Starting phenix.real_space_refine
on Thu Sep 26 00:23:29 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/09_2024/7w4a_32299.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/09_2024/7w4a_32299.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/09_2024/7w4a_32299.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/09_2024/7w4a_32299.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/09_2024/7w4a_32299.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/09_2024/7w4a_32299.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1623 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 9
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     Mg      1      5.21       5
     S      64      5.16       5
     Na      1      4.78       5
     Be      1      3.05       5
     C    6318      2.51       5
     N    1638      2.21       5
     O    1827      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 9855
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 984, 7642
          Classifications: {'peptide': 984}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 47, 'TRANS': 936}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
    Chain: "B"
      Number of atoms: 2076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2076
          Classifications: {'peptide': 261}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 4, 'PTRANS': 17, 'TRANS': 239}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 1, ' NA': 1, '8CK': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 96
          Unusual residues: {'NAG': 3, 'PCW': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 6.73, per 1000 atoms: 0.68
  Number of scatterers: 9855
  At special positions: 0
  Unit cell: (118.064, 91.744, 170.704, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     S      64     16.00
     P       1     15.00
     Mg      1     11.99
     Na      1     11.00
     F       4      9.00
     O    1827      8.00
     N    1638      7.00
     C    6318      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 201 " - pdb=" SG  CYS B 262 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B 301 " - " ASN B  99 "
      " NAG B 302 " - " ASN B 130 "
      " NAG B 303 " - " ASN B 161 "
  Time building additional restraints: 2.97
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2330

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 9 sheets defined
      51.0% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 55
      removed outlier: 3.536A  pdb=" N   GLN A  54 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 65
    Processing helix  chain 'A' and resid 73 through 85
    Processing helix  chain 'A' and resid 96 through 105
    Processing helix  chain 'A' and resid 107 through 130
    Processing helix  chain 'A' and resid 135 through 168
      removed outlier: 4.006A  pdb=" N   LEU A 139 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 171
      No H-bonds generated for 'chain 'A' and resid 169 through 171'
    Processing helix  chain 'A' and resid 270 through 273
    Processing helix  chain 'A' and resid 274 through 286
    Processing helix  chain 'A' and resid 291 through 323
    Processing helix  chain 'A' and resid 325 through 340
    Processing helix  chain 'A' and resid 343 through 363
      removed outlier: 4.440A  pdb=" N   ALA A 347 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LYS A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 379
      removed outlier: 3.540A  pdb=" N   ALA A 372 " --> pdb=" O   ASN A 369 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLU A 374 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   LEU A 376 " --> pdb=" O   VAL A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 438
    Processing helix  chain 'A' and resid 459 through 473
    Processing helix  chain 'A' and resid 475 through 483
      removed outlier: 3.829A  pdb=" N   GLU A 481 " --> pdb=" O   MET A 477 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG A 482 " --> pdb=" O   GLY A 478 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   PHE A 483 " --> pdb=" O   TYR A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 524
    Processing helix  chain 'A' and resid 540 through 556
    Processing helix  chain 'A' and resid 607 through 618
    Processing helix  chain 'A' and resid 629 through 640
    Processing helix  chain 'A' and resid 649 through 658
    Processing helix  chain 'A' and resid 665 through 669
    Processing helix  chain 'A' and resid 675 through 682
    Processing helix  chain 'A' and resid 683 through 694
    Processing helix  chain 'A' and resid 703 through 717
    Processing helix  chain 'A' and resid 727 through 729
      No H-bonds generated for 'chain 'A' and resid 727 through 729'
    Processing helix  chain 'A' and resid 730 through 737
    Processing helix  chain 'A' and resid 748 through 755
    Processing helix  chain 'A' and resid 765 through 791
      removed outlier: 3.795A  pdb=" N   THR A 769 " --> pdb=" O   ALA A 765 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   LYS A 791 " --> pdb=" O   TYR A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 806
      Proline residue:  A 798  - end of helix
    Processing helix  chain 'A' and resid 812 through 822
    Processing helix  chain 'A' and resid 824 through 831
      removed outlier: 3.700A  pdb=" N   SER A 828 " --> pdb=" O   ASP A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 834
      No H-bonds generated for 'chain 'A' and resid 832 through 834'
    Processing helix  chain 'A' and resid 855 through 865
    Processing helix  chain 'A' and resid 865 through 886
    Processing helix  chain 'A' and resid 888 through 893
      removed outlier: 3.532A  pdb=" N   VAL A 893 " --> pdb=" O   PRO A 889 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 900
    Processing helix  chain 'A' and resid 916 through 947
