Starting phenix.real_space_refine
on Fri Aug 22 23:17:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wfs_37498/08_2025/8wfs_37498.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wfs_37498/08_2025/8wfs_37498.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wfs_37498/08_2025/8wfs_37498.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wfs_37498/08_2025/8wfs_37498.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wfs_37498/08_2025/8wfs_37498.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wfs_37498/08_2025/8wfs_37498.cif"
  }
  resolution = 3.36
  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=   0.015
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 2864 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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    3973      2.51       5
     N    1123      2.21       5
     O    1124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6274
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "c"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 884
          Classifications: {'peptide': 118}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 102}
    Chain: "C"
      Number of atoms: 882
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 117, 877
          Classifications: {'peptide': 117}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 102}
      Conformer: "B"
        Number of residues, atoms: 117, 877
          Classifications: {'peptide': 117}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 102}
          bond proxies already assigned to first conformer: 894
    Chain: "E"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 957
          Classifications: {'peptide': 125}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 113}
    Chain: "B"
      Number of atoms: 1035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1035
          Classifications: {'peptide': 140}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 123}
    Chain: "b"
      Number of atoms: 1035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1035
          Classifications: {'peptide': 140}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 123}
    Chain: "X"
      Number of atoms: 1112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1112
          Classifications: {'peptide': 146}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 133}
    Chain: "a"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 179
          Classifications: {'peptide': 22}
          Link IDs: {'PTRANS': 1, 'TRANS': 20}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AALA C 114 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA C 114 " occ=0.50
  Time building chain proxies: 1.38, per 1000 atoms: 0.22
  Number of scatterers: 6274
  At special positions: 0
  Unit cell: (83.7876, 97.7522, 134.275, 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      54     16.00
     O    1124      8.00
     N    1123      7.00
     C    3973      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=26, symmetry=0
    Simple disulfide: pdb=" SG  CYS c   1 " - pdb=" SG  CYS c   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS c   5 " - pdb=" SG  CYS c  14 " distance=2.03
    Simple disulfide: pdb=" SG  CYS c  68 " - pdb=" SG  CYS c  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS c  70 " - pdb=" SG  CYS c 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   1 " - pdb=" SG  CYS C   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   5 " - pdb=" SG  CYS C  14 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  68 " - pdb=" SG  CYS C  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  70 " - pdb=" SG  CYS C 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   4 " - pdb=" SG  CYS E  10 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   8 " - pdb=" SG  CYS E  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  73 " - pdb=" SG  CYS E  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  75 " - pdb=" SG  CYS E 119 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   1 " - pdb=" SG  CYS B   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   5 " - pdb=" SG  CYS B  14 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  68 " - pdb=" SG  CYS B  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  70 " - pdb=" SG  CYS B 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 122 " - pdb=" SG  CYS a 484 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b   1 " - pdb=" SG  CYS b   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b   5 " - pdb=" SG  CYS b  14 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b  68 " - pdb=" SG  CYS b  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b  70 " - pdb=" SG  CYS b 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 122 " - pdb=" SG  CYS a 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X   4 " - pdb=" SG  CYS X  10 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X   8 " - pdb=" SG  CYS X  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X  73 " - pdb=" SG  CYS X  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X  75 " - pdb=" SG  CYS X 119 " 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
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
    NAG-ASN
      " NAG A   1 " - " ASN c  41 "
      " NAG D   1 " - " ASN C  41 "
      " NAG F   1 " - " ASN E  44 "
      " NAG G   1 " - " ASN B  41 "
      " NAG H   1 " - " ASN b  41 "
      " NAG I   1 " - " ASN X  44 "
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 293.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 11 sheets defined
      31.2% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'c' and resid 49 through 53
      removed outlier: 3.545A  pdb=" N   ALA c  52 " --> pdb=" O   LEU c  49 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 69 through 71
      No H-bonds generated for 'chain 'c' and resid 69 through 71'
    Processing helix  chain 'c' and resid 72 through 81
      removed outlier: 4.190A  pdb=" N   GLY c  81 " --> pdb=" O   ALA c  77 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 85 through 89
      removed outlier: 3.541A  pdb=" N   TYR c  88 " --> pdb=" O   ARG c  85 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG c  89 " --> pdb=" O   ALA c  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'c' and resid 85 through 89'
    Processing helix  chain 'c' and resid 96 through 100
      removed outlier: 3.662A  pdb=" N   ARG c 100 " --> pdb=" O   PRO c  97 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 108 through 115
    Processing helix  chain 'C' and resid 69 through 71
      No H-bonds generated for 'chain 'C' and resid 69 through 71'
    Processing helix  chain 'C' and resid 72 through 81
    Processing helix  chain 'C' and resid 96 through 100
      removed outlier: 3.651A  pdb=" N   ARG C 100 " --> pdb=" O   PRO C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 107
    Processing helix  chain 'C' and resid 108 through 115
      removed outlier: 3.754A  pdb=" N   LEU C 112 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ALA C 115 " --> pdb=" O   GLU C 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 77 through 85
    Processing helix  chain 'E' and resid 88 through 95
      removed outlier: 4.089A  pdb=" N   VAL E  95 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 71
      No H-bonds generated for 'chain 'B' and resid 69 through 71'
    Processing helix  chain 'B' and resid 72 through 80
      removed outlier: 3.594A  pdb=" N   ALA B  80 " --> pdb=" O   ARG B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 89
      removed outlier: 3.524A  pdb=" N   TYR B  88 " --> pdb=" O   ARG B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 100
      removed outlier: 3.589A  pdb=" N   ARG B 100 " --> pdb=" O   PRO B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 107
    Processing helix  chain 'B' and resid 108 through 117
      removed outlier: 4.135A  pdb=" N   ALA B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 140
      removed outlier: 3.829A  pdb=" N   GLN B 129 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ALA B 131 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 49 through 53
      removed outlier: 3.908A  pdb=" N   LEU b  53 " --> pdb=" O   LEU b  50 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 69 through 71
      No H-bonds generated for 'chain 'b' and resid 69 through 71'
    Processing helix  chain 'b' and resid 72 through 81
      removed outlier: 3.505A  pdb=" N   GLY b  81 " --> pdb=" O   ALA b  77 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 96 through 100
      removed outlier: 3.551A  pdb=" N   ARG b 100 " --> pdb=" O   PRO b  97 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 103 through 107
    Processing helix  chain 'b' and resid 108 through 116
      removed outlier: 3.798A  pdb=" N   LEU b 112 " --> pdb=" O   ALA b 108 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   CYS b 116 " --> pdb=" O   LEU b 112 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 125 through 140
    Processing helix  chain 'X' and resid 74 through 76
      No H-bonds generated for 'chain 'X' and resid 74 through 76'
    Processing helix  chain 'X' and resid 77 through 88
    Processing helix  chain 'X' and resid 89 through 94
    Processing helix  chain 'X' and resid 130 through 146
      removed outlier: 3.662A  pdb=" N   ALA X 137 " --> pdb=" O   LEU X 133 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLY X 145 " --> pdb=" O   VAL X 141 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU X 146 " --> pdb=" O   ALA X 142 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 483 through 503
      removed outlier: 3.688A  pdb=" N   LEU a 487 " --> pdb=" O   PHE a 483 " (cutoff:3.500A)
      Proline residue:  a 488  - end of helix
      removed outlier: 4.359A  pdb=" N   PHE a 491 " --> pdb=" O   LEU a 487 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL a 493 " --> pdb=" O   LEU a 489 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'c' and resid 6 through 8
    Processing sheet with id=AA2, first strand: chain 'c' and resid 66 through 67
      removed outlier: 7.480A  pdb=" N   TRP c  66 " --> pdb=" O   VAL c  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 8
      removed outlier: 3.658A  pdb=" N   VAL C  36 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 67
      removed outlier: 7.132A  pdb=" N   TRP C  66 " --> pdb=" O   VAL C  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 9 through 13
      removed outlier: 3.660A  pdb=" N   GLY E  17 " --> pdb=" O   LEU E  13 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   LEU E  18 " --> pdb=" O   HIS E  39 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   LEU E  41 " --> pdb=" O   LEU E  18 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   VAL E  20 " --> pdb=" O   LEU E  41 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   LEU E  40 " --> pdb=" O   ASP E  65 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 71 through 72
      removed outlier: 7.077A  pdb=" N   TRP E  71 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 6 through 8
      removed outlier: 6.827A  pdb=" N   LEU B  35 " --> pdb=" O   HIS B  60 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'b' and resid 6 through 8
      removed outlier: 3.522A  pdb=" N   VAL b  36 " --> pdb=" O   VAL b  12 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   LEU b  35 " --> pdb=" O   HIS b  60 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'b' and resid 66 through 67
      removed outlier: 7.041A  pdb=" N   TRP b  66 " --> pdb=" O   VAL b  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'X' and resid 9 through 13
      removed outlier: 6.947A  pdb=" N   LEU X  18 " --> pdb=" O   ARG X  38 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   LEU X  40 " --> pdb=" O   LEU X  18 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL X  20 " --> pdb=" O   LEU X  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'X' and resid 71 through 72
      removed outlier: 6.640A  pdb=" N   TRP X  71 " --> pdb=" O   ALA X  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    149 hydrogen bonds defined for protein.
    351 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: 0.60

