Starting phenix.real_space_refine
on Fri Aug 22 15:59:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fns_50609/08_2025/9fns_50609.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fns_50609/08_2025/9fns_50609.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fns_50609/08_2025/9fns_50609.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fns_50609/08_2025/9fns_50609.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fns_50609/08_2025/9fns_50609.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fns_50609/08_2025/9fns_50609.map"
  }
  resolution = 3.5
  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=   0.001 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    3500      2.51       5
     N     923      2.21       5
     O    1105      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  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: 5542
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1074
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1074
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 137}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1080
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 137}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 946
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 738
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "E"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 930
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "F"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 746
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.36, per 1000 atoms: 0.25
  Number of scatterers: 5542
  At special positions: 0
  Unit cell: (104.92, 79.98, 85.14, 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      14     16.00
     O    1105      8.00
     N     923      7.00
     C    3500      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 137 " - pdb=" SG  CYS D 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 137 " - pdb=" SG  CYS F 202 " distance=2.07

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1000 " - " ASN A 562 "
      " NAG B1000 " - " ASN B 562 "
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 199.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1330

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 19 sheets defined
      1.8% alpha, 39.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 515 through 518
    Processing helix  chain 'C' and resid 28 through 31
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.012A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 464 through 465
    Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 510
      removed outlier: 3.570A  pdb=" N   VAL A 579 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   SER A 582 " --> pdb=" O   GLN A 568 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   GLN A 568 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE A 569 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510
      removed outlier: 5.441A  pdb=" N   THR A 593 " --> pdb=" O   ALA A 477 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 547 through 548
      removed outlier: 4.420A  pdb=" N   PHE A 547 " --> pdb=" O   GLY A 556 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 464 through 465
    Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 510
    Processing sheet with id=AA7, first strand: chain 'B' and resid 478 through 481
      removed outlier: 3.895A  pdb=" N   ILE B 581 " --> pdb=" O   TYR B 493 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 547 through 548
      removed outlier: 4.492A  pdb=" N   PHE B 547 " --> pdb=" O   GLY B 556 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6
      removed outlier: 4.006A  pdb=" N   VAL C  18 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.725A  pdb=" N   THR C 115 " --> pdb=" O   TYR C  94 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TYR C  94 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER C  33 " --> pdb=" O   VAL C  99 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.725A  pdb=" N   THR C 115 " --> pdb=" O   TYR C  94 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TYR C  94 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   CYS C  96 " --> pdb=" O   TRP C 111 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   TRP C 111 " --> pdb=" O   CYS C  96 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ARG C  98 " --> pdb=" O   ASP C 109 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 124 through 126
    Processing sheet with id=AB4, first strand: chain 'D' and resid 133 through 138
    Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 6
      removed outlier: 3.988A  pdb=" N   VAL E  18 " --> pdb=" O   LEU E  83 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.571A  pdb=" N   THR E 118 " --> pdb=" O   GLU E  10 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR E 115 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR E  94 " --> pdb=" O   THR E 115 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER E  33 " --> pdb=" O   VAL E  99 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ILE E  34 " --> pdb=" O   TRP E  50 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   TRP E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   TRP E  36 " --> pdb=" O   MET E  48 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.571A  pdb=" N   THR E 118 " --> pdb=" O   GLU E  10 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR E 115 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR E  94 " --> pdb=" O   THR E 115 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   TYR E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   TRP E 100 " --> pdb=" O   GLY E 108 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   GLY E 108 " --> pdb=" O   TRP E 100 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 125 through 126
      removed outlier: 6.492A  pdb=" N   LEU F 125 " --> pdb=" O   GLU F 220 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'F' and resid 133 through 138
    Processing sheet with id=AC1, first strand: chain 'F' and resid 159 through 162
      removed outlier: 6.943A  pdb=" N   TRP F 149 " --> pdb=" O   LEU F 161 " (cutoff:3.500A)

    186 hydrogen bonds defined for protein.
    459 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: 0.75