      removed outlier: 3.729A  pdb=" N   ALA A 941 " --> pdb=" O   MET A 937 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 944 " --> pdb=" O   ILE A 940 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 980
    Processing helix  chain 'A' and resid 983 through 988
      removed outlier: 3.682A  pdb=" N   ILE A 987 " --> pdb=" O   GLY A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1000
    Processing helix  chain 'A' and resid 1001 through 1022
    Processing helix  chain 'A' and resid 1025 through 1032
    Processing helix  chain 'B' and resid 33 through 66
    Processing helix  chain 'B' and resid 102 through 119
      removed outlier: 4.448A  pdb=" N   TRP B 106 " --> pdb=" O   ASP B 102 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLY B 108 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   LEU B 109 " --> pdb=" O   THR B 105 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   GLY B 119 " --> pdb=" O   ARG B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 4.109A  pdb=" N   GLU B 126 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 164
      removed outlier: 6.253A  pdb=" N   ASN B 161 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   GLY B 164 " --> pdb=" O   ASN B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 223
      removed outlier: 3.809A  pdb=" N   THR B 223 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
      removed outlier: 3.556A  pdb=" N   PHE B 229 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189
      removed outlier: 3.546A  pdb=" N   ARG A 182 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   CYS A 258 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ASP A 223 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   THR A 262 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 5.319A  pdb=" N   GLY A 219 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   GLN A 264 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 5.377A  pdb=" N   ALA A 217 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   LEU A 266 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU A 215 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   VAL A 268 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   ARG A 213 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   CYS A 220 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   ASN A 224 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   GLU A 232 " --> pdb=" O   ASN A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 189
      removed outlier: 3.546A  pdb=" N   ARG A 182 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   CYS A 258 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ASP A 223 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   THR A 262 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 5.319A  pdb=" N   GLY A 219 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   GLN A 264 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 5.377A  pdb=" N   ALA A 217 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   LEU A 266 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU A 215 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   VAL A 268 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   ARG A 213 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367
      removed outlier: 6.138A  pdb=" N   GLY A 740 " --> pdb=" O   MET A 757 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   LEU A 759 " --> pdb=" O   GLY A 740 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ALA A 742 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   VAL A 721 " --> pdb=" O   ILE A 739 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   VAL A 741 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   VAL A 723 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   MET A 743 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   GLY A 725 " --> pdb=" O   MET A 743 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   VAL A 381 " --> pdb=" O   ALA A 722 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   THR A 724 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   CYS A 383 " --> pdb=" O   THR A 724 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   VAL A 622 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 8.342A  pdb=" N   PHE A 699 " --> pdb=" O   VAL A 622 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   MET A 624 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   CYS A 672 " --> pdb=" O   VAL A 698 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408
      removed outlier: 3.562A  pdb=" N   THR A 396 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   SER A 599 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   PHE A 402 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 10.024A  pdb=" N   ALA A 595 " --> pdb=" O   PHE A 402 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   PHE A 564 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU A 562 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   SER A 599 " --> pdb=" O   ARG A 560 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   ARG A 560 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   CYS A 487 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408
      removed outlier: 3.562A  pdb=" N   THR A 396 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   SER A 599 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   PHE A 402 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 10.024A  pdb=" N   ALA A 595 " --> pdb=" O   PHE A 402 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   LEU A 592 " --> pdb=" O   CYS A 527 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   GLY A 596 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908
    Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85
      removed outlier: 3.576A  pdb=" N   VAL B 245 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 99