  Time building geometry restraints manager: 0.65 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: 2060
        1.34 -     1.47: 1427
        1.47 -     1.59: 2898
        1.59 -     1.71: 1
        1.71 -     1.83: 56
  Bond restraints: 6442
  Sorted by residual:
  bond pdb=" CB  PRO c  29 "
       pdb=" CG  PRO c  29 "
    ideal  model  delta    sigma   weight residual
    1.492  1.651 -0.159 5.00e-02 4.00e+02 1.01e+01
  bond pdb=" CB  PRO C   2 "
       pdb=" CG  PRO C   2 "
    ideal  model  delta    sigma   weight residual
    1.492  1.572 -0.080 5.00e-02 4.00e+02 2.54e+00
  bond pdb=" C   ALA B  86 "
       pdb=" N   PRO B  87 "
    ideal  model  delta    sigma   weight residual
    1.334  1.347 -0.013 8.40e-03 1.42e+04 2.38e+00
  bond pdb=" C1  BMA G   3 "
       pdb=" C2  BMA G   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.548 -0.029 2.00e-02 2.50e+03 2.17e+00
  bond pdb=" CG  PRO C   2 "
       pdb=" CD  PRO C   2 "
    ideal  model  delta    sigma   weight residual
    1.503  1.551 -0.048 3.40e-02 8.65e+02 1.95e+00
  ... (remaining 6437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 8639
        2.61 -     5.22: 181
        5.22 -     7.83: 18
        7.83 -    10.45: 9
       10.45 -    13.06: 1
  Bond angle restraints: 8848
  Sorted by residual:
  angle pdb=" CA  PRO c  29 "
        pdb=" N   PRO c  29 "
        pdb=" CD  PRO c  29 "
      ideal   model   delta    sigma   weight residual
     112.00   98.94   13.06 1.40e+00 5.10e-01 8.70e+01
  angle pdb=" N   GLY b 124 "
        pdb=" CA  GLY b 124 "
        pdb=" C   GLY b 124 "
      ideal   model   delta    sigma   weight residual
     115.66  105.40   10.26 1.56e+00 4.11e-01 4.33e+01
  angle pdb=" CA  PRO C   2 "
        pdb=" N   PRO C   2 "
        pdb=" CD  PRO C   2 "
      ideal   model   delta    sigma   weight residual
     112.00  106.47    5.53 1.40e+00 5.10e-01 1.56e+01
  angle pdb=" N   PRO c  29 "
        pdb=" CD  PRO c  29 "
        pdb=" CG  PRO c  29 "
      ideal   model   delta    sigma   weight residual
     103.20   98.14    5.06 1.50e+00 4.44e-01 1.14e+01
  angle pdb=" N   PRO c  29 "
        pdb=" CA  PRO c  29 "
        pdb=" C   PRO c  29 "
      ideal   model   delta    sigma   weight residual
     111.68  116.99   -5.31 1.67e+00 3.59e-01 1.01e+01
  ... (remaining 8843 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.26: 3602
       22.26 -    44.52: 419
       44.52 -    66.78: 71
       66.78 -    89.03: 20
       89.03 -   111.29: 16
  Dihedral angle restraints: 4128
    sinusoidal: 1818
      harmonic: 2310
  Sorted by residual:
  dihedral pdb=" CB  CYS X  73 "
           pdb=" SG  CYS X  73 "
           pdb=" SG  CYS X  97 "
           pdb=" CB  CYS X  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   14.03   78.97     1      1.00e+01 1.00e-02 7.76e+01
  dihedral pdb=" CB  CYS b 122 "
           pdb=" SG  CYS b 122 "
           pdb=" SG  CYS a 485 "
           pdb=" CB  CYS a 485 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  171.92  -78.92     1      1.00e+01 1.00e-02 7.76e+01
  dihedral pdb=" CB  CYS B 122 "
           pdb=" SG  CYS B 122 "
           pdb=" SG  CYS a 484 "
           pdb=" CB  CYS a 484 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.07  -75.07     1      1.00e+01 1.00e-02 7.13e+01
  ... (remaining 4125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 870
       0.056 -    0.111: 160
       0.111 -    0.167: 22
       0.167 -    0.223: 3
       0.223 -    0.278: 5
  Chirality restraints: 1060
  Sorted by residual:
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  PRO c  29 "
            pdb=" N   PRO c  29 "
            pdb=" C   PRO c  29 "
            pdb=" CB  PRO c  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 1057 not shown)

