Starting phenix.real_space_refine
on Wed Sep 17 15:51:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m7o_62355/09_2025/9m7o_62355.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m7o_62355/09_2025/9m7o_62355.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m7o_62355/09_2025/9m7o_62355.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m7o_62355/09_2025/9m7o_62355.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m7o_62355/09_2025/9m7o_62355.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m7o_62355/09_2025/9m7o_62355.cif"
  }
  resolution = 4.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    5985      2.51       5
     N    1547      2.21       5
     O    1767      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9327
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 1161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1161
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 606
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "E"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 591
          Classifications: {'peptide': 76}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 538
          Classifications: {'peptide': 76}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 6431
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 802, 6414
          Classifications: {'peptide': 802}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 36, 'TRANS': 765}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 54
      Conformer: "B"
        Number of residues, atoms: 802, 6414
          Classifications: {'peptide': 802}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 36, 'TRANS': 765}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 54
          bond proxies already assigned to first conformer: 6534
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU D  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU D  73 " occ=0.45
    residue:
      pdb=" N   ARG D  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG D  74 " occ=0.45
    residue:
      pdb=" N   GLY D  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY D  75 " occ=0.25
    residue:
      pdb=" N   GLY D  76 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY D  76 " occ=0.25
  Time building chain proxies: 3.75, per 1000 atoms: 0.40
  Number of scatterers: 9327
  At special positions: 0
  Unit cell: (102.105, 120.769, 94.4194, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O    1767      8.00
     N    1547      7.00
     C    5985      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 607.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2272

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 6 sheets defined
      61.0% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 17
    Processing helix  chain 'B' and resid 60 through 64
    Processing helix  chain 'B' and resid 99 through 114
    Processing helix  chain 'B' and resid 121 through 129
    Processing helix  chain 'B' and resid 131 through 146
      removed outlier: 3.793A  pdb=" N   TYR B 135 " --> pdb=" O   ASP B 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 35
      removed outlier: 3.573A  pdb=" N   LYS D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 35
    Processing helix  chain 'C' and resid 22 through 29
    Processing helix  chain 'C' and resid 37 through 41
    Processing helix  chain 'C' and resid 55 through 59
      removed outlier: 3.817A  pdb=" N   ASP C  58 " --> pdb=" O   THR C  55 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TYR C  59 " --> pdb=" O   LEU C  56 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 55 through 59'
    Processing helix  chain 'A' and resid 118 through 123
    Processing helix  chain 'A' and resid 123 through 142
      removed outlier: 5.550A  pdb=" N   ASP A 129 " --> pdb=" O   ASN A 125 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   PHE A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   SER A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ILE A 134 " --> pdb=" O   PHE A 130 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ALA A 138 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU A 140 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU A 141 " --> pdb=" O   ARG A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 3.974A  pdb=" N   LEU A 147 " --> pdb=" O   THR A 143 " (cutoff:3.500A)
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 170 through 186
      removed outlier: 3.563A  pdb=" N   TYR A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ASN A 175 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR A 186 " --> pdb=" O   GLU A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 193 through 197
      removed outlier: 3.690A  pdb=" N   LYS A 196 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE A 197 " --> pdb=" O   PHE A 194 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 193 through 197'
    Processing helix  chain 'A' and resid 207 through 211
      removed outlier: 3.957A  pdb=" N   PHE A 211 " --> pdb=" O   PRO A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 222
    Processing helix  chain 'A' and resid 227 through 236
    Processing helix  chain 'A' and resid 242 through 273
      removed outlier: 3.768A  pdb=" N   MET A 248 " --> pdb=" O   GLN A 244 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE A 249 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU A 253 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ALA A 255 " --> pdb=" O   GLU A 251 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   GLU A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 293
      removed outlier: 3.766A  pdb=" N   ARG A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   THR A 280 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ASN A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 298
      removed outlier: 4.027A  pdb=" N   ARG A 297 " --> pdb=" O   HIS A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 323
      removed outlier: 3.599A  pdb=" N   ASN A 314 " --> pdb=" O   GLY A 310 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 328
      removed outlier: 3.550A  pdb=" N   LEU A 327 " --> pdb=" O   GLN A 324 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ASP A 328 " --> pdb=" O   PRO A 325 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 324 through 328'
    Processing helix  chain 'A' and resid 331 through 337
      removed outlier: 3.803A  pdb=" N   ILE A 334 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ASP A 335 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 370
    Processing helix  chain 'A' and resid 380 through 396
      removed outlier: 4.070A  pdb=" N   LEU A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 406
      removed outlier: 3.526A  pdb=" N   SER A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 422
      removed outlier: 4.088A  pdb=" N   LYS A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL A 421 " --> pdb=" O   GLU A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 461
      removed outlier: 3.621A  pdb=" N   ARG A 433 " --> pdb=" O   ASP A 429 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   PHE A 434 " --> pdb=" O   VAL A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 485
      removed outlier: 4.661A  pdb=" N   GLU A 468 " --> pdb=" O   SER A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 525
      removed outlier: 3.626A  pdb=" N   TYR A 525 " --> pdb=" O   VAL A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 542
      Proline residue:  A 534  - end of helix
    Processing helix  chain 'A' and resid 552 through 554
      No H-bonds generated for 'chain 'A' and resid 552 through 554'
    Processing helix  chain 'A' and resid 555 through 568
      removed outlier: 3.795A  pdb=" N   VAL A 559 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 589
      removed outlier: 3.705A  pdb=" N   LYS A 578 " --> pdb=" O   ASN A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 606
    Processing helix  chain 'A' and resid 609 through 625
      removed outlier: 3.840A  pdb=" N   ASN A 613 " --> pdb=" O   LEU A 609 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   LEU A 615 " --> pdb=" O   ASN A 611 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   TYR A 616 " --> pdb=" O   LYS A 612 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL A 623 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE A 624 " --> pdb=" O   ASP A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 655
      removed outlier: 3.935A  pdb=" N   SER A 640 " --> pdb=" O   ASP A 636 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ARG A 641 " --> pdb=" O   LYS A 637 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE A 647 " --> pdb=" O   SER A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 669
      removed outlier: 4.513A  pdb=" N   ILE A 663 " --> pdb=" O   LYS A 659 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   SER A 666 " --> pdb=" O   LEU A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 706
      removed outlier: 3.652A  pdb=" N   ARG A 675 " --> pdb=" O   ASP A 671 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 676 " --> pdb=" O   PHE A 672 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASP A 683 " --> pdb=" O   ARG A 679 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A 684 " --> pdb=" O   MET A 680 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR A 685 " --> pdb=" O   LEU A 681 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   PHE A 686 " --> pdb=" O   ASN A 682 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   LEU A 688 " --> pdb=" O   LEU A 684 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   ASP A 689 " --> pdb=" O   THR A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 755
      removed outlier: 4.091A  pdb=" N   ASP A 754 " --> pdb=" O   ILE A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 759
    Processing helix  chain 'A' and resid 764 through 781
      removed outlier: 3.533A  pdb=" N   SER A 778 " --> pdb=" O   TYR A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 787
      removed outlier: 3.674A  pdb=" N   GLY A 785 " --> pdb=" O   GLY A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 813
      removed outlier: 3.791A  pdb=" N   LYS A 804 " --> pdb=" O   LYS A 800 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ALA A 805 " --> pdb=" O   ASP A 801 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 825
    Processing helix  chain 'A' and resid 831 through 845
      removed outlier: 4.193A  pdb=" N   PHE A 835 " --> pdb=" O   ASN A 831 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL A 836 " --> pdb=" O   ARG A 832 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS A 845 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 877
      removed outlier: 3.592A  pdb=" N   GLU A 877 " --> pdb=" O   GLU A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 882 through 886
    Processing helix  chain 'A' and resid 909 through 917
    Processing helix  chain 'A' and resid 930 through 934
      removed outlier: 3.674A  pdb=" N   VAL A 934 " --> pdb=" O   LEU A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 937 through 953
    Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 27
      removed outlier: 6.111A  pdb=" N   HIS B  33 " --> pdb=" O   VAL B  27 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TRP B  34 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE B  55 " --> pdb=" O   TRP B  34 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA B  36 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 16
      removed outlier: 8.875A  pdb=" N   LEU D  67 " --> pdb=" O   GLN D   2 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   PHE D   4 " --> pdb=" O   LEU D  67 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   LEU D  69 " --> pdb=" O   PHE D   4 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LYS D   6 " --> pdb=" O   LEU D  69 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   LEU D  71 " --> pdb=" O   LYS D   6 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE D  45 " --> pdb=" O   CYS D  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 12 through 16
    Processing sheet with id=AA4, first strand: chain 'C' and resid 12 through 15
      removed outlier: 4.079A  pdb=" N   VAL C   5 " --> pdb=" O   ILE C  13 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LEU C  15 " --> pdb=" O   ILE C   3 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE C   3 " --> pdb=" O   LEU C  15 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 44 through 45
    Processing sheet with id=AA6, first strand: chain 'A' and resid 906 through 908