    527 hydrogen bonds defined for protein.
    1497 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: 3.82

  Time building geometry restraints manager: 3.40 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3142
        1.34 -     1.46: 1780
        1.46 -     1.58: 5049
        1.58 -     1.70: 2
        1.70 -     1.82: 95
  Bond restraints: 10068
  Sorted by residual:
  bond pdb=" F3  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.529  1.763 -0.234 2.00e-02 2.50e+03 1.36e+02
  bond pdb=" F2  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.535  1.754 -0.219 2.00e-02 2.50e+03 1.19e+02
  bond pdb=" F1  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.542  1.753 -0.211 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" CG  BFD A 385 "
       pdb=" OD1 BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.269  1.450 -0.181 2.00e-02 2.50e+03 8.15e+01
  bond pdb=" C31 PCW B 304 "
       pdb=" O2  PCW B 304 "
    ideal  model  delta    sigma   weight residual
    1.333  1.454 -0.121 2.00e-02 2.50e+03 3.68e+01
  ... (remaining 10063 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.37: 13603
        3.37 -     6.74: 62
        6.74 -    10.11: 11
       10.11 -    13.48: 1
       13.48 -    16.86: 4
  Bond angle restraints: 13681
  Sorted by residual:
  angle pdb=" F2  BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F3  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     112.60   95.74   16.86 3.00e+00 1.11e-01 3.16e+01
  angle pdb=" OD1 BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F1  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     102.38  118.72  -16.34 3.00e+00 1.11e-01 2.97e+01
  angle pdb=" F1  BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F3  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     111.29   95.71   15.58 3.00e+00 1.11e-01 2.70e+01
  angle pdb=" C   ASN A 792 "
        pdb=" N   ILE A 793 "
        pdb=" CA  ILE A 793 "
      ideal   model   delta    sigma   weight residual
     120.24  123.49   -3.25 6.30e-01 2.52e+00 2.67e+01
  angle pdb=" OD1 BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F3  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     109.93   95.90   14.03 3.00e+00 1.11e-01 2.19e+01
  ... (remaining 13676 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.41: 5728
       22.41 -    44.81: 315
       44.81 -    67.22: 31
       67.22 -    89.62: 15
       89.62 -   112.03: 3
  Dihedral angle restraints: 6092
    sinusoidal: 2475
      harmonic: 3617
  Sorted by residual:
  dihedral pdb=" CB  CYS B 131 "
           pdb=" SG  CYS B 131 "
           pdb=" SG  CYS B 152 "
           pdb=" CB  CYS B 152 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.85   55.15     1      1.00e+01 1.00e-02 4.11e+01
  dihedral pdb=" C3  NAG B 302 "
           pdb=" C1  NAG B 302 "
           pdb=" C2  NAG B 302 "
           pdb=" O5  NAG B 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -55.55   56.48 -112.03     1      3.00e+01 1.11e-03 1.47e+01
  dihedral pdb=" N2  NAG B 302 "
           pdb=" C1  NAG B 302 "
           pdb=" C2  NAG B 302 "
           pdb=" O5  NAG B 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.19  -67.58 -110.61     1      3.00e+01 1.11e-03 1.44e+01
  ... (remaining 6089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1250
       0.053 -    0.106: 256
       0.106 -    0.158: 39
       0.158 -    0.211: 2
       0.211 -    0.264: 2
  Chirality restraints: 1549
  Sorted by residual:
  chirality pdb=" C1  NAG B 302 "
            pdb=" ND2 ASN B 130 "
            pdb=" C2  NAG B 302 "
            pdb=" O5  NAG B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CB  VAL A 930 "
            pdb=" CA  VAL A 930 "
            pdb=" CG1 VAL A 930 "
            pdb=" CG2 VAL A 930 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" C2  PCW B 304 "
            pdb=" C1  PCW B 304 "
            pdb=" C3  PCW B 304 "
            pdb=" O2  PCW B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.52    0.20 2.00e-01 2.50e+01 1.00e+00
  ... (remaining 1546 not shown)

  Planarity restraints: 1757
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 232 "   -0.041 5.00e-02 4.00e+02   6.22e-02 6.19e+00
        pdb=" N   PRO A 233 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 233 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 233 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  99 "    0.001 2.00e-02 2.50e+03   1.92e-02 4.62e+00
        pdb=" CG  ASN B  99 "   -0.024 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  99 "    0.023 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  99 "   -0.020 2.00e-02 2.50e+03
        pdb=" C1  NAG B 301 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 237 "   -0.034 5.00e-02 4.00e+02   5.27e-02 4.44e+00
        pdb=" N   PRO A 238 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 238 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 238 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1754 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 74
        2.62 -     3.19: 8723
        3.19 -     3.76: 15535
        3.76 -     4.33: 21460
        4.33 -     4.90: 35355
  Nonbonded interactions: 81147
  Sorted by model distance:
  nonbonded pdb=" F2  BFD A 385 "
            pdb="MG    MG A1103 "
     model   vdw
     2.048 2.120
  nonbonded pdb=" OD2 BFD A 385 "
            pdb="MG    MG A1103 "
     model   vdw
     2.082 2.170
  nonbonded pdb=" ND2 ASN A 792 "
            pdb=" O   HOH A1201 "
     model   vdw
     2.146 3.120
  nonbonded pdb=" OH  TYR A1011 "
            pdb=" OH  TYR B  43 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" O   SER A 244 "
            pdb=" OG1 THR A 248 "
     model   vdw
     2.240 3.040
  ... (remaining 81142 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.790
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:13.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
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   0.234  10068  Z= 0.365
  Angle     :  0.712  16.855  13681  Z= 0.344
  Chirality :  0.044   0.264   1549
  Planarity :  0.004   0.062   1754
  Dihedral  : 13.796 112.026   3753
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.24), residues: 1238
  helix:  1.76 (0.21), residues: 575
  sheet: -0.01 (0.37), residues: 162
  loop :  0.21 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 427 
 HIS   0.009   0.001   HIS B 114 
 PHE   0.030   0.002   PHE A 124 
 TYR   0.018   0.001   TYR A 802 
 ARG   0.008   0.000   ARG A 844 

