Starting phenix.real_space_refine
on Sun Jun 15 11:52:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tpx_41496/06_2025/8tpx_41496.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tpx_41496/06_2025/8tpx_41496.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tpx_41496/06_2025/8tpx_41496.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tpx_41496/06_2025/8tpx_41496.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tpx_41496/06_2025/8tpx_41496.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tpx_41496/06_2025/8tpx_41496.cif"
  }
  resolution = 3.4
  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=   0.031
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      49      5.16       5
     C   10672      2.51       5
     N    3124      2.21       5
     O    3331      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17177
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6719
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 895, 6675
          Classifications: {'peptide': 895}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 46, 'TRANS': 848}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
      Conformer: "B"
        Number of residues, atoms: 895, 6675
          Classifications: {'peptide': 895}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 46, 'TRANS': 848}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
          bond proxies already assigned to first conformer: 6753
    Chain: "B"
      Number of atoms: 6763
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 901, 6711
          Classifications: {'peptide': 901}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 45, 'TRANS': 855}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
      Conformer: "B"
        Number of residues, atoms: 901, 6711
          Classifications: {'peptide': 901}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 45, 'TRANS': 855}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
          bond proxies already assigned to first conformer: 6779
    Chain: "C"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 560
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'4HH:plan-3': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 1539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1539
          Classifications: {'peptide': 205}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1596
          Classifications: {'peptide': 209}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194}
          Chain breaks: 2
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  AARG A  13 " occ=0.44
      ... (20 atoms not shown)
      pdb=" NH2BARG A  13 " occ=0.56
    residue:
      pdb=" N  AARG A  27 " occ=0.48
      ... (20 atoms not shown)
      pdb=" NH2BARG A  27 " occ=0.52
    residue:
      pdb=" N  AARG A 486 " occ=0.47
      ... (20 atoms not shown)
      pdb=" NH2BARG A 486 " occ=0.53
    residue:
      pdb=" N  AARG B  13 " occ=0.34
      ... (20 atoms not shown)
      pdb=" NH2BARG B  13 " occ=0.66
    residue:
      pdb=" N  AARG B  27 " occ=0.86
      ... (20 atoms not shown)
      pdb=" NH2BARG B  27 " occ=0.14
    residue:
      pdb=" N  AARG B  58 " occ=0.43
      ... (20 atoms not shown)
      pdb=" NH2BARG B  58 " occ=0.57
  Time building chain proxies: 18.27, per 1000 atoms: 1.06
  Number of scatterers: 17177
  At special positions: 0
  Unit cell: (96.8, 117.7, 192.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     P       1     15.00
     O    3331      8.00
     N    3124      7.00
     C   10672      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  24 " - pdb=" SG  CYS H 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  39 " - pdb=" SG  CYS L 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 156 " - pdb=" SG  CYS L 216 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.34
  Conformation dependent library (CDL) restraints added in 3.9 seconds
  