  Planarity restraints: 1135
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE c  28 "    0.089 5.00e-02 4.00e+02   1.24e-01 2.47e+01
        pdb=" N   PRO c  29 "   -0.214 5.00e-02 4.00e+02
        pdb=" CA  PRO c  29 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO c  29 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C   1 "   -0.059 5.00e-02 4.00e+02   8.78e-02 1.23e+01
        pdb=" N   PRO C   2 "    0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO C   2 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO C   2 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO X  51 "   -0.053 5.00e-02 4.00e+02   8.04e-02 1.04e+01
        pdb=" N   PRO X  52 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO X  52 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO X  52 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 1132 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1511
        2.79 -     3.32: 5736
        3.32 -     3.84: 10220
        3.84 -     4.37: 11281
        4.37 -     4.90: 19207
  Nonbonded interactions: 47955
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG c 102 "
            pdb=" OE2 GLU c 111 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" NH1 ARG c  67 "
            pdb=" OD2 ASP c  69 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" O   SER X 126 "
            pdb=" OG  SER X 126 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" NH1 ARG C  89 "
            pdb=" OD1 ASP E  86 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   CYS b 122 "
            pdb=" N   GLY b 124 "
     model   vdw
     2.330 3.120
  ... (remaining 47950 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'b'
}
ncs_group {
  reference = (chain 'C' and (resid 1 through 113 or resid 115 through 117))
  selection = (chain 'c' and (resid 1 through 113 or resid 115 through 117))
}
ncs_group {
  reference = chain 'E'
  selection = (chain 'X' and resid 1 through 125)
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.230
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.159   6482  Z= 0.198
  Angle     :  0.891  13.057   8942  Z= 0.421
  Chirality :  0.048   0.278   1060
  Planarity :  0.008   0.124   1129
  Dihedral  : 19.138 111.292   2556
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 32.97 %
    Favored  : 66.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