    481 hydrogen bonds defined for protein.
    1392 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1584
        1.27 -     1.41: 2238
        1.41 -     1.54: 5614
        1.54 -     1.68: 35
        1.68 -     1.81: 46
  Bond restraints: 9517
  Sorted by residual:
  bond pdb=" CG  PRO A 597 "
       pdb=" CD  PRO A 597 "
    ideal  model  delta    sigma   weight residual
    1.503  1.154  0.349 3.40e-02 8.65e+02 1.06e+02
  bond pdb=" CB  PRO A 597 "
       pdb=" CG  PRO A 597 "
    ideal  model  delta    sigma   weight residual
    1.492  1.141  0.351 5.00e-02 4.00e+02 4.94e+01
  bond pdb=" N   PRO A 597 "
       pdb=" CA  PRO A 597 "
    ideal  model  delta    sigma   weight residual
    1.467  1.511 -0.044 1.21e-02 6.83e+03 1.33e+01
  bond pdb=" C   GLN A 324 "
       pdb=" N   PRO A 325 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.020 1.30e-02 5.92e+03 2.43e+00
  bond pdb=" C   PHE A 490 "
       pdb=" N   PRO A 491 "
    ideal  model  delta    sigma   weight residual
    1.337  1.351 -0.015 1.11e-02 8.12e+03 1.76e+00
  ... (remaining 9512 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.33: 12878
        7.33 -    14.67: 3
       14.67 -    22.00: 0
       22.00 -    29.33: 0
       29.33 -    36.67: 3
  Bond angle restraints: 12884
  Sorted by residual:
  angle pdb=" N   PRO A 597 "
        pdb=" CD  PRO A 597 "
        pdb=" CG  PRO A 597 "
      ideal   model   delta    sigma   weight residual
     103.20   73.76   29.44 1.50e+00 4.44e-01 3.85e+02
  angle pdb=" CA  PRO A 597 "
        pdb=" CB  PRO A 597 "
        pdb=" CG  PRO A 597 "
      ideal   model   delta    sigma   weight residual
     104.50   67.83   36.67 1.90e+00 2.77e-01 3.72e+02
  angle pdb=" CB  PRO A 597 "
        pdb=" CG  PRO A 597 "
        pdb=" CD  PRO A 597 "
      ideal   model   delta    sigma   weight residual
     106.10  138.14  -32.04 3.20e+00 9.77e-02 1.00e+02
  angle pdb=" CA  PRO A 597 "
        pdb=" N   PRO A 597 "
        pdb=" CD  PRO A 597 "
      ideal   model   delta    sigma   weight residual
     112.00  101.62   10.38 1.40e+00 5.10e-01 5.50e+01
  angle pdb=" N   PRO A 597 "
        pdb=" CA  PRO A 597 "
        pdb=" CB  PRO A 597 "
      ideal   model   delta    sigma   weight residual
     103.31   99.42    3.89 8.90e-01 1.26e+00 1.91e+01
  ... (remaining 12879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.68: 5509
       15.68 -    31.36: 236
       31.36 -    47.04: 58
       47.04 -    62.72: 7
       62.72 -    78.40: 8
  Dihedral angle restraints: 5818
    sinusoidal: 2338
      harmonic: 3480
  Sorted by residual:
  dihedral pdb=" N   PRO A 597 "
           pdb=" CG  PRO A 597 "
           pdb=" CD  PRO A 597 "
           pdb=" CB  PRO A 597 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00   95.89  -65.89     1      1.50e+01 4.44e-03 2.52e+01
  dihedral pdb=" CA  GLN A 661 "
           pdb=" C   GLN A 661 "
           pdb=" N   LEU A 662 "
           pdb=" CA  LEU A 662 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.47   21.53     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CA  PRO A 597 "
           pdb=" CB  PRO A 597 "
           pdb=" CG  PRO A 597 "
           pdb=" CD  PRO A 597 "
      ideal   model   delta sinusoidal    sigma   weight residual
      38.00  111.31  -73.31     1      2.00e+01 2.50e-03 1.71e+01
  ... (remaining 5815 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 787
       0.025 -    0.050: 399
       0.050 -    0.075: 179
       0.075 -    0.100: 70
       0.100 -    0.125: 35
  Chirality restraints: 1470
  Sorted by residual:
  chirality pdb=" CA  ILE A 337 "
            pdb=" N   ILE A 337 "
            pdb=" C   ILE A 337 "
            pdb=" CB  ILE A 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.93e-01
  chirality pdb=" CA  ILE D  36 "
            pdb=" N   ILE D  36 "
            pdb=" C   ILE D  36 "
            pdb=" CB  ILE D  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  chirality pdb=" CA  VAL D   5 "
            pdb=" N   VAL D   5 "
            pdb=" C   VAL D   5 "
            pdb=" CB  VAL D   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.70e-01
  ... (remaining 1467 not shown)