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1060
        1.33 -     1.45: 1568
        1.45 -     1.57: 3026
        1.57 -     1.69: 0
        1.69 -     1.82: 20
  Bond restraints: 5674
  Sorted by residual:
  bond pdb=" CA  TYR A 584 "
       pdb=" C   TYR A 584 "
    ideal  model  delta    sigma   weight residual
    1.527  1.476  0.051 1.21e-02 6.83e+03 1.80e+01
  bond pdb=" N   VAL B 501 "
       pdb=" CA  VAL B 501 "
    ideal  model  delta    sigma   weight residual
    1.458  1.503 -0.045 1.08e-02 8.57e+03 1.72e+01
  bond pdb=" N   ILE F 162 "
       pdb=" CA  ILE F 162 "
    ideal  model  delta    sigma   weight residual
    1.456  1.498 -0.041 1.14e-02 7.69e+03 1.32e+01
  bond pdb=" N   VAL E  68 "
       pdb=" CA  VAL E  68 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.042 1.15e-02 7.56e+03 1.32e+01
  bond pdb=" CA  SER D 142 "
       pdb=" CB  SER D 142 "
    ideal  model  delta    sigma   weight residual
    1.528  1.482  0.046 1.35e-02 5.49e+03 1.18e+01
  ... (remaining 5669 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 6960
        2.53 -     5.06: 631
        5.06 -     7.59: 115
        7.59 -    10.12: 37
       10.12 -    12.65: 12
  Bond angle restraints: 7755
  Sorted by residual:
  angle pdb=" N   TYR A 561 "
        pdb=" CA  TYR A 561 "
        pdb=" C   TYR A 561 "
      ideal   model   delta    sigma   weight residual
     111.36  102.09    9.27 1.09e+00 8.42e-01 7.23e+01
  angle pdb=" C   ALA D 157 "
        pdb=" N   PRO D 158 "
        pdb=" CA  PRO D 158 "
      ideal   model   delta    sigma   weight residual
     119.92  128.79   -8.87 1.07e+00 8.73e-01 6.87e+01
  angle pdb=" N   LYS A 534 "
        pdb=" CA  LYS A 534 "
        pdb=" CB  LYS A 534 "
      ideal   model   delta    sigma   weight residual
     110.77   98.12   12.65 1.57e+00 4.06e-01 6.49e+01
  angle pdb=" N   THR A 564 "
        pdb=" CA  THR A 564 "
        pdb=" C   THR A 564 "
      ideal   model   delta    sigma   weight residual
     110.68   99.99   10.69 1.39e+00 5.18e-01 5.92e+01
  angle pdb=" N   GLN B 482 "
        pdb=" CA  GLN B 482 "
        pdb=" CB  GLN B 482 "
      ideal   model   delta    sigma   weight residual
     110.88  121.31  -10.43 1.38e+00 5.25e-01 5.71e+01
  ... (remaining 7750 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.26: 3011
       23.26 -    46.51: 201
       46.51 -    69.77: 63
       69.77 -    93.02: 12
       93.02 -   116.28: 6
  Dihedral angle restraints: 3293
    sinusoidal: 1198
      harmonic: 2095
  Sorted by residual:
  dihedral pdb=" CD  ARG E  67 "
           pdb=" NE  ARG E  67 "
           pdb=" CZ  ARG E  67 "
           pdb=" NH1 ARG E  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   78.05  -78.05     1      1.00e+01 1.00e-02 7.61e+01
  dihedral pdb=" CD  ARG B 512 "
           pdb=" NE  ARG B 512 "
           pdb=" CZ  ARG B 512 "
           pdb=" NH1 ARG B 512 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   70.23  -70.23     1      1.00e+01 1.00e-02 6.35e+01
  dihedral pdb=" N   GLN B 482 "
           pdb=" C   GLN B 482 "
           pdb=" CA  GLN B 482 "
           pdb=" CB  GLN B 482 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  140.55  -17.75     0      2.50e+00 1.60e-01 5.04e+01
  ... (remaining 3290 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.135: 780
       0.135 -    0.269: 96
       0.269 -    0.404: 17
       0.404 -    0.538: 3
       0.538 -    0.673: 1
  Chirality restraints: 897
  Sorted by residual:
  chirality pdb=" CA  GLN B 482 "
            pdb=" N   GLN B 482 "
            pdb=" C   GLN B 482 "
            pdb=" CB  GLN B 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.84    0.67 2.00e-01 2.50e+01 1.13e+01
  chirality pdb=" CA  SER A 533 "
            pdb=" N   SER A 533 "
            pdb=" C   SER A 533 "
            pdb=" CB  SER A 533 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.67e+00
  chirality pdb=" CA  ALA A 504 "
            pdb=" N   ALA A 504 "
            pdb=" C   ALA A 504 "
            pdb=" CB  ALA A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.04    0.44 2.00e-01 2.50e+01 4.88e+00
  ... (remaining 894 not shown)