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4140

  Finding SS restraints...
    Secondary structure from input PDB file:
      74 helices and 16 sheets defined
      34.5% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 31
      removed outlier: 4.274A  pdb=" N   VAL A   8 " --> pdb=" O   ASP A   4 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ALA A   9 " --> pdb=" O   SER A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 60
      removed outlier: 4.392A  pdb=" N   GLU A  59 " --> pdb=" O   GLU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 117
      removed outlier: 3.551A  pdb=" N   ALA A 117 " --> pdb=" O   ARG A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 135
      removed outlier: 3.706A  pdb=" N   ARG A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 144
      removed outlier: 3.730A  pdb=" N   ARG A 144 " --> pdb=" O   HIS A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 191
      removed outlier: 3.749A  pdb=" N   TYR A 188 " --> pdb=" O   GLY A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 203
      No H-bonds generated for 'chain 'A' and resid 201 through 203'
    Processing helix  chain 'A' and resid 204 through 220
    Processing helix  chain 'A' and resid 237 through 245
      removed outlier: 3.763A  pdb=" N   SER A 243 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 285
    Processing helix  chain 'A' and resid 310 through 326
    Processing helix  chain 'A' and resid 328 through 332
      removed outlier: 4.063A  pdb=" N   VAL A 332 " --> pdb=" O   PRO A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 358
      removed outlier: 3.503A  pdb=" N   ILE A 348 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 377
    Processing helix  chain 'A' and resid 379 through 381
      No H-bonds generated for 'chain 'A' and resid 379 through 381'
    Processing helix  chain 'A' and resid 382 through 398
      removed outlier: 3.511A  pdb=" N   LEU A 388 " --> pdb=" O   GLY A 384 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LEU A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 496
      removed outlier: 3.741A  pdb=" N   LEU A 496 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 517
      removed outlier: 3.831A  pdb=" N   ARG A 514 " --> pdb=" O   ALA A 511 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   ALA A 515 " --> pdb=" O   THR A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.729A  pdb=" N   GLU A 537 " --> pdb=" O   ARG A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 582
    Processing helix  chain 'A' and resid 582 through 597
      removed outlier: 3.577A  pdb=" N   ALA A 586 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 610
    Processing helix  chain 'A' and resid 619 through 640
      Proline residue:  A 625  - end of helix
      removed outlier: 4.008A  pdb=" N   SER A 633 " --> pdb=" O   ALA A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 653
      No H-bonds generated for 'chain 'A' and resid 651 through 653'
    Processing helix  chain 'A' and resid 654 through 662
    Processing helix  chain 'A' and resid 666 through 683
      removed outlier: 3.793A  pdb=" N   SER A 683 " --> pdb=" O   ARG A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 704
    Processing helix  chain 'A' and resid 729 through 741
      removed outlier: 3.665A  pdb=" N   GLU A 741 " --> pdb=" O   ASP A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 763 through 771
      removed outlier: 4.007A  pdb=" N   LEU A 767 " --> pdb=" O   ARG A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 807
    Processing helix  chain 'A' and resid 811 through 820
      removed outlier: 3.509A  pdb=" N   GLU A 820 " --> pdb=" O   THR A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 876
    Processing helix  chain 'A' and resid 883 through 888
      removed outlier: 3.730A  pdb=" N   VAL A 886 " --> pdb=" O   ARG A 883 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 31
    Processing helix  chain 'B' and resid 49 through 60
      removed outlier: 3.652A  pdb=" N   LEU B  53 " --> pdb=" O   THR B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 118
      removed outlier: 3.530A  pdb=" N   ALA B 117 " --> pdb=" O   ARG B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 136
      removed outlier: 3.745A  pdb=" N   ARG B 123 " --> pdb=" O   ASP B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 144
    Processing helix  chain 'B' and resid 181 through 191
    Processing helix  chain 'B' and resid 201 through 203
      No H-bonds generated for 'chain 'B' and resid 201 through 203'
    Processing helix  chain 'B' and resid 204 through 219
    Processing helix  chain 'B' and resid 250 through 254
    Processing helix  chain 'B' and resid 278 through 285
    Processing helix  chain 'B' and resid 310 through 326
      removed outlier: 3.679A  pdb=" N   GLN B 314 " --> pdb=" O   SER B 310 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   CYS B 325 " --> pdb=" O   ALA B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 354
      removed outlier: 3.780A  pdb=" N   ALA B 350 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA B 352 " --> pdb=" O   ILE B 348 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   LEU B 353 " --> pdb=" O   GLU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 393
      removed outlier: 3.834A  pdb=" N   GLY B 387 " --> pdb=" O   ALA B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 497
      removed outlier: 3.606A  pdb=" N  AARG B 486 " --> pdb=" O   THR B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 514
      removed outlier: 4.272A  pdb=" N   ARG B 514 " --> pdb=" O   LEU B 510 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 540
    Processing helix  chain 'B' and resid 577 through 582
    Processing helix  chain 'B' and resid 582 through 597
      removed outlier: 3.576A  pdb=" N   ALA B 586 " --> pdb=" O   SER B 582 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 600
      No H-bonds generated for 'chain 'B' and resid 598 through 600'
    Processing helix  chain 'B' and resid 603 through 610
      removed outlier: 3.713A  pdb=" N   VAL B 607 " --> pdb=" O   LYS B 603 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 640
      removed outlier: 3.579A  pdb=" N   GLN B 624 " --> pdb=" O   VAL B 620 " (cutoff:3.500A)
      Proline residue:  B 625  - end of helix
    Processing helix  chain 'B' and resid 653 through 662
      removed outlier: 3.883A  pdb=" N   ALA B 657 " --> pdb=" O   GLN B 653 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 682
    Processing helix  chain 'B' and resid 697 through 704
    Processing helix  chain 'B' and resid 727 through 739
    Processing helix  chain 'B' and resid 758 through 762
      removed outlier: 3.511A  pdb=" N   VAL B 762 " --> pdb=" O   ILE B 759 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 763 through 771
      removed outlier: 3.904A  pdb=" N   LEU B 767 " --> pdb=" O   ARG B 763 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   THR B 769 " --> pdb=" O   GLU B 765 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 797 through 807
    Processing helix  chain 'B' and resid 810 through 822
    Processing helix  chain 'B' and resid 835 through 846
    Processing helix  chain 'B' and resid 864 through 878
      removed outlier: 3.686A  pdb=" N   PHE B 868 " --> pdb=" O   ASP B 864 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   SER B 878 " --> pdb=" O   THR B 874 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 883 through 888
      removed outlier: 3.822A  pdb=" N   VAL B 886 " --> pdb=" O   ARG B 883 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1415 through 1429
      removed outlier: 4.362A  pdb=" N   LEU C1419 " --> pdb=" O   ASN C1415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1441 through 1446
    Processing helix  chain 'C' and resid 1450 through 1463
    Processing helix  chain 'C' and resid 1470 through 1475
    Processing helix  chain 'C' and resid 1477 through 1481
    Processing helix  chain 'H' and resid 30 through 34
      removed outlier: 3.839A  pdb=" N   ASP H  33 " --> pdb=" O   THR H  30 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 178 through 182
      removed outlier: 3.573A  pdb=" N   LEU H 182 " --> pdb=" O   SER H 179 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 143 through 150
      removed outlier: 3.548A  pdb=" N   LEU L 147 " --> pdb=" O   SER L 143 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 204 through 209
    Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199
      removed outlier: 6.295A  pdb=" N   VAL A 150 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   VAL A 199 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   LEU A 152 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   GLY A 228 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ALA A 230 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER A  38 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   GLU A 276 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   ILE A  36 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ALA A 290 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ARG A 293 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ILE A 453 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   SER A 295 " --> pdb=" O   HIS A 451 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   HIS A 451 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   LEU A 297 " --> pdb=" O   ASN A 449 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ASN A 449 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ALA A 334 " --> pdb=" O   ARG A 437 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER A 441 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103
    Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400
      removed outlier: 4.337A  pdb=" N   GLN A 427 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.643A  pdb=" N   VAL A 473 " --> pdb=" O   ALA A 525 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA A 525 " --> pdb=" O   VAL A 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 691 through 692
    Processing sheet with id=AA6, first strand: chain 'B' and resid 196 through 199
      removed outlier: 3.969A  pdb=" N   GLY B 153 " --> pdb=" O   GLY B 228 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA B 230 " --> pdb=" O   GLY B 153 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL B 270 " --> pdb=" O   CYS B  41 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   CYS B  41 " --> pdb=" O   VAL B 270 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   LEU B 272 " --> pdb=" O   MET B  39 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   MET B  39 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   LEU B 274 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL B  37 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ALA B 290 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG B 293 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   ILE B 453 " --> pdb=" O   ARG B 293 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   SER B 295 " --> pdb=" O   HIS B 451 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   HIS B 451 " --> pdb=" O   SER B 295 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   LEU B 297 " --> pdb=" O   ASN B 449 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ASN B 449 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ARG B 437 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ALA B 334 " --> pdb=" O   ARG B 437 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 477
    Processing sheet with id=AA8, first strand: chain 'B' and resid 781 through 782
      removed outlier: 6.792A  pdb=" N   VAL B 560 " --> pdb=" O   ALA B 647 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   VAL B 649 " --> pdb=" O   VAL B 560 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   PHE B 562 " --> pdb=" O   VAL B 649 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 689 through 693
      removed outlier: 3.516A  pdb=" N   GLY B 689 " --> pdb=" O   GLY B 726 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY B 726 " --> pdb=" O   GLY B 689 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   VAL B 722 " --> pdb=" O   VAL B 693 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA B 715 " --> pdb=" O   VAL B 723 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 21 through 22
      removed outlier: 3.862A  pdb=" N   LEU H  22 " --> pdb=" O   LEU H  85 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 47 through 49
    Processing sheet with id=AB3, first strand: chain 'H' and resid 158 through 159
    Processing sheet with id=AB4, first strand: chain 'L' and resid 27 through 29
      removed outlier: 3.672A  pdb=" N   LEU L  27 " --> pdb=" O   LYS L 125 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASP L 127 " --> pdb=" O   LEU L  27 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE L  69 " --> pdb=" O   TRP L  56 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU L  58 " --> pdb=" O   LEU L  67 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   LEU L  67 " --> pdb=" O   LEU L  58 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 35 through 40
    Processing sheet with id=AB6, first strand: chain 'L' and resid 138 through 140
      removed outlier: 3.543A  pdb=" N   LEU L 157 " --> pdb=" O   PHE L 138 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE L 140 " --> pdb=" O   VAL L 155 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   VAL L 155 " --> pdb=" O   PHE L 140 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 216 through 218