  Planarity restraints: 1661
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 596 "    0.047 5.00e-02 4.00e+02   6.56e-02 6.88e+00
        pdb=" N   PRO A 597 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 597 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 597 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  94 "   -0.007 2.00e-02 2.50e+03   1.10e-02 3.01e+00
        pdb=" CG  TRP B  94 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  94 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  94 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  94 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  94 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  94 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  94 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  94 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 286 "    0.006 2.00e-02 2.50e+03   9.56e-03 1.60e+00
        pdb=" CG  PHE A 286 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 286 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 286 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 286 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 286 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 286 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1658 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 116
        2.68 -     3.24: 9283
        3.24 -     3.79: 14094
        3.79 -     4.35: 18886
        4.35 -     4.90: 30086
  Nonbonded interactions: 72465
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 174 "
            pdb=" OE2 GLU A 256 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" OE1 GLU A 404 "
            pdb=" OH  TYR A 540 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OH  TYR A 652 "
            pdb=" OD2 ASP A 754 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   ASP D  39 "
            pdb=" NH1 ARG D  42 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   PHE A 286 "
            pdb=" OH  TYR A 392 "
     model   vdw
     2.247 3.040
  ... (remaining 72460 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 'C' and (resid 1 through 28 or resid 30 through 47 or resid 49 through 76 \ 
))
  selection = (chain 'D' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 4 through 14 or (resid 15 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 16 or (resid 17 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 18 through 19 or (resid 20 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 21 through 28 or (resid 30 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 31 through 33 or (r \ 
esid 34 and (name N or name CA or name C or name O or name CB )) or resid 35 or  \ 
(resid 36 and (name N or name CA or name C or name O or name CB )) or resid 37 t \ 
hrough 38 or (resid 39 through 41 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 42 through 47 or resid 49 through 58 or (resid 59 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resid  \ 
63 and (name N or name CA or name C or name O or name CB )) or resid 64 through  \ 
66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 68 through 70 or (resid 71 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 72 or (resid 73 through 74 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 75 through 76))
  selection = (chain 'E' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 4 through 14 or (resid 15 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 16 or (resid 17 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 18 through 19 or (resid 20 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 21 through 28 or (resid 30 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 31 through 33 or (r \ 
esid 34 and (name N or name CA or name C or name O or name CB )) or resid 35 or  \ 
(resid 36 and (name N or name CA or name C or name O or name CB )) or resid 37 t \ 
hrough 38 or (resid 39 through 41 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 42 through 47 or resid 49 through 58 or (resid 59 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resid  \ 
63 and (name N or name CA or name C or name O or name CB )) or resid 64 through  \ 
66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 68 through 70 or (resid 71 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 72 or (resid 73 through 74 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 75 through 76))
}

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=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.550
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6146
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      :  0.006   0.351   9517  Z= 0.185
  Angle     :  0.769  36.668  12884  Z= 0.424
  Chirality :  0.040   0.125   1470
  Planarity :  0.004   0.066   1661
  Dihedral  : 10.260  78.404   3546
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.25), residues: 1161
  helix:  1.08 (0.21), residues: 619
  sheet: -1.15 (0.51), residues: 99
  loop : -0.30 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 463 
 TYR   0.013   0.001   TYR D  59 
 PHE   0.021   0.001   PHE A 286 
 TRP   0.029   0.004   TRP B  94 
 HIS   0.005   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 9517)
  covalent geometry    : angle       0.76860 (12884)
  hydrogen bonds       : bond        0.20867 (  481)
  hydrogen bonds       : angle       6.29347 ( 1392)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  413 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 413
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 ASP cc_start: 0.7290 (p0) cc_final: 0.7005 (t0)
REVERT: B   61 TYR cc_start: 0.7883 (t80) cc_final: 0.7400 (t80)
REVERT: B  117 ASP cc_start: 0.7598 (m-30) cc_final: 0.7362 (p0)
REVERT: D    8 LEU cc_start: 0.6977 (mt) cc_final: 0.6732 (mt)
REVERT: D   13 ILE cc_start: 0.7835 (pt) cc_final: 0.7602 (mt)
REVERT: D   17 VAL cc_start: 0.7178 (m) cc_final: 0.6955 (p)
REVERT: D   39 ASP cc_start: 0.6110 (p0) cc_final: 0.5498 (p0)
REVERT: E   26 VAL cc_start: 0.9564 (t) cc_final: 0.9216 (t)
REVERT: E   39 ASP cc_start: 0.8438 (p0) cc_final: 0.7693 (p0)
REVERT: E   43 LEU cc_start: 0.8235 (mt) cc_final: 0.8021 (mt)
REVERT: E   48 LYS cc_start: 0.8083 (mtmm) cc_final: 0.7827 (mmtt)
REVERT: E   49 GLN cc_start: 0.4791 (tt0) cc_final: 0.3990 (pm20)
REVERT: A  190 ILE cc_start: 0.8728 (mm) cc_final: 0.8467 (tt)
REVERT: A  355 THR cc_start: 0.7446 (m) cc_final: 0.6424 (p)
REVERT: A  401 LEU cc_start: 0.7977 (pp) cc_final: 0.7700 (pp)
REVERT: A  441 LYS cc_start: 0.7024 (ttpp) cc_final: 0.6739 (ptmt)
REVERT: A  454 PHE cc_start: 0.6746 (m-10) cc_final: 0.6094 (m-10)
REVERT: A  459 PHE cc_start: 0.7939 (t80) cc_final: 0.7670 (t80)
REVERT: A  468 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7796 (mp0)
REVERT: A  479 PHE cc_start: 0.8171 (t80) cc_final: 0.7914 (t80)
REVERT: A  526 TYR cc_start: 0.7528 (m-10) cc_final: 0.7252 (m-80)
REVERT: A  541 ILE cc_start: 0.8157 (tp) cc_final: 0.7586 (mm)
REVERT: A  583 GLN cc_start: 0.7451 (tt0) cc_final: 0.6968 (mt0)
REVERT: A  612 LYS cc_start: 0.8448 (mttm) cc_final: 0.8243 (mmtm)
REVERT: A  620 ASP cc_start: 0.8418 (t0) cc_final: 0.7913 (t70)
REVERT: A  695 LEU cc_start: 0.6908 (mt) cc_final: 0.6683 (mp)
REVERT: A  732 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7363 (mtp85)
REVERT: A  745 MET cc_start: 0.8314 (mmt) cc_final: 0.8056 (mtt)
REVERT: A  793 GLN cc_start: 0.5058 (mm-40) cc_final: 0.4767 (mp10)
REVERT: A  802 LEU cc_start: 0.8418 (tp) cc_final: 0.8088 (tt)
REVERT: A  916 LEU cc_start: 0.8149 (mt) cc_final: 0.7859 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 413
  average time/residue: 0.1302
  time to fit residues: 70.3673
Evaluate side-chains
  199 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0000
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    1.1790

