90) cc_final: 0.7383 (t-90)
REVERT: B  380 ASP cc_start: 0.8847 (t70) cc_final: 0.8448 (t0)
REVERT: C    3 ASP cc_start: 0.5893 (OUTLIER) cc_final: 0.5377 (t0)
REVERT: C   46 GLU cc_start: 0.5709 (mm-30) cc_final: 0.5404 (mm-30)
REVERT: D   89 LYS cc_start: 0.8463 (tttt) cc_final: 0.8183 (ttmm)
  outliers start: 29
  outliers final: 23
  residues processed: 125
  average time/residue: 0.2663
  time to fit residues: 49.9070
Evaluate side-chains
  116 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1021 HIS
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain B residue   11 HIS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   86 GLU
Chi-restraints excluded: chain C residue  120 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 140 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0870
   chunk 147 optimal weight:    1.9990
   chunk 167 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 155 optimal weight:    2.9990
   chunk 69 optimal weight:    8.9990
   chunk 97 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.6762

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

Flipped N/Q/H residues before XYZ refinement:
B 250 HIS
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.124890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.093484 restraints weight = 24909.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.097684 restraints weight = 14342.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.099771 restraints weight = 8663.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3410
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3410
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  13629  Z= 0.102
  Angle     :  0.510   7.246  18511  Z= 0.248
  Chirality :  0.041   0.187   2069
  Planarity :  0.004   0.063   2415
  Dihedral  :  3.825  44.308   1862
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.22 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 10.73 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.22), residues: 1681
  helix:  2.61 (0.21), residues: 626
  sheet:  0.97 (0.34), residues: 244
  loop : -0.05 (0.23), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 102 
 HIS   0.007   0.001   HIS A 988 
 PHE   0.016   0.001   PHE A 350 
 TYR   0.017   0.001   TYR A 511 
 ARG   0.003   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  596)
  hydrogen bonds       : angle       4.20590 ( 1680)
  metal coordination   : bond        0.00381 (    8)
  metal coordination   : angle       2.89143 (   18)
  covalent geometry    : bond        0.00234 (13621)
  covalent geometry    : angle       0.50220 (18493)

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

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

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 90
  time to evaluate  : 1.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8225 (mtp) cc_final: 0.7761 (mtt)
REVERT: A  315 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8541 (p90)
REVERT: A  388 MET cc_start: 0.8129 (tmm) cc_final: 0.7426 (tmm)
REVERT: A  466 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5961 (tt0)
REVERT: A  487 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7158 (mm-30)
REVERT: A  564 MET cc_start: 0.8322 (ttp) cc_final: 0.7873 (mmt)
REVERT: A  620 THR cc_start: 0.8339 (p) cc_final: 0.8031 (t)
REVERT: A  725 ARG cc_start: 0.6574 (mtt180) cc_final: 0.6260 (mtt90)
REVERT: A  877 ASP cc_start: 0.7727 (t0) cc_final: 0.7514 (t0)
REVERT: A  905 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8826 (mt-10)
REVERT: A  937 MET cc_start: 0.8258 (tpp) cc_final: 0.7736 (tpp)
REVERT: B  304 TYR cc_start: 0.8427 (t80) cc_final: 0.7844 (t80)
REVERT: B  380 ASP cc_start: 0.8803 (t70) cc_final: 0.8422 (t0)
REVERT: C    3 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.5371 (t0)
REVERT: C   46 GLU cc_start: 0.5837 (mm-30) cc_final: 0.5509 (mm-30)
REVERT: D   89 LYS cc_start: 0.8619 (tttt) cc_final: 0.8352 (ttmm)
  outliers start: 32
  outliers final: 27
  residues processed: 111
  average time/residue: 0.2609
  time to fit residues: 43.9948
Evaluate side-chains
  117 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 87
  time to evaluate  : 1.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  790 ILE
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1021 HIS
Chi-restraints excluded: chain B residue   11 HIS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   86 GLU
Chi-restraints excluded: chain C residue  120 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 125 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 72 optimal weight:   10.0000
   chunk 108 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 145 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
B 250 HIS
** C  52 ASN ** 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 = 0.3764 r_free = 0.3764 target = 0.123536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.091703 restraints weight = 24955.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.096008 restraints weight = 14562.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.097582 restraints weight = 9023.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3383
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3383
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13629  Z= 0.118
  Angle     :  0.523   7.330  18511  Z= 0.257
  Chirality :  0.042   0.196   2069
  Planarity :  0.004   0.062   2415
  Dihedral  :  3.899  44.107   1862
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.64 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.80 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.22), residues: 1681
  helix:  2.58 (0.21), residues: 625
  sheet:  0.90 (0.34), residues: 246
  loop : -0.09 (0.23), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 102 
 HIS   0.006   0.001   HIS A 988 
 PHE   0.017   0.001   PHE A 350 
 TYR   0.013   0.001   TYR C  61 
 ARG   0.003   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03613 (  596)
  hydrogen bonds       : angle       4.26284 ( 1680)
  metal coordination   : bond        0.00495 (    8)
  metal coordination   : angle       2.83304 (   18)
  covalent geometry    : bond        0.00276 (13621)
  covalent geometry    : angle       0.51524 (18493)