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 1.106 
Fit side-chains
REVERT: A  140 TYR cc_start: 0.6553 (m-10) cc_final: 0.6270 (m-10)
REVERT: A  213 ARG cc_start: 0.5596 (ttt-90) cc_final: 0.5284 (ttt180)
REVERT: A  220 CYS cc_start: 0.6849 (t) cc_final: 0.6577 (t)
REVERT: A  260 GLU cc_start: 0.5871 (mt-10) cc_final: 0.5612 (mt-10)
REVERT: A  314 THR cc_start: 0.6909 (t) cc_final: 0.6619 (p)
REVERT: A  320 MET cc_start: 0.6875 (mmp) cc_final: 0.6515 (mmp)
REVERT: A  333 PHE cc_start: 0.7257 (t80) cc_final: 0.6890 (t80)
REVERT: A  369 ASN cc_start: 0.7437 (p0) cc_final: 0.7182 (p0)
REVERT: A  425 GLU cc_start: 0.4301 (pm20) cc_final: 0.3772 (tm-30)
REVERT: A  585 MET cc_start: -0.1063 (mmt) cc_final: -0.1434 (mmt)
REVERT: A  652 ASP cc_start: 0.5905 (m-30) cc_final: 0.5649 (m-30)
REVERT: A  743 MET cc_start: 0.8061 (mmm) cc_final: 0.7789 (mpp)
REVERT: A  970 PHE cc_start: 0.7261 (t80) cc_final: 0.7056 (t80)
REVERT: B  147 HIS cc_start: 0.6754 (t-90) cc_final: 0.6450 (t-170)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 1.2926
  time to fit residues: 191.7466
Evaluate side-chains
  108 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN
A 706 GLN
A 924 GLN
A 986 ASN
B 146 ASN
B 289 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10068  Z= 0.242
  Angle     :  0.584   6.261  13681  Z= 0.302
  Chirality :  0.045   0.262   1549
  Planarity :  0.005   0.062   1754
  Dihedral  :  8.182  93.404   1480
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  6.54 %
    Favored  : 91.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.24), residues: 1238
  helix:  1.82 (0.21), residues: 564
  sheet: -0.06 (0.37), residues: 162
  loop :  0.17 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 998 
 HIS   0.007   0.001   HIS B 227 
 PHE   0.018   0.002   PHE A 932 
 TYR   0.019   0.002   TYR A 802 
 ARG   0.004   0.001   ARG A 278 

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6715 (m-10) cc_final: 0.6422 (m-10)
REVERT: A  193 GLN cc_start: 0.6283 (mm-40) cc_final: 0.5762 (mm-40)
REVERT: A  213 ARG cc_start: 0.5747 (ttt-90) cc_final: 0.5366 (ttt180)
REVERT: A  260 GLU cc_start: 0.5949 (mt-10) cc_final: 0.5697 (mt-10)
REVERT: A  320 MET cc_start: 0.6481 (mmp) cc_final: 0.6231 (mmp)
REVERT: A  333 PHE cc_start: 0.7333 (t80) cc_final: 0.6972 (t80)
REVERT: A  425 GLU cc_start: 0.4157 (pm20) cc_final: 0.3773 (tm-30)
REVERT: A  516 MET cc_start: 0.4316 (tmt) cc_final: 0.3964 (tmt)
REVERT: A  585 MET cc_start: -0.1018 (mmt) cc_final: -0.1227 (mmt)
REVERT: A  652 ASP cc_start: 0.5852 (m-30) cc_final: 0.5570 (m-30)
REVERT: B  114 HIS cc_start: 0.6425 (OUTLIER) cc_final: 0.6103 (t-90)
REVERT: B  135 LYS cc_start: 0.7461 (ptpp) cc_final: 0.7228 (ptpp)
REVERT: B  147 HIS cc_start: 0.6747 (t-90) cc_final: 0.6504 (t-170)
REVERT: B  258 VAL cc_start: 0.7810 (p) cc_final: 0.7543 (m)
  outliers start: 19
  outliers final: 7
  residues processed: 127
  average time/residue: 1.1538
  time to fit residues: 158.7035
Evaluate side-chains
  121 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  906 ASP
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 93 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 112 optimal weight:    0.6980
   chunk 121 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 111 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
A 986 ASN
B 289 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10068  Z= 0.163
  Angle     :  0.510   8.129  13681  Z= 0.259
  Chirality :  0.042   0.194   1549
  Planarity :  0.004   0.059   1754
  Dihedral  :  7.666  88.201   1480
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.10 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.24), residues: 1238
  helix:  2.11 (0.22), residues: 565
  sheet:  0.06 (0.38), residues: 162
  loop :  0.21 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 915 
 HIS   0.005   0.001   HIS B 227 
 PHE   0.015   0.001   PHE A 970 
 TYR   0.015   0.001   TYR A 802 
 ARG   0.003   0.000   ARG A 278 