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

Flipped N/Q/H residues before XYZ refinement:
D  41 GLN
D  49 GLN
A 162 HIS
A 176 ASN
A 257 HIS
A 371 ASN
A 394 HIS
A 494 GLN
A 665 GLN
A 694 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.092392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.065616 restraints weight = 75989.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.068494 restraints weight = 40220.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.070438 restraints weight = 26600.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.071759 restraints weight = 20116.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.072688 restraints weight = 16561.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3446
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9517  Z= 0.163
  Angle     :  0.701  13.088  12884  Z= 0.355
  Chirality :  0.044   0.175   1470
  Planarity :  0.005   0.067   1661
  Dihedral  :  4.010  24.104   1254
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.05 %
    Favored  : 97.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.25), residues: 1161
  helix:  1.08 (0.21), residues: 630
  sheet: -0.92 (0.54), residues: 88
  loop : -0.15 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 909 
 TYR   0.034   0.002   TYR A 653 
 PHE   0.023   0.002   PHE A 311 
 TRP   0.031   0.004   TRP B 142 
 HIS   0.010   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9517)
  covalent geometry    : angle       0.70130 (12884)
  hydrogen bonds       : bond        0.05351 (  481)
  hydrogen bonds       : angle       5.05316 ( 1392)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 265
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.0569 (ttp) cc_final: 0.0193 (ttp)
REVERT: B   38 ILE cc_start: 0.8937 (pt) cc_final: 0.8510 (mm)
REVERT: B   51 PHE cc_start: 0.7448 (m-80) cc_final: 0.6984 (m-10)
REVERT: B   57 PHE cc_start: 0.6437 (m-80) cc_final: 0.5600 (m-10)
REVERT: B   61 TYR cc_start: 0.8385 (t80) cc_final: 0.7882 (t80)
REVERT: B   75 TYR cc_start: 0.7116 (t80) cc_final: 0.6852 (t80)
REVERT: B  117 ASP cc_start: 0.8108 (m-30) cc_final: 0.7750 (p0)
REVERT: B  142 TRP cc_start: 0.7394 (m-10) cc_final: 0.6830 (m-10)
REVERT: D   39 ASP cc_start: 0.7467 (p0) cc_final: 0.7253 (p0)
REVERT: E    1 MET cc_start: 0.7727 (mmp) cc_final: 0.7294 (mmp)
REVERT: E    3 ILE cc_start: 0.7570 (tt) cc_final: 0.7285 (mm)
REVERT: E   25 ASN cc_start: 0.9216 (t0) cc_final: 0.8950 (t0)
REVERT: E   26 VAL cc_start: 0.9338 (t) cc_final: 0.8996 (t)
REVERT: E   48 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7883 (mmtt)
REVERT: C   56 LEU cc_start: 0.4431 (tp) cc_final: 0.4033 (mt)
REVERT: A  293 ASN cc_start: 0.6927 (m-40) cc_final: 0.6542 (m110)
REVERT: A  354 GLU cc_start: 0.7387 (tp30) cc_final: 0.7118 (tp30)
REVERT: A  442 MET cc_start: 0.8534 (mpp) cc_final: 0.8236 (mpp)
REVERT: A  456 LEU cc_start: 0.8786 (mm) cc_final: 0.8583 (mm)
REVERT: A  459 PHE cc_start: 0.8260 (t80) cc_final: 0.8001 (t80)
REVERT: A  524 LYS cc_start: 0.8127 (ptmt) cc_final: 0.7845 (ptpp)
REVERT: A  557 SER cc_start: 0.8496 (m) cc_final: 0.8132 (p)
REVERT: A  564 MET cc_start: 0.7553 (mmt) cc_final: 0.7221 (mmm)
REVERT: A  583 GLN cc_start: 0.7590 (tt0) cc_final: 0.7146 (mt0)
REVERT: A  613 ASN cc_start: 0.8078 (m-40) cc_final: 0.7562 (m-40)
REVERT: A  620 ASP cc_start: 0.8553 (t0) cc_final: 0.8152 (t70)
REVERT: A  732 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7479 (mtp85)
REVERT: A  745 MET cc_start: 0.8518 (mmt) cc_final: 0.8315 (mtt)
REVERT: A  749 GLU cc_start: 0.8420 (tt0) cc_final: 0.8187 (tt0)
REVERT: A  793 GLN cc_start: 0.5369 (mm-40) cc_final: 0.4832 (mp10)
REVERT: A  889 LEU cc_start: 0.7294 (mt) cc_final: 0.7057 (tp)
REVERT: A  916 LEU cc_start: 0.8702 (mt) cc_final: 0.8413 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 266
  average time/residue: 0.0958
  time to fit residues: 36.3271
Evaluate side-chains
  175 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 28 optimal weight:   30.0000
   chunk 89 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 114 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 49 optimal weight:    9.9990
   chunk 47 optimal weight:   10.0000
   chunk 26 optimal weight:    0.1980
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 HIS
A 371 ASN
A 915 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.091640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.064354 restraints weight = 73040.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.067184 restraints weight = 39191.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.069052 restraints weight = 25978.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.070331 restraints weight = 19635.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.071216 restraints weight = 16168.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3413
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3413
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.4770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9517  Z= 0.149
  Angle     :  0.635   9.123  12884  Z= 0.320
  Chirality :  0.045   0.228   1470
  Planarity :  0.004   0.041   1661
  Dihedral  :  4.054  24.320   1254
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.24), residues: 1161
  helix:  1.14 (0.21), residues: 628
  sheet: -0.80 (0.57), residues: 80
  loop : -0.12 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  72 
 TYR   0.013   0.002   TYR A 174 
 PHE   0.019   0.002   PHE A 311 
 TRP   0.013   0.002   TRP B 142 
 HIS   0.012   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9517)
  covalent geometry    : angle       0.63464 (12884)
  hydrogen bonds       : bond        0.04585 (  481)
  hydrogen bonds       : angle       4.66347 ( 1392)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.392 
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: B   51 PHE cc_start: 0.7472 (m-80) cc_final: 0.7267 (m-80)
REVERT: B  117 ASP cc_start: 0.8162 (m-30) cc_final: 0.7669 (p0)
REVERT: B  127 ILE cc_start: 0.8482 (mm) cc_final: 0.8086 (tp)
REVERT: B  142 TRP cc_start: 0.7342 (m-10) cc_final: 0.7004 (m-10)
REVERT: D   39 ASP cc_start: 0.7497 (p0) cc_final: 0.7078 (p0)
REVERT: E    3 ILE cc_start: 0.7786 (tt) cc_final: 0.7392 (tp)
REVERT: E    6 LYS cc_start: 0.7358 (ttmt) cc_final: 0.6944 (tptm)
REVERT: E   43 LEU cc_start: 0.8284 (mt) cc_final: 0.7983 (mt)
REVERT: E   48 LYS cc_start: 0.8170 (mtmm) cc_final: 0.7841 (mmtt)
REVERT: C   56 LEU cc_start: 0.4898 (tp) cc_final: 0.4528 (mt)
REVERT: A  312 MET cc_start: 0.7593 (tmm) cc_final: 0.7325 (tmm)
REVERT: A  355 THR cc_start: 0.7608 (p) cc_final: 0.7349 (p)
REVERT: A  401 LEU cc_start: 0.7715 (pp) cc_final: 0.7477 (pp)
REVERT: A  442 MET cc_start: 0.8506 (mpp) cc_final: 0.8295 (mmt)
REVERT: A  456 LEU cc_start: 0.8955 (mm) cc_final: 0.8734 (mm)
REVERT: A  459 PHE cc_start: 0.8298 (t80) cc_final: 0.8057 (t80)
REVERT: A  524 LYS cc_start: 0.8229 (ptmt) cc_final: 0.7753 (ptmt)
REVERT: A  557 SER cc_start: 0.8562 (m) cc_final: 0.8166 (p)
REVERT: A  583 GLN cc_start: 0.7587 (tt0) cc_final: 0.7127 (mt0)
REVERT: A  620 ASP cc_start: 0.8596 (t0) cc_final: 0.8176 (t70)
REVERT: A  732 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7459 (mtp85)
REVERT: A  749 GLU cc_start: 0.8375 (tt0) cc_final: 0.8140 (tt0)
REVERT: A  793 GLN cc_start: 0.5515 (mm-40) cc_final: 0.4856 (mp10)
REVERT: A  808 THR cc_start: 0.8894 (m) cc_final: 0.8612 (m)
REVERT: A  916 LEU cc_start: 0.8565 (mt) cc_final: 0.8318 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.0983
  time to fit residues: 33.2647
Evaluate side-chains
  167 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0030
   chunk 2 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 78 optimal weight:    3.9990
   chunk 42 optimal weight:    0.3980
   chunk 41 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9980
   overall best weight:    2.0794