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: -1.77 (0.29), residues: 797
  helix: -1.26 (0.39), residues: 161
  sheet: -1.45 (0.69), residues: 68
  loop : -1.15 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG b  89 
 TYR   0.032   0.002   TYR a 492 
 PHE   0.008   0.001   PHE c  28 
 TRP   0.037   0.001   TRP b 123 
 HIS   0.002   0.001   HIS E  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 6442)
  covalent geometry    : angle       0.86553 ( 8848)
  SS BOND              : bond        0.00246 (   26)
  SS BOND              : angle       1.63006 (   52)
  hydrogen bonds       : bond        0.23842 (  149)
  hydrogen bonds       : angle       8.41223 (  351)
  link_BETA1-4         : bond        0.00334 (    8)
  link_BETA1-4         : angle       2.74733 (   24)
  link_NAG-ASN         : bond        0.00390 (    6)
  link_NAG-ASN         : angle       2.88739 (   18)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 131
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: b  113 ARG cc_start: 0.7548 (mtp85) cc_final: 0.7257 (mtp85)
  outliers start: 6
  outliers final: 2
  residues processed: 134
  average time/residue: 0.1958
  time to fit residues: 29.9295
Evaluate side-chains
  132 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0050
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0020
   chunk 74 optimal weight:    0.0870
   overall best weight:    0.2380

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

Flipped N/Q/H residues before XYZ refinement:
c  64 ASN
C  40 ASN
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 115 GLN
B  64 ASN
b  40 ASN
X 115 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.138888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.122891 restraints weight = 10183.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 2.54
r_work: 0.3467 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.0808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6482  Z= 0.136
  Angle     :  0.794   9.521   8942  Z= 0.360
  Chirality :  0.044   0.185   1060
  Planarity :  0.006   0.063   1129
  Dihedral  : 12.608  86.947   1177
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 29.98 %
    Favored  : 66.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

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: -1.34 (0.30), residues: 797
  helix: -0.12 (0.41), residues: 165
  sheet: -1.49 (0.67), residues: 68
  loop : -1.10 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  89 
 TYR   0.031   0.002   TYR a 492 
 PHE   0.004   0.001   PHE X  55 
 TRP   0.026   0.001   TRP b 123 
 HIS   0.003   0.001   HIS c  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6442)
  covalent geometry    : angle       0.77479 ( 8848)
  SS BOND              : bond        0.00218 (   26)
  SS BOND              : angle       1.19965 (   52)
  hydrogen bonds       : bond        0.05057 (  149)
  hydrogen bonds       : angle       5.75840 (  351)
  link_BETA1-4         : bond        0.00428 (    8)
  link_BETA1-4         : angle       2.64051 (   24)
  link_NAG-ASN         : bond        0.00411 (    6)
  link_NAG-ASN         : angle       2.14692 (   18)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ARG cc_start: 0.8200 (tpp-160) cc_final: 0.7995 (tpp80)
REVERT: E   21 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6756 (t70)
REVERT: b   76 ARG cc_start: 0.8161 (tpt90) cc_final: 0.7946 (tmt170)
REVERT: b  138 LEU cc_start: -0.2972 (OUTLIER) cc_final: -0.3450 (tp)
REVERT: X   62 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7888 (pt0)
  outliers start: 22
  outliers final: 9
  residues processed: 145
  average time/residue: 0.1891
  time to fit residues: 31.2648
Evaluate side-chains
  136 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue   12 VAL
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain b residue  138 LEU
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  112 THR
Chi-restraints excluded: chain X residue  115 GLN
Chi-restraints excluded: chain X residue  116 LEU
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 57 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0770
   chunk 48 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0570
   chunk 53 optimal weight:    0.3980
   chunk 35 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.3256