    589 hydrogen bonds defined for protein.
    1650 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: 5.63

  Time building geometry restraints manager: 5.08 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 3329
        1.32 -     1.45: 4237
        1.45 -     1.57: 9866
        1.57 -     1.69: 2
        1.69 -     1.81: 79
  Bond restraints: 17513
  Sorted by residual:
  bond pdb=" N   ASN B 351 "
       pdb=" CA  ASN B 351 "
    ideal  model  delta    sigma   weight residual
    1.458  1.501 -0.044 1.42e-02 4.96e+03 9.41e+00
  bond pdb=" C   PRO A  50 "
       pdb=" O   PRO A  50 "
    ideal  model  delta    sigma   weight residual
    1.235  1.202  0.033 1.30e-02 5.92e+03 6.29e+00
  bond pdb=" N   ASP B 355 "
       pdb=" CA  ASP B 355 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.33e-02 5.65e+03 5.54e+00
  bond pdb=" N   VAL A  47 "
       pdb=" CA  VAL A  47 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.25e-02 6.40e+03 5.43e+00
  bond pdb=" CA  ALA B 352 "
       pdb=" CB  ALA B 352 "
    ideal  model  delta    sigma   weight residual
    1.531  1.494  0.037 1.59e-02 3.96e+03 5.33e+00
  ... (remaining 17508 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 23486
        2.58 -     5.15: 291
        5.15 -     7.73: 29
        7.73 -    10.31: 5
       10.31 -    12.88: 5
  Bond angle restraints: 23816
  Sorted by residual:
  angle pdb=" N   LEU B 353 "
        pdb=" CA  LEU B 353 "
        pdb=" C   LEU B 353 "
      ideal   model   delta    sigma   weight residual
     113.18  101.30   11.88 1.21e+00 6.83e-01 9.64e+01
  angle pdb=" N   ASP B 355 "
        pdb=" CA  ASP B 355 "
        pdb=" C   ASP B 355 "
      ideal   model   delta    sigma   weight residual
     113.28  101.67   11.61 1.22e+00 6.72e-01 9.06e+01
  angle pdb=" N   LEU B 354 "
        pdb=" CA  LEU B 354 "
        pdb=" C   LEU B 354 "
      ideal   model   delta    sigma   weight residual
     113.28  102.35   10.93 1.22e+00 6.72e-01 8.03e+01
  angle pdb=" C   TYR B 159 "
        pdb=" CA  TYR B 159 "
        pdb=" CB  TYR B 159 "
      ideal   model   delta    sigma   weight residual
     116.63  110.86    5.77 1.16e+00 7.43e-01 2.48e+01
  angle pdb=" C   VAL A  47 "
        pdb=" N   ASN A  48 "
        pdb=" CA  ASN A  48 "
      ideal   model   delta    sigma   weight residual
     122.11  114.87    7.24 1.59e+00 3.96e-01 2.08e+01
  ... (remaining 23811 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 9330
       17.95 -    35.89: 877
       35.89 -    53.84: 233
       53.84 -    71.78: 35
       71.78 -    89.73: 15
  Dihedral angle restraints: 10490
    sinusoidal: 4019
      harmonic: 6471
  Sorted by residual:
  dihedral pdb=" CB  CYS L  39 "
           pdb=" SG  CYS L  39 "
           pdb=" SG  CYS L 109 "
           pdb=" CB  CYS L 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  155.49  -62.49     1      1.00e+01 1.00e-02 5.17e+01
  dihedral pdb=" CA  THR B 410 "
           pdb=" C   THR B 410 "
           pdb=" N   PRO B 411 "
           pdb=" CA  PRO B 411 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.83  -27.17     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  ASP B  74 "
           pdb=" C   ASP B  74 "
           pdb=" N   LEU B  75 "
           pdb=" CA  LEU B  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.26  -25.74     0      5.00e+00 4.00e-02 2.65e+01
  ... (remaining 10487 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 2307
       0.060 -    0.119: 344
       0.119 -    0.178: 26
       0.178 -    0.238: 1
       0.238 -    0.297: 2
  Chirality restraints: 2680
  Sorted by residual:
  chirality pdb=" CA  LEU B 353 "
            pdb=" N   LEU B 353 "
            pdb=" C   LEU B 353 "
            pdb=" CB  LEU B 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CA  LEU B 354 "
            pdb=" N   LEU B 354 "
            pdb=" C   LEU B 354 "
            pdb=" CB  LEU B 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CB  VAL A 174 "
            pdb=" CA  VAL A 174 "
            pdb=" CG1 VAL A 174 "
            pdb=" CG2 VAL A 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 2677 not shown)