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6627 (m-10) cc_final: 0.6350 (m-10)
REVERT: A  193 GLN cc_start: 0.6415 (mm-40) cc_final: 0.5789 (mm-40)
REVERT: A  213 ARG cc_start: 0.5757 (ttt-90) cc_final: 0.5391 (ttt180)
REVERT: A  260 GLU cc_start: 0.5946 (mt-10) cc_final: 0.5708 (mt-10)
REVERT: A  333 PHE cc_start: 0.7340 (t80) cc_final: 0.7042 (t80)
REVERT: A  425 GLU cc_start: 0.4222 (pm20) cc_final: 0.3821 (tm-30)
REVERT: A  516 MET cc_start: 0.4480 (tmt) cc_final: 0.4258 (tmt)
REVERT: A  585 MET cc_start: -0.1061 (mmt) cc_final: -0.1312 (mmt)
REVERT: A  652 ASP cc_start: 0.5873 (m-30) cc_final: 0.5597 (m-30)
REVERT: A  686 GLU cc_start: 0.5723 (tp30) cc_final: 0.5522 (tp30)
REVERT: B  114 HIS cc_start: 0.6399 (OUTLIER) cc_final: 0.6063 (t-90)
REVERT: B  135 LYS cc_start: 0.7434 (ptpp) cc_final: 0.7185 (ptpp)
REVERT: B  147 HIS cc_start: 0.6734 (t-90) cc_final: 0.6493 (t-170)
  outliers start: 14
  outliers final: 5
  residues processed: 129
  average time/residue: 1.1205
  time to fit residues: 156.4130
Evaluate side-chains
  116 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0770
   chunk 75 optimal weight:    0.0970
   chunk 113 optimal weight:    0.9980
   chunk 119 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.5936

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

Flipped N/Q/H residues before XYZ refinement:
A 986 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10068  Z= 0.149
  Angle     :  0.498   9.077  13681  Z= 0.251
  Chirality :  0.042   0.175   1549
  Planarity :  0.004   0.055   1754
  Dihedral  :  7.321  84.341   1480
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.81 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.24), residues: 1238
  helix:  2.24 (0.22), residues: 565
  sheet:  0.16 (0.38), residues: 162
  loop :  0.26 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 401 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.013   0.001   PHE A 161 
 TYR   0.014   0.001   TYR A 802 
 ARG   0.003   0.000   ARG A 278 

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6626 (m-10) cc_final: 0.6356 (m-10)
REVERT: A  193 GLN cc_start: 0.6298 (mm-40) cc_final: 0.5739 (mm-40)
REVERT: A  213 ARG cc_start: 0.5760 (ttt-90) cc_final: 0.5542 (ttt180)
REVERT: A  260 GLU cc_start: 0.5983 (mt-10) cc_final: 0.5755 (mt-10)
REVERT: A  320 MET cc_start: 0.6165 (mmp) cc_final: 0.5841 (mmt)
REVERT: A  333 PHE cc_start: 0.7294 (t80) cc_final: 0.7035 (t80)
REVERT: A  425 GLU cc_start: 0.4289 (pm20) cc_final: 0.3799 (tm-30)
REVERT: A  516 MET cc_start: 0.4461 (tmt) cc_final: 0.4194 (tmt)
REVERT: A  585 MET cc_start: -0.1068 (mmt) cc_final: -0.1384 (mmt)
REVERT: A  652 ASP cc_start: 0.5875 (m-30) cc_final: 0.5596 (m-30)
REVERT: A  696 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6748 (mt-10)
REVERT: B  114 HIS cc_start: 0.6414 (OUTLIER) cc_final: 0.6070 (t-90)
REVERT: B  135 LYS cc_start: 0.7376 (ptpp) cc_final: 0.7115 (ptpp)
REVERT: B  147 HIS cc_start: 0.6753 (t-90) cc_final: 0.6505 (t-170)
  outliers start: 14
  outliers final: 9
  residues processed: 129
  average time/residue: 1.1122
  time to fit residues: 155.7408
Evaluate side-chains
  120 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 89 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 102 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 107 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 986 ASN
B 289 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10068  Z= 0.232
  Angle     :  0.556   8.628  13681  Z= 0.283
  Chirality :  0.044   0.230   1549
  Planarity :  0.005   0.059   1754
  Dihedral  :  7.595  81.657   1480
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 11.47 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.24), residues: 1238
  helix:  2.03 (0.21), residues: 564
  sheet:  0.08 (0.38), residues: 162
  loop :  0.16 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 915 
 HIS   0.005   0.001   HIS B 227 
 PHE   0.017   0.002   PHE A 932 
 TYR   0.018   0.002   TYR A 802 
 ARG   0.003   0.001   ARG A 692 