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 115 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.138305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.121939 restraints weight = 10098.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.52
r_work: 0.3464 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3314
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3314
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.1002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6482  Z= 0.144
  Angle     :  0.770   9.175   8942  Z= 0.348
  Chirality :  0.044   0.201   1060
  Planarity :  0.006   0.056   1129
  Dihedral  : 10.657  78.196   1176
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 30.61 %
    Favored  : 65.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

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: -1.26 (0.29), residues: 797
  helix:  0.23 (0.42), residues: 159
  sheet: -1.52 (0.66), residues: 68
  loop : -1.11 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  89 
 TYR   0.030   0.002   TYR a 492 
 PHE   0.004   0.001   PHE a 491 
 TRP   0.025   0.001   TRP b 123 
 HIS   0.002   0.000   HIS E  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6442)
  covalent geometry    : angle       0.74954 ( 8848)
  SS BOND              : bond        0.00222 (   26)
  SS BOND              : angle       1.20303 (   52)
  hydrogen bonds       : bond        0.04515 (  149)
  hydrogen bonds       : angle       5.43555 (  351)
  link_BETA1-4         : bond        0.00344 (    8)
  link_BETA1-4         : angle       2.66413 (   24)
  link_NAG-ASN         : bond        0.00362 (    6)
  link_NAG-ASN         : angle       2.21044 (   18)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   21 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7040 (t70)
REVERT: B   17 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7552 (mtm180)
REVERT: b   76 ARG cc_start: 0.8324 (tpt90) cc_final: 0.8104 (tmt170)
REVERT: b  138 LEU cc_start: -0.3139 (OUTLIER) cc_final: -0.3652 (tp)
REVERT: X  124 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.6876 (pp30)
  outliers start: 25
  outliers final: 10
  residues processed: 149
  average time/residue: 0.1737
  time to fit residues: 29.5928
Evaluate side-chains
  138 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain b residue  138 LEU
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 70 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** c  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.136484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.120113 restraints weight = 10213.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.54
r_work: 0.3432 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6482  Z= 0.206
  Angle     :  0.799   9.384   8942  Z= 0.360
  Chirality :  0.046   0.205   1060
  Planarity :  0.006   0.053   1129
  Dihedral  :  9.366  68.532   1176
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 29.36 %
    Favored  : 65.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

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: -1.29 (0.29), residues: 797
  helix: -0.01 (0.41), residues: 165
  sheet: -1.55 (0.66), residues: 68
  loop : -1.07 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  89 
 TYR   0.030   0.002   TYR a 492 
 PHE   0.005   0.001   PHE C  28 
 TRP   0.026   0.001   TRP b 123 
 HIS   0.003   0.001   HIS B  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 6442)
  covalent geometry    : angle       0.77849 ( 8848)
  SS BOND              : bond        0.00295 (   26)
  SS BOND              : angle       1.28699 (   52)
  hydrogen bonds       : bond        0.04623 (  149)
  hydrogen bonds       : angle       5.41647 (  351)
  link_BETA1-4         : bond        0.00256 (    8)
  link_BETA1-4         : angle       2.60298 (   24)
  link_NAG-ASN         : bond        0.00406 (    6)
  link_NAG-ASN         : angle       2.31528 (   18)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ARG cc_start: 0.8375 (tpp80) cc_final: 0.8138 (tpp-160)
REVERT: E   95 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7818 (t)
REVERT: b  138 LEU cc_start: -0.3023 (OUTLIER) cc_final: -0.3550 (tp)
REVERT: X  124 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6870 (pp30)
  outliers start: 31
  outliers final: 18
  residues processed: 153
  average time/residue: 0.1493
  time to fit residues: 26.3772
Evaluate side-chains
  147 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain b residue  138 LEU
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 18 optimal weight:    0.1980
   chunk 42 optimal weight:    0.0970
   chunk 29 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** c  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.136843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.120424 restraints weight = 10318.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.56
r_work: 0.3440 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6482  Z= 0.176
  Angle     :  0.781   9.272   8942  Z= 0.353
  Chirality :  0.045   0.221   1060
  Planarity :  0.006   0.050   1129
  Dihedral  :  8.159  56.248   1175
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 27.47 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