  Planarity restraints: 3172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  46 "   -0.025 2.00e-02 2.50e+03   5.09e-02 2.59e+01
        pdb=" C   GLY A  46 "    0.088 2.00e-02 2.50e+03
        pdb=" O   GLY A  46 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   VAL A  47 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 355 "    0.024 2.00e-02 2.50e+03   4.96e-02 2.46e+01
        pdb=" C   ASP B 355 "   -0.086 2.00e-02 2.50e+03
        pdb=" O   ASP B 355 "    0.032 2.00e-02 2.50e+03
        pdb=" N   THR B 356 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 354 "   -0.015 2.00e-02 2.50e+03   3.15e-02 9.94e+00
        pdb=" C   LEU B 354 "    0.054 2.00e-02 2.50e+03
        pdb=" O   LEU B 354 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP B 355 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 3169 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 2536
        2.75 -     3.29: 18103
        3.29 -     3.83: 28225
        3.83 -     4.36: 31250
        4.36 -     4.90: 52990
  Nonbonded interactions: 133104
  Sorted by model distance:
  nonbonded pdb=" OG1 THR H  73 "
            pdb=" OD1 ASN H  88 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG1 THR B 666 "
            pdb=" OE1 GLU B 668 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   LEU A 637 "
            pdb=" OG  SER A 640 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OH  TYR A  90 "
            pdb=" O   LEU A 248 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" N   GLU C1431 "
            pdb=" OE1 GLU C1431 "
     model   vdw
     2.233 3.120
  ... (remaining 133099 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 3 through 12 or resid 14 through 26 or resid 28 through 47 \ 
 or resid 49 through 57 or resid 59 through 95 or (resid 96 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 97 through 485 or resid 487 throug \ 
h 908))
  selection = (chain 'B' and (resid 3 through 12 or resid 14 through 26 or resid 28 through 47 \ 
 or resid 49 through 57 or resid 59 through 162 or resid 171 through 485 or resi \ 
d 487 through 595 or (resid 596 through 597 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 598 through 908))
}

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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             8.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.650
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     50.880
  Find NCS groups from input model:        0.720
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   64.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
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      :  0.003   0.044  17517  Z= 0.158
  Angle     :  0.692  12.883  23824  Z= 0.376
  Chirality :  0.042   0.297   2680
  Planarity :  0.005   0.075   3172
  Dihedral  : 15.184  89.726   6338
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 14.08 %
    Favored  : 85.16 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 17.01 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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: -1.36 (0.19), residues: 2278
  helix:  1.43 (0.21), residues: 681
  sheet: -0.55 (0.33), residues: 281
  loop : -2.42 (0.17), residues: 1316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  54 
 HIS   0.007   0.001   HIS A 832 
 PHE   0.011   0.001   PHE B 157 
 TYR   0.019   0.001   TYR A 906 
 ARG   0.007   0.000   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16714 (  589)
  hydrogen bonds       : angle       6.45322 ( 1650)
  SS BOND              : bond        0.00202 (    4)
  SS BOND              : angle       0.69614 (    8)
  covalent geometry    : bond        0.00321 (17513)
  covalent geometry    : angle       0.69165 (23816)

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

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

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 1.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 3
  residues processed: 83
  average time/residue: 0.3669
  time to fit residues: 45.3701
Evaluate side-chains
  69 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 2.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ARG
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain B residue  585 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 226
   random chunks:
   chunk 190 optimal weight:    0.7980
   chunk 171 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 115 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 177 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 131 optimal weight:    0.5980
   chunk 205 optimal weight:    0.0470
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.050988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.034643 restraints weight = 510795.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 11.63
r_work: 0.2640 rms_B_bonded: 10.36 restraints_weight: 2.0000
r_work: 0.2767 rms_B_bonded: 6.61 restraints_weight: 4.0000
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2766
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.2766
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.0827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  17517  Z= 0.134
  Angle     :  0.655  13.917  23824  Z= 0.334
  Chirality :  0.042   0.279   2680
  Planarity :  0.005   0.079   3172
  Dihedral  :  5.190  58.023   2527
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 13.37 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.06 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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: -1.33 (0.18), residues: 2278
  helix:  1.66 (0.21), residues: 700
  sheet: -0.97 (0.31), residues: 307
  loop : -2.50 (0.17), residues: 1271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  54 
 HIS   0.005   0.001   HIS B 519 
 PHE   0.020   0.001   PHE B 157 
 TYR   0.020   0.001   TYR A 906 
 ARG   0.006   0.000   ARG C1439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03942 (  589)
  hydrogen bonds       : angle       4.60034 ( 1650)
  SS BOND              : bond        0.00181 (    4)
  SS BOND              : angle       0.58709 (    8)
  covalent geometry    : bond        0.00293 (17513)
  covalent geometry    : angle       0.65528 (23816)