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

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

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 93
  time to evaluate  : 1.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8173 (mtp) cc_final: 0.7670 (mtm)
REVERT: A  315 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8503 (p90)
REVERT: A  388 MET cc_start: 0.8119 (tmm) cc_final: 0.7390 (tmm)
REVERT: A  466 GLU cc_start: 0.6218 (mt-10) cc_final: 0.5897 (tt0)
REVERT: A  514 LYS cc_start: 0.5306 (mptt) cc_final: 0.5099 (mmtt)
REVERT: A  564 MET cc_start: 0.8355 (ttp) cc_final: 0.7941 (mmt)
REVERT: A  620 THR cc_start: 0.8347 (p) cc_final: 0.8063 (t)
REVERT: A  905 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8881 (mt-10)
REVERT: A  937 MET cc_start: 0.8270 (tpp) cc_final: 0.7769 (tpp)
REVERT: B  304 TYR cc_start: 0.8588 (t80) cc_final: 0.8004 (t80)
REVERT: B  380 ASP cc_start: 0.8863 (t70) cc_final: 0.8476 (t0)
REVERT: C    3 ASP cc_start: 0.6380 (OUTLIER) cc_final: 0.5817 (t0)
REVERT: C   46 GLU cc_start: 0.5842 (mm-30) cc_final: 0.5519 (mm-30)
REVERT: D   89 LYS cc_start: 0.8590 (tttt) cc_final: 0.8297 (ttmm)
  outliers start: 31
  outliers final: 24
  residues processed: 114
  average time/residue: 0.2860
  time to fit residues: 49.9330
Evaluate side-chains
  116 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain A residue  731 THR
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  790 ILE
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1021 HIS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue   86 GLU
Chi-restraints excluded: chain C residue  120 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 86 optimal weight:    0.0770
   chunk 146 optimal weight:    3.9990
   chunk 122 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 150 optimal weight:    0.7980
   chunk 152 optimal weight:    3.9990
   chunk 77 optimal weight:    8.9990
   chunk 103 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 HIS
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.124240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.092602 restraints weight = 24962.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.096701 restraints weight = 14338.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.098534 restraints weight = 8732.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3391
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3391
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  13629  Z= 0.105
  Angle     :  0.522   9.826  18511  Z= 0.255
  Chirality :  0.041   0.191   2069
  Planarity :  0.004   0.063   2415
  Dihedral  :  3.856  43.804   1862
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.16 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.59 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.22), residues: 1681
  helix:  2.63 (0.21), residues: 625
  sheet:  0.96 (0.34), residues: 241
  loop : -0.07 (0.23), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 102 
 HIS   0.006   0.001   HIS A 988 
 PHE   0.016   0.001   PHE A 350 
 TYR   0.017   0.001   TYR A 511 
 ARG   0.004   0.000   ARG A 725 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03394 (  596)
  hydrogen bonds       : angle       4.22007 ( 1680)
  metal coordination   : bond        0.00443 (    8)
  metal coordination   : angle       2.99061 (   18)
  covalent geometry    : bond        0.00243 (13621)
  covalent geometry    : angle       0.51436 (18493)

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

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

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3362 Ramachandran restraints generated.
    1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 91
  time to evaluate  : 1.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8112 (mtp) cc_final: 0.7699 (mtm)
REVERT: A  315 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8504 (p90)
REVERT: A  388 MET cc_start: 0.8103 (tmm) cc_final: 0.7375 (tmm)
REVERT: A  466 GLU cc_start: 0.6316 (mt-10) cc_final: 0.5983 (tt0)
REVERT: A  487 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6986 (mm-30)
REVERT: A  564 MET cc_start: 0.8328 (ttp) cc_final: 0.7937 (mmt)
REVERT: A  620 THR cc_start: 0.8331 (p) cc_final: 0.8029 (t)
REVERT: A  905 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8881 (mt-10)
REVERT: A  937 MET cc_start: 0.8272 (tpp) cc_final: 0.7770 (tpp)
REVERT: B  304 TYR cc_start: 0.8607 (t80) cc_final: 0.8058 (t80)
REVERT: B  380 ASP cc_start: 0.8854 (t70) cc_final: 0.8462 (t0)
REVERT: C    3 ASP cc_start: 0.6409 (OUTLIER) cc_final: 0.5821 (t0)
REVERT: C   46 GLU cc_start: 0.5780 (mm-30) cc_final: 0.5453 (mm-30)
REVERT: D   89 LYS cc_start: 0.8578 (tttt) cc_final: 0.8298 (ttmm)
  outliers start: 31
  outliers final: 25
  residues processed: 112
  average time/residue: 0.2593
  time to fit residues: 43.7949
Evaluate side-chains
  118 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 90
  time to evaluate  : 1.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain A residue  731 THR
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  790 ILE
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1021 HIS
Chi-restraints excluded: chain B residue   11 HIS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue  120 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 28 optimal weight:    0.2980
   chunk 133 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9980
   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 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 HIS
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.124061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.092103 restraints weight = 25023.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.096994 restraints weight = 14394.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.098426 restraints weight = 8704.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3391
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3391
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13629  Z= 0.112
  Angle     :  0.520   7.375  18511  Z= 0.254
  Chirality :  0.041   0.192   2069
  Planarity :  0.004   0.063   2415
  Dihedral  :  3.866  43.504   1862
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.34 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.80 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.22), residues: 1681
  helix:  2.64 (0.21), residues: 625
  sheet:  0.94 (0.34), residues: 241
  loop : -0.07 (0.23), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 102 
 HIS   0.006   0.001   HIS A 988 
 PHE   0.016   0.001   PHE A 350 
 TYR   0.012   0.001   TYR C  61 
 ARG   0.003   0.000   ARG A1060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03424 (  596)
  hydrogen bonds       : angle       4.23013 ( 1680)
  metal coordination   : bond        0.00467 (    8)
  metal coordination   : angle       3.00602 (   18)
  covalent geometry    : bond        0.00263 (13621)
  covalent geometry    : angle       0.51149 (18493)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5256.99 seconds
wall clock time: 94 minutes 41.18 seconds (5681.18 seconds total)