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: -1.29 (0.30), residues: 797
  helix:  0.23 (0.42), residues: 153
  sheet: -1.55 (0.67), residues: 68
  loop : -1.13 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  89 
 TYR   0.029   0.002   TYR a 492 
 PHE   0.006   0.001   PHE c  28 
 TRP   0.023   0.001   TRP B  78 
 HIS   0.003   0.001   HIS B  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 6442)
  covalent geometry    : angle       0.75943 ( 8848)
  SS BOND              : bond        0.00259 (   26)
  SS BOND              : angle       1.39427 (   52)
  hydrogen bonds       : bond        0.04219 (  149)
  hydrogen bonds       : angle       5.24855 (  351)
  link_BETA1-4         : bond        0.00297 (    8)
  link_BETA1-4         : angle       2.48106 (   24)
  link_NAG-ASN         : bond        0.00359 (    6)
  link_NAG-ASN         : angle       2.35369 (   18)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7946 (tpp-160)
REVERT: E   21 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7081 (t70)
REVERT: E   95 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7815 (t)
REVERT: B   72 LEU cc_start: 0.8763 (tt) cc_final: 0.8552 (tp)
REVERT: b   21 TRP cc_start: 0.8382 (OUTLIER) cc_final: 0.7916 (t-100)
REVERT: X   62 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8250 (pt0)
REVERT: X  124 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.6891 (pp30)
  outliers start: 39
  outliers final: 24
  residues processed: 153
  average time/residue: 0.1758
  time to fit residues: 30.9112
Evaluate side-chains
  155 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   15 THR
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   50 VAL
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  116 LEU
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 5 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
c  40 ASN
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  72 HIS
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.135388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.119170 restraints weight = 10257.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.53
r_work: 0.3417 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6482  Z= 0.235
  Angle     :  0.838  10.153   8942  Z= 0.377
  Chirality :  0.048   0.253   1060
  Planarity :  0.006   0.051   1129
  Dihedral  :  7.604  54.902   1175
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 28.57 %
    Favored  : 65.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

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: -1.45 (0.30), residues: 797
  helix: -0.13 (0.42), residues: 159
  sheet: -1.58 (0.68), residues: 68
  loop : -1.18 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  89 
 TYR   0.025   0.002   TYR a 492 
 PHE   0.006   0.001   PHE C  28 
 TRP   0.026   0.002   TRP B  78 
 HIS   0.004   0.001   HIS B  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 ( 6442)
  covalent geometry    : angle       0.81677 ( 8848)
  SS BOND              : bond        0.00364 (   26)
  SS BOND              : angle       1.60747 (   52)
  hydrogen bonds       : bond        0.04647 (  149)
  hydrogen bonds       : angle       5.43457 (  351)
  link_BETA1-4         : bond        0.00272 (    8)
  link_BETA1-4         : angle       2.40983 (   24)
  link_NAG-ASN         : bond        0.00447 (    6)
  link_NAG-ASN         : angle       2.42817 (   18)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 136
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c   76 ARG cc_start: 0.7719 (tpt170) cc_final: 0.7066 (tpt170)
REVERT: E   21 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7131 (t70)
REVERT: B   70 CYS cc_start: 0.7689 (t) cc_final: 0.7371 (t)
REVERT: b   21 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7945 (t-100)
REVERT: X   62 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8241 (pt0)
REVERT: X  124 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.6940 (pp30)
  outliers start: 38
  outliers final: 24
  residues processed: 163
  average time/residue: 0.1586
  time to fit residues: 30.0681
Evaluate side-chains
  159 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   15 THR
Chi-restraints excluded: chain X residue   18 LEU
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   50 VAL
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  110 ARG
Chi-restraints excluded: chain X residue  116 LEU
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 42 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9990
   chunk 2 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0980
   chunk 60 optimal weight:    0.0020
   chunk 20 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.2388

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.138092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.121652 restraints weight = 10141.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.54
r_work: 0.3455 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6482  Z= 0.129
  Angle     :  0.774   9.135   8942  Z= 0.350
  Chirality :  0.044   0.256   1060
  Planarity :  0.006   0.048   1129
  Dihedral  :  6.809  51.801   1175
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 29.20 %
    Favored  : 65.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