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

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

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 1.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  599 MET cc_start: 0.9362 (tmm) cc_final: 0.9009 (tmm)
REVERT: A  791 MET cc_start: 0.8388 (mmm) cc_final: 0.7520 (mmm)
REVERT: C 1444 GLU cc_start: 0.4637 (tp30) cc_final: 0.4339 (tp30)
REVERT: H  129 PHE cc_start: 0.8452 (t80) cc_final: 0.7380 (t80)
REVERT: L  155 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8322 (t)
  outliers start: 29
  outliers final: 14
  residues processed: 100
  average time/residue: 0.3104
  time to fit residues: 48.4050
Evaluate side-chains
  85 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 1.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 MET
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue  266 PHE
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  585 PHE
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   63 GLU
Chi-restraints excluded: chain H residue   85 LEU
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain L residue  155 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 226
   random chunks:
   chunk 129 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 117 optimal weight:    0.5980
   chunk 194 optimal weight:    7.9990
   chunk 188 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 139 optimal weight:    2.9990
   chunk 161 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 201 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  15 GLN
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.050120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.034006 restraints weight = 440035.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 10.85
r_work: 0.2614 rms_B_bonded: 10.02 restraints_weight: 2.0000
r_work: 0.2740 rms_B_bonded: 6.31 restraints_weight: 4.0000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  17517  Z= 0.155
  Angle     :  0.662  14.530  23824  Z= 0.337
  Chirality :  0.042   0.166   2680
  Planarity :  0.005   0.081   3172
  Dihedral  :  5.224  59.317   2523
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 13.95 %
    Favored  : 85.47 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.72 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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: -1.34 (0.18), residues: 2278
  helix:  1.73 (0.21), residues: 699
  sheet: -1.08 (0.31), residues: 310
  loop : -2.52 (0.17), residues: 1269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  54 
 HIS   0.005   0.001   HIS B 519 
 PHE   0.015   0.001   PHE B 157 
 TYR   0.020   0.001   TYR A 906 
 ARG   0.007   0.000   ARG C1458 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03962 (  589)
  hydrogen bonds       : angle       4.43041 ( 1650)
  SS BOND              : bond        0.00242 (    4)
  SS BOND              : angle       0.54682 (    8)
  covalent geometry    : bond        0.00348 (17513)
  covalent geometry    : angle       0.66229 (23816)

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

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

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 69
  time to evaluate  : 1.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 MET cc_start: 0.9342 (tpp) cc_final: 0.9047 (ttm)
REVERT: A  599 MET cc_start: 0.9395 (tmm) cc_final: 0.9010 (tmm)
REVERT: C 1439 ARG cc_start: 0.8970 (mtm110) cc_final: 0.8744 (mtm110)
REVERT: H  129 PHE cc_start: 0.8298 (t80) cc_final: 0.7663 (t80)
  outliers start: 36
  outliers final: 22
  residues processed: 102
  average time/residue: 0.2972
  time to fit residues: 46.7542
Evaluate side-chains
  91 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 1.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  824 ASP
Chi-restraints excluded: chain A residue  835 VAL
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  266 PHE
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  585 PHE
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   38 TRP
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   85 LEU
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain L residue  106 VAL
Chi-restraints excluded: chain L residue  185 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 226
   random chunks:
   chunk 159 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 123 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 167 optimal weight:    0.0270
   chunk 17 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 58 optimal weight:    8.9990
   chunk 49 optimal weight:    0.0070
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.5056

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.050930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.034720 restraints weight = 480735.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 11.63
r_work: 0.2641 rms_B_bonded: 10.31 restraints_weight: 2.0000
r_work: 0.2765 rms_B_bonded: 6.61 restraints_weight: 4.0000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2764
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.2764
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  17517  Z= 0.117
  Angle     :  0.635  15.345  23824  Z= 0.323
  Chirality :  0.042   0.150   2680
  Planarity :  0.004   0.075   3172
  Dihedral  :  5.155  57.455   2523
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 12.93 %
    Favored  : 86.49 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.89 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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: -1.32 (0.18), residues: 2278
  helix:  1.76 (0.21), residues: 694
  sheet: -1.00 (0.31), residues: 315
  loop : -2.53 (0.17), residues: 1269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  54 
 HIS   0.006   0.001   HIS B 519 
 PHE   0.014   0.001   PHE B 157 
 TYR   0.024   0.001   TYR B 802 
 ARG   0.006   0.000   ARG A 480 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03264 (  589)
  hydrogen bonds       : angle       4.25623 ( 1650)
  SS BOND              : bond        0.00201 (    4)
  SS BOND              : angle       0.52711 (    8)
  covalent geometry    : bond        0.00258 (17513)
  covalent geometry    : angle       0.63535 (23816)

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

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

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 73
  time to evaluate  : 1.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.8952 (ttt) cc_final: 0.8640 (ttt)
REVERT: A  599 MET cc_start: 0.9313 (tmm) cc_final: 0.9045 (tmm)
REVERT: A  681 MET cc_start: 0.9605 (tmm) cc_final: 0.9298 (tmm)
REVERT: C 1444 GLU cc_start: 0.4828 (tp30) cc_final: 0.4554 (tp30)
REVERT: C 1458 ARG cc_start: 0.8397 (mtp180) cc_final: 0.8112 (mmm-85)
REVERT: H  129 PHE cc_start: 0.8242 (t80) cc_final: 0.7657 (t80)
REVERT: H  173 PHE cc_start: 0.6005 (OUTLIER) cc_final: 0.4913 (t80)
REVERT: L  110 MET cc_start: 0.9156 (mmm) cc_final: 0.8742 (mmm)
  outliers start: 37
  outliers final: 27
  residues processed: 107
  average time/residue: 0.3093
  time to fit residues: 51.0581
Evaluate side-chains
  101 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 1.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  172 TYR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  824 ASP
Chi-restraints excluded: chain A residue  835 VAL
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   73 TRP
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   38 TRP
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   85 LEU
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  173 PHE
Chi-restraints excluded: chain H residue  214 VAL
Chi-restraints excluded: chain L residue  106 VAL
Chi-restraints excluded: chain L residue  185 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 226
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 215 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 115 optimal weight:    0.4980
   chunk 211 optimal weight:    2.9990
   chunk 198 optimal weight:    0.8980
   chunk 217 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 203 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.049236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.032994 restraints weight = 467162.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 11.17
r_work: 0.2569 rms_B_bonded: 10.00 restraints_weight: 2.0000
r_work: 0.2692 rms_B_bonded: 6.44 restraints_weight: 4.0000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.2691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  17517  Z= 0.210
  Angle     :  0.713  15.865  23824  Z= 0.361
  Chirality :  0.044   0.181   2680
  Planarity :  0.005   0.081   3172
  Dihedral  :  5.289  57.933   2521
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  : 14.44 %
    Favored  : 85.03 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.68 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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: -1.36 (0.18), residues: 2278
  helix:  1.75 (0.21), residues: 694
  sheet: -1.07 (0.31), residues: 318
  loop : -2.56 (0.17), residues: 1266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  54 
 HIS   0.006   0.001   HIS B 412 
 PHE   0.013   0.002   PHE B 264 
 TYR   0.020   0.002   TYR B 802 
 ARG   0.008   0.000   ARG H  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04308 (  589)
  hydrogen bonds       : angle       4.42773 ( 1650)
  SS BOND              : bond        0.00272 (    4)
  SS BOND              : angle       0.55869 (    8)
  covalent geometry    : bond        0.00469 (17513)
  covalent geometry    : angle       0.71259 (23816)