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

Flipped N/Q/H residues before XYZ refinement:
B 126 HIS
D  40 GLN
A 371 ASN
A 915 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.089483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.062081 restraints weight = 87930.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.064981 restraints weight = 43360.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.066925 restraints weight = 27963.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.068226 restraints weight = 20805.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.069110 restraints weight = 17005.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3366
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3365 r_free = 0.3365    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3365
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.5312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9517  Z= 0.147
  Angle     :  0.621   8.758  12884  Z= 0.313
  Chirality :  0.044   0.201   1470
  Planarity :  0.004   0.041   1661
  Dihedral  :  4.101  26.097   1254
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.24), residues: 1161
  helix:  1.31 (0.21), residues: 620
  sheet: -0.53 (0.59), residues: 80
  loop : -0.11 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  54 
 TYR   0.014   0.002   TYR A 642 
 PHE   0.022   0.002   PHE A 265 
 TRP   0.024   0.003   TRP B  94 
 HIS   0.011   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9517)
  covalent geometry    : angle       0.62079 (12884)
  hydrogen bonds       : bond        0.04218 (  481)
  hydrogen bonds       : angle       4.49930 ( 1392)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.410 
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: B   75 TYR cc_start: 0.7173 (t80) cc_final: 0.6949 (t80)
REVERT: B  117 ASP cc_start: 0.8038 (m-30) cc_final: 0.7669 (p0)
REVERT: B  127 ILE cc_start: 0.8408 (mm) cc_final: 0.7961 (tp)
REVERT: B  135 TYR cc_start: 0.7573 (t80) cc_final: 0.7188 (t80)
REVERT: B  142 TRP cc_start: 0.7417 (m-10) cc_final: 0.6907 (m-10)
REVERT: E    6 LYS cc_start: 0.7265 (ttmt) cc_final: 0.6897 (tptt)
REVERT: E   25 ASN cc_start: 0.9235 (t0) cc_final: 0.8999 (t0)
REVERT: E   48 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7854 (mmtt)
REVERT: A  214 LYS cc_start: 0.7956 (mttm) cc_final: 0.7749 (mmtp)
REVERT: A  312 MET cc_start: 0.7625 (tmm) cc_final: 0.7422 (tmm)
REVERT: A  323 SER cc_start: 0.8712 (p) cc_final: 0.8374 (p)
REVERT: A  401 LEU cc_start: 0.7702 (pp) cc_final: 0.7450 (pp)
REVERT: A  456 LEU cc_start: 0.8968 (mm) cc_final: 0.8702 (mm)
REVERT: A  459 PHE cc_start: 0.8333 (t80) cc_final: 0.8031 (t80)
REVERT: A  524 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7921 (ptmm)
REVERT: A  557 SER cc_start: 0.8677 (m) cc_final: 0.8279 (p)
REVERT: A  583 GLN cc_start: 0.7635 (tt0) cc_final: 0.6987 (mt0)
REVERT: A  620 ASP cc_start: 0.8639 (t0) cc_final: 0.8257 (t70)
REVERT: A  640 SER cc_start: 0.8029 (m) cc_final: 0.7505 (p)
REVERT: A  732 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7433 (mtp85)
REVERT: A  745 MET cc_start: 0.8431 (mtm) cc_final: 0.8061 (mtm)
REVERT: A  749 GLU cc_start: 0.8246 (tt0) cc_final: 0.7864 (tt0)
REVERT: A  808 THR cc_start: 0.8845 (m) cc_final: 0.8504 (m)
REVERT: A  916 LEU cc_start: 0.8561 (mt) cc_final: 0.8284 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0947
  time to fit residues: 29.6755
Evaluate side-chains
  151 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9980
   chunk 68 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 98 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    3.5786