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ASP cc_start: 0.5598 (OUTLIER) cc_final: 0.5353 (m-30)
REVERT: A  140 TYR cc_start: 0.6672 (m-10) cc_final: 0.6426 (m-10)
REVERT: A  193 GLN cc_start: 0.6400 (mm-40) cc_final: 0.5750 (mm-40)
REVERT: A  213 ARG cc_start: 0.5770 (ttt-90) cc_final: 0.5469 (ttt180)
REVERT: A  260 GLU cc_start: 0.6137 (mt-10) cc_final: 0.5846 (mt-10)
REVERT: A  320 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.6042 (mmt)
REVERT: A  333 PHE cc_start: 0.7311 (t80) cc_final: 0.7064 (t80)
REVERT: A  425 GLU cc_start: 0.4296 (pm20) cc_final: 0.3867 (tm-30)
REVERT: A  477 MET cc_start: 0.4812 (tpt) cc_final: 0.4595 (tpp)
REVERT: A  516 MET cc_start: 0.4473 (tmt) cc_final: 0.4232 (tmt)
REVERT: A  585 MET cc_start: -0.0921 (mmt) cc_final: -0.1352 (mmt)
REVERT: A  652 ASP cc_start: 0.5872 (m-30) cc_final: 0.5615 (m-30)
REVERT: A  680 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6381 (ttpp)
REVERT: A  696 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6759 (mt-10)
REVERT: B  114 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.6067 (t-90)
REVERT: B  147 HIS cc_start: 0.6722 (t-90) cc_final: 0.6459 (t-170)
  outliers start: 25
  outliers final: 13
  residues processed: 129
  average time/residue: 1.1655
  time to fit residues: 162.5897
Evaluate side-chains
  125 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  906 ASP
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 107 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 119 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN
A 986 ASN
B 289 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10068  Z= 0.163
  Angle     :  0.512   9.749  13681  Z= 0.258
  Chirality :  0.042   0.174   1549
  Planarity :  0.004   0.056   1754
  Dihedral  :  7.292  79.311   1480
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.18 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.24), residues: 1238
  helix:  2.18 (0.22), residues: 565
  sheet:  0.13 (0.39), residues: 162
  loop :  0.19 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 915 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.013   0.001   PHE A 932 
 TYR   0.015   0.001   TYR A 802 
 ARG   0.002   0.000   ARG A 278 

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6661 (m-10) cc_final: 0.6350 (m-10)
REVERT: A  193 GLN cc_start: 0.6406 (mm-40) cc_final: 0.5817 (mm-40)
REVERT: A  213 ARG cc_start: 0.5773 (ttt-90) cc_final: 0.5482 (ttt180)
REVERT: A  260 GLU cc_start: 0.6089 (mt-10) cc_final: 0.5822 (mt-10)
REVERT: A  320 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.6064 (mmt)
REVERT: A  333 PHE cc_start: 0.7255 (t80) cc_final: 0.7025 (t80)
REVERT: A  425 GLU cc_start: 0.4341 (pm20) cc_final: 0.3897 (tm-30)
REVERT: A  477 MET cc_start: 0.4885 (tpt) cc_final: 0.3285 (ppp)
REVERT: A  516 MET cc_start: 0.4477 (tmt) cc_final: 0.4213 (tmt)
REVERT: A  585 MET cc_start: -0.0717 (mmt) cc_final: -0.1168 (mmt)
REVERT: A  652 ASP cc_start: 0.5812 (m-30) cc_final: 0.5536 (m-30)
REVERT: A  680 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6378 (ttpp)
REVERT: A  696 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6725 (mt-10)
REVERT: B  114 HIS cc_start: 0.6400 (OUTLIER) cc_final: 0.6063 (t-90)
REVERT: B  135 LYS cc_start: 0.7353 (ptpp) cc_final: 0.6930 (mtmm)
REVERT: B  147 HIS cc_start: 0.6712 (t-90) cc_final: 0.6447 (t-170)
  outliers start: 20
  outliers final: 11
  residues processed: 127
  average time/residue: 1.2127
  time to fit residues: 166.4049
Evaluate side-chains
  122 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 119 optimal weight:    5.9990
   chunk 74 optimal weight:    0.1980
   chunk 72 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 369 ASN
A 415 GLN
A 986 ASN
B 289 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10068  Z= 0.217
  Angle     :  0.554   9.286  13681  Z= 0.281
  Chirality :  0.044   0.219   1549
  Planarity :  0.005   0.058   1754
  Dihedral  :  7.491  77.767   1480
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.65 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.24), residues: 1238
  helix:  2.03 (0.21), residues: 565
  sheet:  0.01 (0.39), residues: 162
  loop :  0.16 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 915 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.017   0.002   PHE A 932 
 TYR   0.017   0.002   TYR A 802 
 ARG   0.002   0.000   ARG A 701 