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

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

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 70
  time to evaluate  : 2.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 MET cc_start: 0.9289 (tpp) cc_final: 0.9045 (ttm)
REVERT: A  599 MET cc_start: 0.9346 (tmm) cc_final: 0.9017 (tmm)
REVERT: H  173 PHE cc_start: 0.6239 (OUTLIER) cc_final: 0.5458 (t80)
  outliers start: 38
  outliers final: 27
  residues processed: 106
  average time/residue: 0.3173
  time to fit residues: 51.3928
Evaluate side-chains
  96 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 1.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  172 TYR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  824 ASP
Chi-restraints excluded: chain A residue  835 VAL
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  266 PHE
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   38 TRP
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   85 LEU
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  173 PHE
Chi-restraints excluded: chain H residue  214 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  106 VAL
Chi-restraints excluded: chain L residue  185 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 226
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 163 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 220 optimal weight:   10.0000
   chunk 148 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0000
   chunk 4 optimal weight:    0.0470
   overall best weight:    0.4682

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN
** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 207 HIS ** 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 = 0.3434 r_free = 0.3434 target = 0.050524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.034209 restraints weight = 435491.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 10.52
r_work: 0.2647 rms_B_bonded: 9.78 restraints_weight: 2.0000
r_work: 0.2766 rms_B_bonded: 6.53 restraints_weight: 4.0000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2764
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.2764
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  17517  Z= 0.117
  Angle     :  0.668  16.269  23824  Z= 0.332
  Chirality :  0.042   0.184   2680
  Planarity :  0.004   0.077   3172
  Dihedral  :  5.128  58.310   2521
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 12.31 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.35 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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: -1.35 (0.18), residues: 2278
  helix:  1.75 (0.21), residues: 695
  sheet: -1.02 (0.32), residues: 297
  loop : -2.55 (0.17), residues: 1286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 907 
 HIS   0.007   0.001   HIS B 519 
 PHE   0.011   0.001   PHE B 157 
 TYR   0.021   0.001   TYR A 906 
 ARG   0.009   0.000   ARG C1439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03272 (  589)
  hydrogen bonds       : angle       4.20964 ( 1650)
  SS BOND              : bond        0.00222 (    4)
  SS BOND              : angle       0.56503 (    8)
  covalent geometry    : bond        0.00259 (17513)
  covalent geometry    : angle       0.66793 (23816)

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

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

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 72
  time to evaluate  : 1.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 LEU cc_start: 0.9348 (tt) cc_final: 0.8820 (pp)
REVERT: B  246 ARG cc_start: 0.8793 (ttt90) cc_final: 0.8585 (ttt-90)
REVERT: B  791 MET cc_start: 0.9018 (ppp) cc_final: 0.7849 (ppp)
REVERT: C 1444 GLU cc_start: 0.4576 (tp30) cc_final: 0.4248 (tp30)
REVERT: C 1475 HIS cc_start: 0.3920 (p90) cc_final: 0.3705 (p-80)
REVERT: H   21 ARG cc_start: 0.9059 (tpt170) cc_final: 0.8638 (tpt170)
REVERT: H  173 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5033 (t80)
REVERT: L  110 MET cc_start: 0.9168 (mmm) cc_final: 0.8775 (mmm)
  outliers start: 36
  outliers final: 31
  residues processed: 104
  average time/residue: 0.3057
  time to fit residues: 48.6443
Evaluate side-chains
  103 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 71
  time to evaluate  : 1.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  172 TYR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  824 ASP
Chi-restraints excluded: chain A residue  835 VAL
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   73 TRP
Chi-restraints excluded: chain B residue   98 ASP
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   38 TRP
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   85 LEU
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  173 PHE
Chi-restraints excluded: chain H residue  214 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  106 VAL
Chi-restraints excluded: chain L residue  185 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 226
   random chunks:
   chunk 220 optimal weight:    7.9990
   chunk 94 optimal weight:    0.6980
   chunk 196 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 130 optimal weight:    4.9990
   chunk 131 optimal weight:    0.2980
   chunk 212 optimal weight:    0.3980
   chunk 71 optimal weight:    8.9990
   chunk 20 optimal weight:    0.4980
   chunk 117 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.050764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.034411 restraints weight = 443218.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 10.66
r_work: 0.2654 rms_B_bonded: 9.91 restraints_weight: 2.0000
r_work: 0.2780 rms_B_bonded: 6.39 restraints_weight: 4.0000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17517  Z= 0.114
  Angle     :  0.654  13.936  23824  Z= 0.324
  Chirality :  0.042   0.173   2680
  Planarity :  0.004   0.076   3172
  Dihedral  :  4.982  59.191   2521
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  : 13.51 %
    Favored  : 85.96 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.35 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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: -1.25 (0.19), residues: 2278
  helix:  1.89 (0.21), residues: 691
  sheet: -1.02 (0.31), residues: 311
  loop : -2.51 (0.17), residues: 1276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  54 
 HIS   0.005   0.001   HIS B 519 
 PHE   0.030   0.001   PHE H 129 
 TYR   0.021   0.001   TYR A 906 
 ARG   0.011   0.000   ARG C1439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03076 (  589)
  hydrogen bonds       : angle       4.10791 ( 1650)
  SS BOND              : bond        0.00196 (    4)
  SS BOND              : angle       0.53668 (    8)
  covalent geometry    : bond        0.00252 (17513)
  covalent geometry    : angle       0.65444 (23816)