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: -1.38 (0.29), residues: 797
  helix:  0.15 (0.43), residues: 153
  sheet: -1.60 (0.67), residues: 68
  loop : -1.19 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  89 
 TYR   0.024   0.001   TYR a 492 
 PHE   0.004   0.001   PHE a 491 
 TRP   0.042   0.002   TRP a 498 
 HIS   0.001   0.000   HIS B  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6442)
  covalent geometry    : angle       0.75377 ( 8848)
  SS BOND              : bond        0.00211 (   26)
  SS BOND              : angle       1.36402 (   52)
  hydrogen bonds       : bond        0.03918 (  149)
  hydrogen bonds       : angle       5.30480 (  351)
  link_BETA1-4         : bond        0.00366 (    8)
  link_BETA1-4         : angle       2.32485 (   24)
  link_NAG-ASN         : bond        0.00372 (    6)
  link_NAG-ASN         : angle       2.45131 (   18)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ARG cc_start: 0.8299 (tpp80) cc_final: 0.8074 (tpp-160)
REVERT: E   21 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7001 (t70)
REVERT: b  113 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7315 (mtp85)
REVERT: X   62 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8238 (pt0)
REVERT: X  124 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7048 (pp30)
  outliers start: 34
  outliers final: 24
  residues processed: 149
  average time/residue: 0.1738
  time to fit residues: 29.7914
Evaluate side-chains
  151 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   15 THR
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   47 LEU
Chi-restraints excluded: chain X residue   50 VAL
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  110 ARG
Chi-restraints excluded: chain X residue  112 THR
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0670
   chunk 64 optimal weight:    0.6980
   chunk 20 optimal weight:    0.1980
   chunk 52 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.3518

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.137452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.121149 restraints weight = 10264.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.53
r_work: 0.3451 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3302
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3302
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6482  Z= 0.149
  Angle     :  0.786   9.318   8942  Z= 0.353
  Chirality :  0.045   0.287   1060
  Planarity :  0.006   0.048   1129
  Dihedral  :  6.400  46.805   1175
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 30.14 %
    Favored  : 65.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

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: -1.41 (0.29), residues: 797
  helix: -0.02 (0.41), residues: 159
  sheet: -1.54 (0.67), residues: 68
  loop : -1.18 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  89 
 TYR   0.026   0.001   TYR a 492 
 PHE   0.005   0.001   PHE c  28 
 TRP   0.034   0.002   TRP a 498 
 HIS   0.002   0.001   HIS B  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6442)
  covalent geometry    : angle       0.76653 ( 8848)
  SS BOND              : bond        0.00253 (   26)
  SS BOND              : angle       1.37073 (   52)
  hydrogen bonds       : bond        0.03911 (  149)
  hydrogen bonds       : angle       5.35633 (  351)
  link_BETA1-4         : bond        0.00318 (    8)
  link_BETA1-4         : angle       2.29620 (   24)
  link_NAG-ASN         : bond        0.00384 (    6)
  link_NAG-ASN         : angle       2.45226 (   18)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ARG cc_start: 0.8294 (tpp80) cc_final: 0.8070 (tpp-160)
REVERT: E   21 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6957 (t70)
REVERT: b   21 TRP cc_start: 0.8376 (OUTLIER) cc_final: 0.7950 (t-100)
REVERT: X   62 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8243 (pt0)
REVERT: X  124 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7060 (pp30)
  outliers start: 29
  outliers final: 23
  residues processed: 147
  average time/residue: 0.1605
  time to fit residues: 27.2558
Evaluate side-chains
  153 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   15 THR
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   47 LEU
Chi-restraints excluded: chain X residue   50 VAL
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  110 ARG
Chi-restraints excluded: chain X residue  112 THR
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0060
   chunk 53 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0870
   overall best weight:    0.4574

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.137390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.121597 restraints weight = 10318.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.53
r_work: 0.3451 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3298
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3298
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6482  Z= 0.173
  Angle     :  0.793   9.313   8942  Z= 0.357
  Chirality :  0.046   0.318   1060
  Planarity :  0.006   0.047   1129
  Dihedral  :  6.156  38.856   1175
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 29.36 %
    Favored  : 65.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