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 ASP cc_start: 0.5624 (OUTLIER) cc_final: 0.5382 (m-30)
REVERT: A  140 TYR cc_start: 0.6638 (m-10) cc_final: 0.6360 (m-10)
REVERT: A  193 GLN cc_start: 0.6474 (mm-40) cc_final: 0.5864 (mm-40)
REVERT: A  213 ARG cc_start: 0.5768 (ttt-90) cc_final: 0.5479 (ttt180)
REVERT: A  260 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5910 (mt-10)
REVERT: A  320 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.6130 (mmt)
REVERT: A  333 PHE cc_start: 0.7336 (t80) cc_final: 0.7111 (t80)
REVERT: A  425 GLU cc_start: 0.4302 (pm20) cc_final: 0.3915 (tm-30)
REVERT: A  477 MET cc_start: 0.4764 (tpt) cc_final: 0.3227 (ppp)
REVERT: A  516 MET cc_start: 0.4466 (tmt) cc_final: 0.4183 (tmt)
REVERT: A  585 MET cc_start: -0.0589 (mmt) cc_final: -0.1124 (mmt)
REVERT: A  652 ASP cc_start: 0.5843 (m-30) cc_final: 0.5579 (m-30)
REVERT: A  680 LYS cc_start: 0.6759 (OUTLIER) cc_final: 0.6434 (ttpp)
REVERT: A  686 GLU cc_start: 0.5408 (mp0) cc_final: 0.4972 (mp0)
REVERT: A  696 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6824 (mt-10)
REVERT: B  114 HIS cc_start: 0.6364 (OUTLIER) cc_final: 0.6041 (t-90)
REVERT: B  126 GLU cc_start: 0.5990 (mm-30) cc_final: 0.5689 (mm-30)
REVERT: B  147 HIS cc_start: 0.6727 (t-90) cc_final: 0.6455 (t-170)
  outliers start: 23
  outliers final: 14
  residues processed: 131
  average time/residue: 1.1349
  time to fit residues: 160.8186
Evaluate side-chains
  125 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  906 ASP
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0970
   chunk 71 optimal weight:    0.0970
   chunk 36 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0050
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.3590

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

Flipped N/Q/H residues before XYZ refinement:
A 369 ASN
A 986 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10068  Z= 0.144
  Angle     :  0.519  10.827  13681  Z= 0.258
  Chirality :  0.042   0.162   1549
  Planarity :  0.004   0.055   1754
  Dihedral  :  7.207  75.684   1480
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.79 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.24), residues: 1238
  helix:  2.26 (0.22), residues: 565
  sheet:  0.16 (0.39), residues: 162
  loop :  0.25 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 401 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.013   0.001   PHE A 161 
 TYR   0.016   0.001   TYR A 157 
 ARG   0.002   0.000   ARG A 278 

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 1.117 
Fit side-chains
REVERT: A  140 TYR cc_start: 0.6618 (m-10) cc_final: 0.6258 (m-10)
REVERT: A  193 GLN cc_start: 0.6338 (mm-40) cc_final: 0.5820 (mm-40)
REVERT: A  213 ARG cc_start: 0.5783 (ttt-90) cc_final: 0.5508 (ttt180)
REVERT: A  260 GLU cc_start: 0.6085 (mt-10) cc_final: 0.5791 (mt-10)
REVERT: A  320 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.6035 (mmt)
REVERT: A  333 PHE cc_start: 0.7263 (t80) cc_final: 0.7056 (t80)
REVERT: A  425 GLU cc_start: 0.4201 (pm20) cc_final: 0.3821 (tm-30)
REVERT: A  477 MET cc_start: 0.4879 (tpt) cc_final: 0.3214 (ppp)
REVERT: A  516 MET cc_start: 0.4505 (tmt) cc_final: 0.4237 (tmt)
REVERT: A  585 MET cc_start: -0.0567 (mmt) cc_final: -0.1145 (mmt)
REVERT: A  652 ASP cc_start: 0.5809 (m-30) cc_final: 0.5540 (m-30)
REVERT: A  686 GLU cc_start: 0.5419 (mp0) cc_final: 0.5032 (mp0)
REVERT: A  696 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6793 (mt-10)
REVERT: B  114 HIS cc_start: 0.6340 (OUTLIER) cc_final: 0.6004 (t-90)
REVERT: B  135 LYS cc_start: 0.7326 (ptpp) cc_final: 0.6935 (mtmm)
REVERT: B  147 HIS cc_start: 0.6723 (t-90) cc_final: 0.6477 (t-170)
  outliers start: 13
  outliers final: 6
  residues processed: 127
  average time/residue: 1.1398
  time to fit residues: 157.2328
Evaluate side-chains
  123 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 111 optimal weight:    7.9990
   chunk 67 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0030
   chunk 87 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.1994

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

Flipped N/Q/H residues before XYZ refinement:
A 369 ASN
A 898 GLN
A 971 GLN
A 986 ASN
B 289 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10068  Z= 0.201
  Angle     :  0.563  10.500  13681  Z= 0.283
  Chirality :  0.044   0.238   1549
  Planarity :  0.005   0.059   1754
  Dihedral  :  7.342  75.583   1480
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.17 %
    Favored  : 83.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.24), residues: 1238
  helix:  2.13 (0.22), residues: 566
  sheet:  0.07 (0.39), residues: 162
  loop :  0.19 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 915 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.021   0.002   PHE A 970 
 TYR   0.019   0.002   TYR B  60 
 ARG   0.002   0.000   ARG A 692 