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

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

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 73
  time to evaluate  : 1.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 LEU cc_start: 0.9348 (tt) cc_final: 0.8789 (pp)
REVERT: A  599 MET cc_start: 0.9249 (tmm) cc_final: 0.8920 (tmm)
REVERT: A  898 THR cc_start: 0.6556 (p) cc_final: 0.6270 (p)
REVERT: B  791 MET cc_start: 0.9083 (ppp) cc_final: 0.7759 (ppp)
REVERT: C 1444 GLU cc_start: 0.4563 (tp30) cc_final: 0.4226 (tp30)
REVERT: H   21 ARG cc_start: 0.9060 (tpt170) cc_final: 0.8671 (tpt170)
REVERT: H  173 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.4844 (t80)
REVERT: L  110 MET cc_start: 0.9121 (mmm) cc_final: 0.8874 (mmm)
  outliers start: 38
  outliers final: 30
  residues processed: 109
  average time/residue: 0.3138
  time to fit residues: 52.9281
Evaluate side-chains
  104 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 73
  time to evaluate  : 1.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  172 TYR
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  824 ASP
Chi-restraints excluded: chain A residue  835 VAL
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   98 ASP
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  173 PHE
Chi-restraints excluded: chain H residue  214 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  106 VAL
Chi-restraints excluded: chain L residue  185 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 226
   random chunks:
   chunk 156 optimal weight:    1.9990
   chunk 205 optimal weight:    9.9990
   chunk 138 optimal weight:    1.9990
   chunk 67 optimal weight:    8.9990
   chunk 172 optimal weight:    0.9990
   chunk 149 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0870
   chunk 180 optimal weight:    4.9990
   chunk 198 optimal weight:    0.8980
   chunk 171 optimal weight:    1.9990
   chunk 155 optimal weight:    2.9990
   overall best weight:    1.1964

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1483 GLN
** H 207 HIS ** 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 = 0.3406 r_free = 0.3406 target = 0.049633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.033426 restraints weight = 427348.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 10.33
r_work: 0.2614 rms_B_bonded: 9.50 restraints_weight: 2.0000
r_work: 0.2732 rms_B_bonded: 6.36 restraints_weight: 4.0000
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.2730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  17517  Z= 0.161
  Angle     :  0.685  13.936  23824  Z= 0.342
  Chirality :  0.043   0.189   2680
  Planarity :  0.005   0.078   3172
  Dihedral  :  5.116  59.565   2521
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  : 13.42 %
    Favored  : 86.10 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.46 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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 (0.19), residues: 2278
  helix:  1.95 (0.21), residues: 688
  sheet: -1.10 (0.30), residues: 323
  loop : -2.55 (0.17), residues: 1267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  54 
 HIS   0.006   0.001   HIS B 519 
 PHE   0.009   0.001   PHE A 264 
 TYR   0.019   0.001   TYR A 906 
 ARG   0.010   0.000   ARG C1439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 (  589)
  hydrogen bonds       : angle       4.20886 ( 1650)
  SS BOND              : bond        0.00243 (    4)
  SS BOND              : angle       0.67623 (    8)
  covalent geometry    : bond        0.00364 (17513)
  covalent geometry    : angle       0.68517 (23816)

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

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

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 69
  time to evaluate  : 1.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 MET cc_start: 0.9338 (tpp) cc_final: 0.9050 (ttm)
REVERT: A  791 MET cc_start: 0.8212 (mmm) cc_final: 0.7606 (mmm)
REVERT: B  791 MET cc_start: 0.9095 (ppp) cc_final: 0.7828 (ppp)
REVERT: H  173 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.5142 (t80)
  outliers start: 37
  outliers final: 33
  residues processed: 103
  average time/residue: 0.3359
  time to fit residues: 53.3148
Evaluate side-chains
  101 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 67
  time to evaluate  : 2.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  141 HIS
Chi-restraints excluded: chain A residue  172 TYR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  824 ASP
Chi-restraints excluded: chain A residue  835 VAL
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   98 ASP
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  266 PHE
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   38 TRP
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  173 PHE
Chi-restraints excluded: chain H residue  214 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  106 VAL
Chi-restraints excluded: chain L residue  185 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 226
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 216 optimal weight:    0.7980
   chunk 208 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 169 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0070
   chunk 116 optimal weight:    0.5980
   chunk 100 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.050531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.034066 restraints weight = 525086.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 11.47
r_work: 0.2633 rms_B_bonded: 10.13 restraints_weight: 2.0000
r_work: 0.2751 rms_B_bonded: 6.81 restraints_weight: 4.0000
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  17517  Z= 0.114
  Angle     :  0.671  17.512  23824  Z= 0.331
  Chirality :  0.042   0.177   2680
  Planarity :  0.004   0.077   3172
  Dihedral  :  5.021  59.465   2521
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 13.06 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.75 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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: -1.24 (0.19), residues: 2278
  helix:  1.95 (0.21), residues: 690
  sheet: -1.01 (0.32), residues: 304
  loop : -2.53 (0.17), residues: 1284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  54 
 HIS   0.006   0.001   HIS B 519 
 PHE   0.030   0.001   PHE H 129 
 TYR   0.019   0.001   TYR A 906 
 ARG   0.015   0.000   ARG C1439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03135 (  589)
  hydrogen bonds       : angle       4.09209 ( 1650)
  SS BOND              : bond        0.00227 (    4)
  SS BOND              : angle       0.65117 (    8)
  covalent geometry    : bond        0.00253 (17513)
  covalent geometry    : angle       0.67055 (23816)