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

Flipped N/Q/H residues before XYZ refinement:
** E   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 GLN
A 254 GLN
A 344 ASN
A 915 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.086912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.060789 restraints weight = 67272.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.063187 restraints weight = 37024.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.064826 restraints weight = 25389.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.065906 restraints weight = 19735.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.066712 restraints weight = 16680.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.6078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086   9517  Z= 0.201
  Angle     :  0.717  11.571  12884  Z= 0.365
  Chirality :  0.047   0.227   1470
  Planarity :  0.005   0.033   1661
  Dihedral  :  4.525  26.544   1254
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.24), residues: 1161
  helix:  1.05 (0.20), residues: 614
  sheet: -0.64 (0.57), residues: 81
  loop : -0.22 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 868 
 TYR   0.022   0.002   TYR A 642 
 PHE   0.032   0.002   PHE A 748 
 TRP   0.016   0.002   TRP B  94 
 HIS   0.009   0.002   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 9517)
  covalent geometry    : angle       0.71706 (12884)
  hydrogen bonds       : bond        0.04509 (  481)
  hydrogen bonds       : angle       4.71548 ( 1392)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  100 LEU cc_start: 0.9024 (tp) cc_final: 0.8802 (tp)
REVERT: B  127 ILE cc_start: 0.8275 (mm) cc_final: 0.7868 (tp)
REVERT: B  135 TYR cc_start: 0.7630 (t80) cc_final: 0.7231 (t80)
REVERT: B  138 THR cc_start: 0.8679 (m) cc_final: 0.8416 (m)
REVERT: D   24 GLU cc_start: 0.7770 (tp30) cc_final: 0.7275 (tp30)
REVERT: D   51 GLU cc_start: 0.5897 (pm20) cc_final: 0.5485 (pm20)
REVERT: D   54 ARG cc_start: 0.7171 (mmm-85) cc_final: 0.6772 (mmm-85)
REVERT: D   64 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6887 (mm-30)
REVERT: E    6 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6941 (tptt)
REVERT: E   25 ASN cc_start: 0.9221 (t0) cc_final: 0.9017 (t0)
REVERT: E   43 LEU cc_start: 0.8212 (mt) cc_final: 0.8000 (mt)
REVERT: E   48 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7809 (mmtt)
REVERT: A  187 PHE cc_start: 0.8202 (m-80) cc_final: 0.7914 (m-80)
REVERT: A  211 PHE cc_start: 0.7694 (m-80) cc_final: 0.6795 (m-80)
REVERT: A  214 LYS cc_start: 0.8239 (mttm) cc_final: 0.7931 (mmtp)
REVERT: A  281 ASP cc_start: 0.8036 (m-30) cc_final: 0.7825 (m-30)
REVERT: A  456 LEU cc_start: 0.8976 (mm) cc_final: 0.8689 (mm)
REVERT: A  459 PHE cc_start: 0.8355 (t80) cc_final: 0.8071 (t80)
REVERT: A  524 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7806 (ptpp)
REVERT: A  557 SER cc_start: 0.8931 (m) cc_final: 0.8375 (p)
REVERT: A  600 MET cc_start: 0.8035 (mmt) cc_final: 0.7821 (mmt)
REVERT: A  620 ASP cc_start: 0.8621 (t0) cc_final: 0.8256 (t70)
REVERT: A  732 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7447 (mtp85)
REVERT: A  745 MET cc_start: 0.8327 (mtm) cc_final: 0.8084 (mtm)
REVERT: A  749 GLU cc_start: 0.8408 (tt0) cc_final: 0.7776 (tt0)
REVERT: A  808 THR cc_start: 0.8870 (m) cc_final: 0.8503 (m)
REVERT: A  916 LEU cc_start: 0.8660 (mt) cc_final: 0.8304 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0965
  time to fit residues: 28.7438
Evaluate side-chains
  145 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 104 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 98 optimal weight:    7.9990
   chunk 108 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 126 HIS
** E   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
A 457 GLN
A 793 GLN
A 812 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.084490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.059228 restraints weight = 56209.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.061389 restraints weight = 33922.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.062764 restraints weight = 23821.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.063713 restraints weight = 18953.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.064354 restraints weight = 16365.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.6725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.090   9517  Z= 0.274
  Angle     :  0.823   9.157  12884  Z= 0.420
  Chirality :  0.050   0.215   1470
  Planarity :  0.006   0.073   1661
  Dihedral  :  5.137  27.212   1254
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.13 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.23), residues: 1161
  helix:  0.42 (0.20), residues: 614
  sheet: -0.85 (0.64), residues: 57
  loop : -0.49 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 868 
 TYR   0.026   0.003   TYR A 642 
 PHE   0.034   0.003   PHE A 748 
 TRP   0.044   0.006   TRP B 142 
 HIS   0.011   0.002   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 9517)
  covalent geometry    : angle       0.82282 (12884)
  hydrogen bonds       : bond        0.04988 (  481)
  hydrogen bonds       : angle       5.10733 ( 1392)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   39 MET cc_start: 0.8161 (mpp) cc_final: 0.7924 (mpp)
REVERT: B  100 LEU cc_start: 0.9165 (tp) cc_final: 0.8919 (tp)
REVERT: B  117 ASP cc_start: 0.7967 (m-30) cc_final: 0.7590 (p0)
REVERT: B  127 ILE cc_start: 0.8272 (mm) cc_final: 0.7847 (tp)
REVERT: B  138 THR cc_start: 0.8575 (m) cc_final: 0.8323 (m)
REVERT: B  142 TRP cc_start: 0.7416 (m-10) cc_final: 0.6944 (m-10)
REVERT: D   24 GLU cc_start: 0.7528 (tp30) cc_final: 0.7129 (tp30)
REVERT: D   33 LYS cc_start: 0.6259 (ptmt) cc_final: 0.5993 (ptmm)
REVERT: D   64 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6757 (mt-10)
REVERT: D   69 LEU cc_start: 0.8549 (tp) cc_final: 0.8291 (tp)
REVERT: D   72 ARG cc_start: 0.5236 (ptm160) cc_final: 0.4852 (ptp-110)
REVERT: E    4 PHE cc_start: 0.6829 (m-80) cc_final: 0.6500 (m-80)
REVERT: E    6 LYS cc_start: 0.7346 (ttmt) cc_final: 0.6859 (tptm)
REVERT: E   43 LEU cc_start: 0.8321 (mt) cc_final: 0.8103 (mt)
REVERT: E   48 LYS cc_start: 0.8175 (mtmm) cc_final: 0.7828 (mmtt)
REVERT: C   68 HIS cc_start: 0.6918 (m90) cc_final: 0.6586 (m90)
REVERT: A  187 PHE cc_start: 0.8288 (m-80) cc_final: 0.7867 (m-80)
REVERT: A  211 PHE cc_start: 0.7767 (m-80) cc_final: 0.6834 (m-80)
REVERT: A  214 LYS cc_start: 0.8284 (mttm) cc_final: 0.8000 (mmtp)
REVERT: A  251 GLU cc_start: 0.8485 (mp0) cc_final: 0.7842 (tt0)
REVERT: A  312 MET cc_start: 0.7763 (tmm) cc_final: 0.7377 (tmm)
REVERT: A  456 LEU cc_start: 0.8875 (mm) cc_final: 0.8603 (mm)
REVERT: A  459 PHE cc_start: 0.8448 (t80) cc_final: 0.8144 (t80)
REVERT: A  524 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7989 (ptpp)
REVERT: A  557 SER cc_start: 0.8935 (m) cc_final: 0.8323 (p)
REVERT: A  620 ASP cc_start: 0.8722 (t0) cc_final: 0.8416 (t70)
REVERT: A  732 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7420 (mtp85)
REVERT: A  745 MET cc_start: 0.8409 (mtm) cc_final: 0.8186 (mtm)
REVERT: A  749 GLU cc_start: 0.8273 (tt0) cc_final: 0.8000 (tt0)
REVERT: A  916 LEU cc_start: 0.8992 (mt) cc_final: 0.8433 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0936
  time to fit residues: 24.8853
Evaluate side-chains
  138 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 113 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   chunk 102 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** E   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  25 ASN
E  60 ASN
A 699 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.084954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.057865 restraints weight = 95169.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.060616 restraints weight = 44655.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.062454 restraints weight = 28569.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.063658 restraints weight = 21366.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.064501 restraints weight = 17649.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3262
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3262
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.7092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   9517  Z= 0.206
  Angle     :  0.723  11.125  12884  Z= 0.367
  Chirality :  0.048   0.194   1470
  Planarity :  0.005   0.050   1661
  Dihedral  :  5.008  26.994   1254
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.13 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.37 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.24), residues: 1161
  helix:  0.58 (0.20), residues: 614
  sheet: -1.12 (0.58), residues: 68
  loop : -0.53 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 868 
 TYR   0.022   0.002   TYR A 174 
 PHE   0.018   0.002   PHE A 853 
 TRP   0.030   0.003   TRP B 142 
 HIS   0.010   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 9517)
  covalent geometry    : angle       0.72319 (12884)
  hydrogen bonds       : bond        0.04501 (  481)
  hydrogen bonds       : angle       4.98488 ( 1392)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   39 MET cc_start: 0.8198 (mpp) cc_final: 0.7940 (mpp)
REVERT: B  100 LEU cc_start: 0.9157 (tp) cc_final: 0.8893 (tp)
REVERT: B  117 ASP cc_start: 0.7910 (m-30) cc_final: 0.7577 (p0)
REVERT: B  138 THR cc_start: 0.8692 (m) cc_final: 0.8467 (m)
REVERT: B  142 TRP cc_start: 0.7557 (m-10) cc_final: 0.7349 (m-10)
REVERT: D   24 GLU cc_start: 0.7600 (tp30) cc_final: 0.7239 (tp30)
REVERT: D   33 LYS cc_start: 0.6318 (ptmt) cc_final: 0.6097 (ptmm)
REVERT: D   64 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6722 (mt-10)
REVERT: D   72 ARG cc_start: 0.5487 (ptm160) cc_final: 0.5012 (ptp-110)
REVERT: E    4 PHE cc_start: 0.6848 (m-80) cc_final: 0.6582 (m-80)
REVERT: E    6 LYS cc_start: 0.7352 (ttmt) cc_final: 0.6891 (tptm)
REVERT: E   43 LEU cc_start: 0.8441 (mt) cc_final: 0.8174 (mt)
REVERT: C   68 HIS cc_start: 0.6860 (m90) cc_final: 0.6470 (m90)
REVERT: A  187 PHE cc_start: 0.8241 (m-80) cc_final: 0.7831 (m-80)
REVERT: A  211 PHE cc_start: 0.7759 (m-80) cc_final: 0.6820 (m-80)
REVERT: A  214 LYS cc_start: 0.8255 (mttm) cc_final: 0.7981 (mmtp)
REVERT: A  459 PHE cc_start: 0.8309 (t80) cc_final: 0.7934 (t80)
REVERT: A  525 TYR cc_start: 0.8629 (m-80) cc_final: 0.7869 (m-10)
REVERT: A  557 SER cc_start: 0.8830 (m) cc_final: 0.8268 (p)
REVERT: A  583 GLN cc_start: 0.8013 (tt0) cc_final: 0.7187 (mt0)
REVERT: A  620 ASP cc_start: 0.8695 (t0) cc_final: 0.8446 (t70)
REVERT: A  732 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7467 (mtp85)
REVERT: A  745 MET cc_start: 0.8409 (mtm) cc_final: 0.8177 (mtm)
REVERT: A  749 GLU cc_start: 0.8272 (tt0) cc_final: 0.7943 (tt0)
REVERT: A  808 THR cc_start: 0.8901 (m) cc_final: 0.8647 (m)
REVERT: A  916 LEU cc_start: 0.8880 (mt) cc_final: 0.8374 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0974
  time to fit residues: 24.4948
Evaluate side-chains
  142 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9990
   chunk 11 optimal weight:    9.9990
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:   20.0000
   chunk 36 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0170
   chunk 99 optimal weight:    0.1980
   overall best weight:    0.6020