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6663 (m-10) cc_final: 0.6316 (m-10)
REVERT: A  193 GLN cc_start: 0.6428 (mm-40) cc_final: 0.5826 (mm-40)
REVERT: A  213 ARG cc_start: 0.5772 (ttt-90) cc_final: 0.5490 (ttt180)
REVERT: A  260 GLU cc_start: 0.6126 (mt-10) cc_final: 0.5860 (mt-10)
REVERT: A  320 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.6019 (mmt)
REVERT: A  333 PHE cc_start: 0.7303 (t80) cc_final: 0.7102 (t80)
REVERT: A  425 GLU cc_start: 0.4217 (pm20) cc_final: 0.3819 (tm-30)
REVERT: A  477 MET cc_start: 0.4836 (tpt) cc_final: 0.3251 (ppp)
REVERT: A  516 MET cc_start: 0.4499 (tmt) cc_final: 0.4198 (tmt)
REVERT: A  585 MET cc_start: -0.0648 (mmt) cc_final: -0.1303 (mmt)
REVERT: A  652 ASP cc_start: 0.5840 (m-30) cc_final: 0.5575 (m-30)
REVERT: A  680 LYS cc_start: 0.6812 (OUTLIER) cc_final: 0.6495 (ttpp)
REVERT: A  686 GLU cc_start: 0.5350 (mp0) cc_final: 0.4961 (mp0)
REVERT: A  696 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6844 (mt-10)
REVERT: B  114 HIS cc_start: 0.6362 (OUTLIER) cc_final: 0.6040 (t-90)
REVERT: B  135 LYS cc_start: 0.7331 (ptpp) cc_final: 0.6859 (mtmm)
REVERT: B  147 HIS cc_start: 0.6748 (t-90) cc_final: 0.6459 (t-170)
  outliers start: 16
  outliers final: 11
  residues processed: 124
  average time/residue: 1.1315
  time to fit residues: 152.6511
Evaluate side-chains
  124 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  906 ASP
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 117 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0980
   chunk 55 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 113 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 369 ASN
A 971 GLN
A 986 ASN
B 289 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10068  Z= 0.162
  Angle     :  0.530  10.290  13681  Z= 0.266
  Chirality :  0.043   0.179   1549
  Planarity :  0.004   0.058   1754
  Dihedral  :  7.150  74.195   1480
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.07 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.24), residues: 1238
  helix:  2.23 (0.22), residues: 565
  sheet:  0.12 (0.39), residues: 162
  loop :  0.21 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 106 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.021   0.001   PHE A 970 
 TYR   0.016   0.001   TYR B  98 
 ARG   0.002   0.000   ARG A 278 

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6620 (m-10) cc_final: 0.6321 (m-10)
REVERT: A  193 GLN cc_start: 0.6320 (mm-40) cc_final: 0.5794 (mm-40)
REVERT: A  213 ARG cc_start: 0.5811 (ttt-90) cc_final: 0.5525 (ttt180)
REVERT: A  260 GLU cc_start: 0.6168 (mt-10) cc_final: 0.5903 (mt-10)
REVERT: A  320 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.5990 (mmt)
REVERT: A  333 PHE cc_start: 0.7281 (t80) cc_final: 0.7078 (t80)
REVERT: A  425 GLU cc_start: 0.4203 (pm20) cc_final: 0.3823 (tm-30)
REVERT: A  477 MET cc_start: 0.4865 (tpt) cc_final: 0.3266 (ppp)
REVERT: A  516 MET cc_start: 0.4517 (tmt) cc_final: 0.4246 (tmt)
REVERT: A  585 MET cc_start: -0.0589 (mmt) cc_final: -0.1231 (mmt)
REVERT: A  652 ASP cc_start: 0.5811 (m-30) cc_final: 0.5549 (m-30)
REVERT: A  686 GLU cc_start: 0.5416 (mp0) cc_final: 0.5054 (mp0)
REVERT: A  696 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6846 (mt-10)
REVERT: B  114 HIS cc_start: 0.6357 (OUTLIER) cc_final: 0.6023 (t-90)
REVERT: B  147 HIS cc_start: 0.6751 (t-90) cc_final: 0.6474 (t-170)
  outliers start: 13
  outliers final: 11
  residues processed: 119
  average time/residue: 1.1272
  time to fit residues: 145.6778
Evaluate side-chains
  123 residues out of total 1059 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  906 ASP
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 90 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0070
   chunk 41 optimal weight:    0.9980
   chunk 101 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A 986 ASN
B 289 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.181302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.131960 restraints weight = 11407.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.63
r_work: 0.3233 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10068  Z= 0.154
  Angle     :  0.526  10.212  13681  Z= 0.263
  Chirality :  0.042   0.163   1549
  Planarity :  0.004   0.058   1754
  Dihedral  :  7.011  72.981   1480
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.26 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.24), residues: 1238
  helix:  2.29 (0.22), residues: 564
  sheet:  0.10 (0.39), residues: 162
  loop :  0.22 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 106 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.013   0.001   PHE A 932 
 TYR   0.015   0.001   TYR A 802 
 ARG   0.002   0.000   ARG A  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4082.13 seconds
wall clock time: 74 minutes 25.27 seconds (4465.27 seconds total)