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: -1.40 (0.30), residues: 797
  helix: -0.02 (0.41), residues: 159
  sheet: -1.58 (0.66), residues: 68
  loop : -1.17 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  89 
 TYR   0.025   0.002   TYR a 492 
 PHE   0.006   0.001   PHE a 491 
 TRP   0.033   0.002   TRP a 498 
 HIS   0.002   0.001   HIS B  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 6442)
  covalent geometry    : angle       0.77098 ( 8848)
  SS BOND              : bond        0.00274 (   26)
  SS BOND              : angle       1.54556 (   52)
  hydrogen bonds       : bond        0.04056 (  149)
  hydrogen bonds       : angle       5.34606 (  351)
  link_BETA1-4         : bond        0.00289 (    8)
  link_BETA1-4         : angle       2.27882 (   24)
  link_NAG-ASN         : bond        0.00426 (    6)
  link_NAG-ASN         : angle       2.50436 (   18)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ARG cc_start: 0.8362 (tpp80) cc_final: 0.8137 (tpp-160)
REVERT: E   21 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6920 (t70)
REVERT: b   21 TRP cc_start: 0.8399 (OUTLIER) cc_final: 0.7955 (t-100)
REVERT: X   62 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8247 (pt0)
REVERT: X  124 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7029 (pp30)
  outliers start: 30
  outliers final: 25
  residues processed: 149
  average time/residue: 0.1699
  time to fit residues: 29.2481
Evaluate side-chains
  157 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   15 THR
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   18 LEU
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   47 LEU
Chi-restraints excluded: chain X residue   50 VAL
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  110 ARG
Chi-restraints excluded: chain X residue  112 THR
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.3980
   chunk 73 optimal weight:    0.0050
   chunk 19 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0270
   chunk 17 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0570
   chunk 10 optimal weight:    0.2980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.1570

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

Flipped N/Q/H residues before XYZ refinement:
c  40 ASN
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.139647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.123651 restraints weight = 10263.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.54
r_work: 0.3481 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3485
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6482  Z= 0.117
  Angle     :  0.762   9.201   8942  Z= 0.341
  Chirality :  0.043   0.299   1060
  Planarity :  0.006   0.046   1129
  Dihedral  :  5.572  37.584   1175
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 29.98 %
    Favored  : 65.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    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: -1.32 (0.30), residues: 797
  helix:  0.07 (0.41), residues: 165
  sheet: -1.68 (0.66), residues: 68
  loop : -1.11 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  89 
 TYR   0.024   0.001   TYR a 492 
 PHE   0.004   0.001   PHE a 491 
 TRP   0.027   0.001   TRP a 498 
 HIS   0.002   0.001   HIS B 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6442)
  covalent geometry    : angle       0.74093 ( 8848)
  SS BOND              : bond        0.00225 (   26)
  SS BOND              : angle       1.35187 (   52)
  hydrogen bonds       : bond        0.03480 (  149)
  hydrogen bonds       : angle       5.18483 (  351)
  link_BETA1-4         : bond        0.00356 (    8)
  link_BETA1-4         : angle       2.28159 (   24)
  link_NAG-ASN         : bond        0.00387 (    6)
  link_NAG-ASN         : angle       2.47635 (   18)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ARG cc_start: 0.8159 (tpp80) cc_final: 0.7934 (tpp-160)
REVERT: C   72 LEU cc_start: 0.8718 (tp) cc_final: 0.8269 (tp)
REVERT: E   21 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6580 (t70)
REVERT: b   21 TRP cc_start: 0.8289 (OUTLIER) cc_final: 0.7747 (t-100)
REVERT: X   62 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7969 (pt0)
REVERT: X  124 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6802 (pp30)
  outliers start: 29
  outliers final: 23
  residues processed: 144
  average time/residue: 0.1677
  time to fit residues: 27.7765
Evaluate side-chains
  146 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   15 THR
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   47 LEU
Chi-restraints excluded: chain X residue   50 VAL
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  110 ARG
Chi-restraints excluded: chain X residue  112 THR
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 42 optimal weight:    0.1980
   chunk 62 optimal weight:    0.0050
   chunk 35 optimal weight:    0.0070
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.3012

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.138811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.122808 restraints weight = 10266.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.54
r_work: 0.3471 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3320
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3320
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6482  Z= 0.136
  Angle     :  0.762   9.029   8942  Z= 0.341
  Chirality :  0.044   0.326   1060
  Planarity :  0.006   0.046   1129
  Dihedral  :  5.418  36.451   1175
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 30.46 %
    Favored  : 65.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    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: -1.29 (0.30), residues: 797
  helix:  0.14 (0.41), residues: 165
  sheet: -1.70 (0.66), residues: 68
  loop : -1.10 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  89 
 TYR   0.026   0.001   TYR a 492 
 PHE   0.005   0.001   PHE c  28 
 TRP   0.028   0.001   TRP a 498 
 HIS   0.002   0.000   HIS B 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6442)
  covalent geometry    : angle       0.74098 ( 8848)
  SS BOND              : bond        0.00218 (   26)
  SS BOND              : angle       1.36830 (   52)
  hydrogen bonds       : bond        0.03576 (  149)
  hydrogen bonds       : angle       5.14634 (  351)
  link_BETA1-4         : bond        0.00312 (    8)
  link_BETA1-4         : angle       2.23697 (   24)
  link_NAG-ASN         : bond        0.00408 (    6)
  link_NAG-ASN         : angle       2.52182 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2059.06 seconds
wall clock time: 35 minutes 41.02 seconds (2141.02 seconds total)