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

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

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 69
  time to evaluate  : 1.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 LEU cc_start: 0.9379 (tt) cc_final: 0.8858 (pp)
REVERT: A  599 MET cc_start: 0.9246 (tmm) cc_final: 0.8922 (tmm)
REVERT: A  690 MET cc_start: 0.7432 (mmt) cc_final: 0.7229 (mmp)
REVERT: A  791 MET cc_start: 0.8112 (mmm) cc_final: 0.7490 (mmm)
REVERT: B  791 MET cc_start: 0.9138 (ppp) cc_final: 0.7865 (ppp)
REVERT: C 1444 GLU cc_start: 0.4785 (tp30) cc_final: 0.4435 (tp30)
REVERT: H  173 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5048 (t80)
REVERT: L  110 MET cc_start: 0.9117 (mmm) cc_final: 0.8747 (mmm)
  outliers start: 35
  outliers final: 33
  residues processed: 102
  average time/residue: 0.3291
  time to fit residues: 51.8422
Evaluate side-chains
  103 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 69
  time to evaluate  : 1.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  141 HIS
Chi-restraints excluded: chain A residue  172 TYR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  824 ASP
Chi-restraints excluded: chain A residue  835 VAL
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   98 ASP
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   38 TRP
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  173 PHE
Chi-restraints excluded: chain H residue  214 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  106 VAL
Chi-restraints excluded: chain L residue  185 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 226
   random chunks:
   chunk 214 optimal weight:    3.9990
   chunk 144 optimal weight:    5.9990
   chunk 213 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0980
   chunk 152 optimal weight:    0.5980
   chunk 162 optimal weight:    8.9990
   chunk 220 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0570
   chunk 198 optimal weight:    7.9990
   chunk 207 optimal weight:    0.0770
   overall best weight:    0.3658

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.051228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.034730 restraints weight = 568545.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 12.02
r_work: 0.2657 rms_B_bonded: 10.69 restraints_weight: 2.0000
r_work: 0.2781 rms_B_bonded: 6.96 restraints_weight: 4.0000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  17517  Z= 0.110
  Angle     :  0.657  18.873  23824  Z= 0.322
  Chirality :  0.042   0.187   2680
  Planarity :  0.004   0.074   3172
  Dihedral  :  4.847  59.800   2521
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  : 12.66 %
    Favored  : 86.81 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.92 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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: -1.16 (0.19), residues: 2278
  helix:  2.02 (0.21), residues: 689
  sheet: -0.91 (0.31), residues: 315
  loop : -2.49 (0.17), residues: 1274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 429 
 HIS   0.005   0.001   HIS B 519 
 PHE   0.008   0.001   PHE A 264 
 TYR   0.020   0.001   TYR A 906 
 ARG   0.013   0.000   ARG C1439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02825 (  589)
  hydrogen bonds       : angle       3.99600 ( 1650)
  SS BOND              : bond        0.00234 (    4)
  SS BOND              : angle       0.63846 (    8)
  covalent geometry    : bond        0.00244 (17513)
  covalent geometry    : angle       0.65729 (23816)

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

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

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4556 Ramachandran restraints generated.
    2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 72
  time to evaluate  : 1.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 LEU cc_start: 0.9366 (tt) cc_final: 0.8835 (pp)
REVERT: A  791 MET cc_start: 0.8201 (mmm) cc_final: 0.7183 (mmm)
REVERT: A  898 THR cc_start: 0.6835 (p) cc_final: 0.6536 (p)
REVERT: B  791 MET cc_start: 0.9169 (ppp) cc_final: 0.7885 (ppp)
REVERT: C 1444 GLU cc_start: 0.4693 (tp30) cc_final: 0.4362 (tp30)
REVERT: H  173 PHE cc_start: 0.6066 (OUTLIER) cc_final: 0.4836 (t80)
REVERT: L  110 MET cc_start: 0.9045 (mmm) cc_final: 0.8675 (mmm)
  outliers start: 31
  outliers final: 29
  residues processed: 101
  average time/residue: 0.3262
  time to fit residues: 50.9056
Evaluate side-chains
  98 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 68
  time to evaluate  : 1.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  172 TYR
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  824 ASP
Chi-restraints excluded: chain A residue  835 VAL
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   98 ASP
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  762 VAL
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    7 VAL
Chi-restraints excluded: chain H residue   38 TRP
Chi-restraints excluded: chain H residue   47 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain H residue  158 THR
Chi-restraints excluded: chain H residue  173 PHE
Chi-restraints excluded: chain H residue  214 VAL
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  106 VAL
Chi-restraints excluded: chain L residue  185 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 226
   random chunks:
   chunk 97 optimal weight:    0.0170
   chunk 180 optimal weight:    2.9990
   chunk 198 optimal weight:    5.9990
   chunk 220 optimal weight:    0.0370
   chunk 44 optimal weight:    0.8980
   chunk 175 optimal weight:    0.9990
   chunk 60 optimal weight:    0.1980
   chunk 10 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0370
   chunk 115 optimal weight:    0.4980
   chunk 126 optimal weight:    0.9980
   overall best weight:    0.1574

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 717 ASN
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  52 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.051683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.035333 restraints weight = 479530.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 11.26
r_work: 0.2692 rms_B_bonded: 10.35 restraints_weight: 2.0000
r_work: 0.2814 rms_B_bonded: 6.74 restraints_weight: 4.0000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.2813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  17517  Z= 0.109
  Angle     :  0.668  19.517  23824  Z= 0.327
  Chirality :  0.042   0.226   2680
  Planarity :  0.004   0.073   3172
  Dihedral  :  4.708  59.523   2521
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 12.53 %
    Favored  : 87.03 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.08 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.54 %
    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: -1.12 (0.19), residues: 2278
  helix:  2.13 (0.21), residues: 675
  sheet: -0.97 (0.31), residues: 325
  loop : -2.45 (0.17), residues: 1278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 429 
 HIS   0.005   0.001   HIS B 519 
 PHE   0.008   0.001   PHE A 264 
 TYR   0.020   0.001   TYR A 906 
 ARG   0.013   0.000   ARG C1439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02835 (  589)
  hydrogen bonds       : angle       3.96198 ( 1650)
  SS BOND              : bond        0.00237 (    4)
  SS BOND              : angle       0.63064 (    8)
  covalent geometry    : bond        0.00237 (17513)
  covalent geometry    : angle       0.66813 (23816)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14404.88 seconds
wall clock time: 250 minutes 15.76 seconds (15015.76 seconds total)