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

Flipped N/Q/H residues before XYZ refinement:
** E   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  25 ASN
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.087030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.061926 restraints weight = 53297.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.064043 restraints weight = 31685.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.065480 restraints weight = 22603.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.066462 restraints weight = 18019.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.067089 restraints weight = 15474.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3319
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3319
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.7037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9517  Z= 0.128
  Angle     :  0.649   8.941  12884  Z= 0.328
  Chirality :  0.045   0.189   1470
  Planarity :  0.004   0.040   1661
  Dihedral  :  4.552  24.949   1254
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.17 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.24), residues: 1161
  helix:  0.95 (0.20), residues: 616
  sheet: -0.98 (0.57), residues: 69
  loop : -0.42 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 233 
 TYR   0.013   0.001   TYR A 392 
 PHE   0.031   0.002   PHE A 748 
 TRP   0.031   0.002   TRP B 142 
 HIS   0.009   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9517)
  covalent geometry    : angle       0.64944 (12884)
  hydrogen bonds       : bond        0.03988 (  481)
  hydrogen bonds       : angle       4.68934 ( 1392)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.630 
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: B   39 MET cc_start: 0.8215 (mpp) cc_final: 0.7906 (mpp)
REVERT: B   75 TYR cc_start: 0.7088 (t80) cc_final: 0.6690 (t80)
REVERT: B  100 LEU cc_start: 0.9109 (tp) cc_final: 0.8848 (tp)
REVERT: B  117 ASP cc_start: 0.8023 (m-30) cc_final: 0.7625 (p0)
REVERT: B  127 ILE cc_start: 0.8318 (mm) cc_final: 0.7896 (tp)
REVERT: B  142 TRP cc_start: 0.7392 (m-10) cc_final: 0.6785 (m-10)
REVERT: D    1 MET cc_start: 0.6081 (ttt) cc_final: 0.4981 (tmm)
REVERT: D   24 GLU cc_start: 0.7577 (tp30) cc_final: 0.7158 (tp30)
REVERT: D   33 LYS cc_start: 0.6114 (ptmt) cc_final: 0.5868 (ptmm)
REVERT: D   72 ARG cc_start: 0.5600 (ptm160) cc_final: 0.5093 (ptp-110)
REVERT: E    4 PHE cc_start: 0.6965 (m-80) cc_final: 0.6685 (m-80)
REVERT: E    6 LYS cc_start: 0.7331 (ttmt) cc_final: 0.6966 (tptp)
REVERT: E    8 LEU cc_start: 0.8320 (tp) cc_final: 0.7848 (pt)
REVERT: E   43 LEU cc_start: 0.8274 (mt) cc_final: 0.8061 (mt)
REVERT: C   58 ASP cc_start: 0.4687 (m-30) cc_final: 0.3359 (p0)
REVERT: C   68 HIS cc_start: 0.6767 (m90) cc_final: 0.6345 (m90)
REVERT: A  187 PHE cc_start: 0.8201 (m-80) cc_final: 0.7756 (m-80)
REVERT: A  214 LYS cc_start: 0.8108 (mttm) cc_final: 0.7883 (mmtp)
REVERT: A  251 GLU cc_start: 0.8472 (mp0) cc_final: 0.7730 (tt0)
REVERT: A  312 MET cc_start: 0.7702 (tmm) cc_final: 0.7292 (tmm)
REVERT: A  459 PHE cc_start: 0.8382 (t80) cc_final: 0.7832 (t80)
REVERT: A  525 TYR cc_start: 0.8545 (m-80) cc_final: 0.7838 (m-10)
REVERT: A  557 SER cc_start: 0.8864 (m) cc_final: 0.8349 (p)
REVERT: A  583 GLN cc_start: 0.7829 (tt0) cc_final: 0.7045 (mt0)
REVERT: A  620 ASP cc_start: 0.8646 (t0) cc_final: 0.8331 (t70)
REVERT: A  732 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7391 (mtp85)
REVERT: A  745 MET cc_start: 0.8332 (mtm) cc_final: 0.8033 (mtm)
REVERT: A  749 GLU cc_start: 0.8225 (tt0) cc_final: 0.7888 (tt0)
REVERT: A  808 THR cc_start: 0.8785 (m) cc_final: 0.8507 (m)
REVERT: A  916 LEU cc_start: 0.8907 (mt) cc_final: 0.8291 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0973
  time to fit residues: 28.0578
Evaluate side-chains
  151 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0670
   chunk 89 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 111 optimal weight:    0.8980
   overall best weight:    0.7918

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

Flipped N/Q/H residues before XYZ refinement:
** E   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  25 ASN
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 ASN
A 457 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.087545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.061389 restraints weight = 74562.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.065095 restraints weight = 39160.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.066531 restraints weight = 21422.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.066960 restraints weight = 16950.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.067027 restraints weight = 15719.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.7105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9517  Z= 0.127
  Angle     :  0.651  10.328  12884  Z= 0.322
  Chirality :  0.045   0.217   1470
  Planarity :  0.004   0.038   1661
  Dihedral  :  4.373  25.943   1254
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.01 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.49 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.24), residues: 1161
  helix:  1.14 (0.21), residues: 615
  sheet: -0.72 (0.60), residues: 69
  loop : -0.32 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 233 
 TYR   0.018   0.002   TYR D  59 
 PHE   0.017   0.001   PHE A 311 
 TRP   0.027   0.002   TRP B 142 
 HIS   0.011   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9517)
  covalent geometry    : angle       0.65067 (12884)
  hydrogen bonds       : bond        0.03848 (  481)
  hydrogen bonds       : angle       4.61348 ( 1392)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   39 MET cc_start: 0.8284 (mpp) cc_final: 0.7950 (mpp)
REVERT: B   75 TYR cc_start: 0.7380 (t80) cc_final: 0.7053 (t80)
REVERT: B  100 LEU cc_start: 0.9045 (tp) cc_final: 0.8796 (tp)
REVERT: B  117 ASP cc_start: 0.8052 (m-30) cc_final: 0.7667 (p0)
REVERT: B  127 ILE cc_start: 0.8243 (mm) cc_final: 0.7822 (tp)
REVERT: B  142 TRP cc_start: 0.7484 (m-10) cc_final: 0.7066 (m-10)
REVERT: D   24 GLU cc_start: 0.7484 (tp30) cc_final: 0.7117 (tp30)
REVERT: D   72 ARG cc_start: 0.5456 (ptm160) cc_final: 0.4945 (ptp-110)
REVERT: E    4 PHE cc_start: 0.6916 (m-80) cc_final: 0.6662 (m-80)
REVERT: E    6 LYS cc_start: 0.7316 (ttmt) cc_final: 0.6941 (tptp)
REVERT: E    8 LEU cc_start: 0.8314 (tp) cc_final: 0.7807 (pt)
REVERT: C   58 ASP cc_start: 0.4506 (m-30) cc_final: 0.3422 (p0)
REVERT: C   68 HIS cc_start: 0.6853 (m90) cc_final: 0.6423 (m90)
REVERT: A  187 PHE cc_start: 0.8149 (m-80) cc_final: 0.7738 (m-80)
REVERT: A  214 LYS cc_start: 0.8099 (mttm) cc_final: 0.7824 (mmtp)
REVERT: A  270 LYS cc_start: 0.7454 (mmtt) cc_final: 0.6746 (mmmm)
REVERT: A  293 ASN cc_start: 0.6885 (m-40) cc_final: 0.6322 (m110)
REVERT: A  312 MET cc_start: 0.7691 (tmm) cc_final: 0.7434 (tmm)
REVERT: A  323 SER cc_start: 0.8450 (p) cc_final: 0.8202 (p)
REVERT: A  459 PHE cc_start: 0.8387 (t80) cc_final: 0.7841 (t80)
REVERT: A  472 PHE cc_start: 0.9146 (t80) cc_final: 0.8868 (t80)
REVERT: A  557 SER cc_start: 0.8826 (m) cc_final: 0.8278 (p)
REVERT: A  583 GLN cc_start: 0.7779 (tt0) cc_final: 0.7004 (mt0)
REVERT: A  620 ASP cc_start: 0.8566 (t0) cc_final: 0.8204 (t70)
REVERT: A  732 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7463 (mtp85)
REVERT: A  749 GLU cc_start: 0.8171 (tt0) cc_final: 0.7738 (tt0)
REVERT: A  808 THR cc_start: 0.8819 (m) cc_final: 0.8391 (m)
REVERT: A  916 LEU cc_start: 0.8951 (mt) cc_final: 0.8336 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0877
  time to fit residues: 24.6451
Evaluate side-chains
  140 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 114 optimal weight:    6.9990
   chunk 77 optimal weight:    0.5980
   chunk 68 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
E   2 GLN
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 438 GLN    B

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.086323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.062061 restraints weight = 51953.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.063984 restraints weight = 32024.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.065319 restraints weight = 23259.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.066200 restraints weight = 18737.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.066853 restraints weight = 16229.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.7283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9517  Z= 0.144
  Angle     :  0.665   9.653  12884  Z= 0.332
  Chirality :  0.046   0.276   1470
  Planarity :  0.004   0.037   1661
  Dihedral  :  4.425  25.699   1254
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.27 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.49 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.25), residues: 1161
  helix:  1.16 (0.21), residues: 615
  sheet: -0.86 (0.60), residues: 70
  loop : -0.31 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 868 
 TYR   0.016   0.001   TYR A 174 
 PHE   0.016   0.001   PHE A 265 
 TRP   0.022   0.002   TRP B 142 
 HIS   0.007   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9517)
  covalent geometry    : angle       0.66515 (12884)
  hydrogen bonds       : bond        0.03902 (  481)
  hydrogen bonds       : angle       4.68312 ( 1392)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   39 MET cc_start: 0.8255 (mpp) cc_final: 0.7917 (mpp)
REVERT: B   75 TYR cc_start: 0.7431 (t80) cc_final: 0.7019 (t80)
REVERT: B  100 LEU cc_start: 0.9122 (tp) cc_final: 0.8876 (tp)
REVERT: B  117 ASP cc_start: 0.7973 (m-30) cc_final: 0.7607 (p0)
REVERT: B  127 ILE cc_start: 0.8330 (mm) cc_final: 0.7907 (tp)
REVERT: B  142 TRP cc_start: 0.7504 (m-10) cc_final: 0.6978 (m-10)
REVERT: D   24 GLU cc_start: 0.7527 (tp30) cc_final: 0.7161 (tp30)
REVERT: D   72 ARG cc_start: 0.5679 (ptm160) cc_final: 0.5118 (ptp-110)
REVERT: E    4 PHE cc_start: 0.6923 (m-80) cc_final: 0.6689 (m-80)
REVERT: E    6 LYS cc_start: 0.7323 (ttmt) cc_final: 0.6955 (tptp)
REVERT: E   48 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7840 (mmtt)
REVERT: C   58 ASP cc_start: 0.4803 (m-30) cc_final: 0.3561 (p0)
REVERT: A  187 PHE cc_start: 0.8402 (m-80) cc_final: 0.7935 (m-80)
REVERT: A  214 LYS cc_start: 0.8296 (mttm) cc_final: 0.7938 (mmtp)
REVERT: A  251 GLU cc_start: 0.8486 (mp0) cc_final: 0.8188 (mp0)
REVERT: A  312 MET cc_start: 0.7572 (tmm) cc_final: 0.7231 (tmm)
REVERT: A  323 SER cc_start: 0.8439 (p) cc_final: 0.8201 (p)
REVERT: A  459 PHE cc_start: 0.8394 (t80) cc_final: 0.7863 (t80)
REVERT: A  472 PHE cc_start: 0.9198 (t80) cc_final: 0.8941 (t80)
REVERT: A  557 SER cc_start: 0.8877 (m) cc_final: 0.8353 (p)
REVERT: A  583 GLN cc_start: 0.7784 (tt0) cc_final: 0.6985 (mt0)
REVERT: A  620 ASP cc_start: 0.8659 (t0) cc_final: 0.8352 (t70)
REVERT: A  675 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7619 (ptt90)
REVERT: A  732 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7533 (mtp85)
REVERT: A  749 GLU cc_start: 0.8298 (tt0) cc_final: 0.7852 (tt0)
REVERT: A  808 THR cc_start: 0.8813 (m) cc_final: 0.8439 (m)
REVERT: A  916 LEU cc_start: 0.9008 (mt) cc_final: 0.8346 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.0894
  time to fit residues: 24.2331
Evaluate side-chains
  137 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 75 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0670
   chunk 110 optimal weight:    9.9990
   chunk 94 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 93 optimal weight:    8.9990
   chunk 102 optimal weight:    8.9990
   overall best weight:    1.2922

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

Flipped N/Q/H residues before XYZ refinement:
E  25 ASN
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.087064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.061858 restraints weight = 58895.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.064166 restraints weight = 33948.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.065701 restraints weight = 23464.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.066716 restraints weight = 18423.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.067388 restraints weight = 15638.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.7334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9517  Z= 0.128
  Angle     :  0.651   9.439  12884  Z= 0.322
  Chirality :  0.045   0.276   1470
  Planarity :  0.004   0.035   1661
  Dihedral  :  4.309  25.412   1254
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.93 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.29 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.25), residues: 1161
  helix:  1.26 (0.21), residues: 617
  sheet: -0.77 (0.61), residues: 70
  loop : -0.35 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 233 
 TYR   0.019   0.002   TYR A 204 
 PHE   0.018   0.001   PHE A 748 
 TRP   0.024   0.002   TRP B 142 
 HIS   0.008   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9517)
  covalent geometry    : angle       0.65103 (12884)
  hydrogen bonds       : bond        0.03691 (  481)
  hydrogen bonds       : angle       4.58051 ( 1392)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2147.76 seconds
wall clock time: 37 minutes 52.23 seconds (2272.23 seconds total)