  Planarity restraints: 976
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E  67 "    1.086 9.50e-02 1.11e+02   4.86e-01 1.43e+02
        pdb=" NE  ARG E  67 "   -0.065 2.00e-02 2.50e+03
        pdb=" CZ  ARG E  67 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG E  67 "    0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG E  67 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 512 "   -1.028 9.50e-02 1.11e+02   4.61e-01 1.28e+02
        pdb=" NE  ARG B 512 "    0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 512 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 512 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 512 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F 138 "    0.540 9.50e-02 1.11e+02   2.42e-01 3.58e+01
        pdb=" NE  ARG F 138 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG F 138 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG F 138 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG F 138 "    0.019 2.00e-02 2.50e+03
  ... (remaining 973 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 3
        2.19 -     2.86: 2167
        2.86 -     3.54: 6482
        3.54 -     4.22: 11633
        4.22 -     4.90: 20816
  Nonbonded interactions: 41101
  Sorted by model distance:
  nonbonded pdb=" O   SER C   7 "
            pdb=" CG2 THR C 115 "
     model   vdw
     1.508 3.460
  nonbonded pdb=" O   ASP B 515 "
            pdb=" OD1 ASP B 515 "
     model   vdw
     1.546 3.040
  nonbonded pdb=" OG1 THR A 476 "
            pdb=" OG1 THR A 497 "
     model   vdw
     2.086 3.040
  nonbonded pdb=" CG  ARG B 466 "
            pdb=" OD2 ASP B 469 "
     model   vdw
     2.210 3.440
  nonbonded pdb=" O   PRO D 122 "
            pdb=" OG1 THR D 217 "
     model   vdw
     2.238 3.040
  ... (remaining 41096 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 'B' and (resid 461 through 465 or (resid 466 through 467 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 468 through 1000))
}
ncs_group {
  reference = (chain 'C' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 2 through 9 or (resid 10 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 11 or (resid 12 through 13 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 14 through 120))
  selection = (chain 'E' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 20 through 120))
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'F' and (resid 122 through 217 or (resid 218 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 219 or (resid 220 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 221))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.570
  Find NCS groups from input model:        0.090
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
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      :  0.009   0.060   5680  Z= 0.632
  Angle     :  1.648  13.174   7769  Z= 1.096
  Chirality :  0.100   0.673    897
  Planarity :  0.024   0.486    974
  Dihedral  : 18.272 116.280   1951
  Min Nonbonded Distance : 1.508

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.52 %
    Favored  : 97.34 %
  Rotamer:
    Outliers : 11.00 %
    Allowed  : 11.00 %
    Favored  : 78.00 %
  Cbeta Deviations :  2.71 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.07 (0.29), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.99 (0.27), residues: 335
  loop : -1.70 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 175 
 TYR   0.025   0.002   TYR A 557 
 PHE   0.021   0.002   PHE B 547 
 TRP   0.012   0.001   TRP C 100 
 HIS   0.006   0.001   HIS A 602 

Details of bonding type rmsd
  covalent geometry    : bond        0.00875 ( 5674)
  covalent geometry    : angle       1.64024 ( 7755)
  SS BOND              : bond        0.01948 (    4)
  SS BOND              : angle       1.46575 (    8)
  hydrogen bonds       : bond        0.28678 (  173)
  hydrogen bonds       : angle       9.83644 (  459)
  link_NAG-ASN         : bond        0.01127 (    2)
  link_NAG-ASN         : angle       6.08992 (    6)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 106
  time to evaluate  : 0.128 
Fit side-chains
REVERT: B  487 SER cc_start: 0.9440 (OUTLIER) cc_final: 0.9045 (p)
REVERT: B  490 ASN cc_start: 0.8137 (m-40) cc_final: 0.7754 (t0)
REVERT: C   78 THR cc_start: 0.8480 (p) cc_final: 0.8203 (p)
REVERT: E   65 GLN cc_start: 0.8310 (tp-100) cc_final: 0.8099 (tp-100)
REVERT: E   78 THR cc_start: 0.8487 (p) cc_final: 0.8247 (p)
REVERT: F  204 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8798 (tm-30)
  outliers start: 65
  outliers final: 31
  residues processed: 153
  average time/residue: 0.0814
  time to fit residues: 15.6201
Evaluate side-chains
  135 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  557 TYR
Chi-restraints excluded: chain B residue  560 ASN
Chi-restraints excluded: chain B residue  563 THR
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  107 ARG
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  107 ARG
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  162 ILE
Chi-restraints excluded: chain F residue  166 SER
Chi-restraints excluded: chain F residue  168 LEU
Chi-restraints excluded: chain F residue  202 CYS
Chi-restraints excluded: chain F residue  204 GLN
Chi-restraints excluded: chain F residue  213 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0170
   chunk 62 optimal weight:    0.0010
   chunk 51 optimal weight:    0.0030
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0570
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.1552

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

Flipped N/Q/H residues before XYZ refinement:
A 602 HIS
C  62 GLN
C  65 GLN
C 113 GLN
E 106 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.130202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.105404 restraints weight = 8201.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.109173 restraints weight = 4115.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.111653 restraints weight = 2704.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.113147 restraints weight = 2071.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.114291 restraints weight = 1749.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5680  Z= 0.099
  Angle     :  0.560   8.877   7769  Z= 0.289
  Chirality :  0.044   0.240    897
  Planarity :  0.004   0.055    974
  Dihedral  :  8.813  83.595    890
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.82 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 12.01 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.30), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.37 (0.27), residues: 347
  loop : -1.23 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  67 
 TYR   0.013   0.001   TYR E  54 
 PHE   0.014   0.001   PHE B 500 
 TRP   0.013   0.001   TRP E 100 
 HIS   0.005   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 5674)
  covalent geometry    : angle       0.55860 ( 7755)
  SS BOND              : bond        0.00468 (    4)
  SS BOND              : angle       0.63859 (    8)
  hydrogen bonds       : bond        0.03602 (  173)
  hydrogen bonds       : angle       6.52032 (  459)
  link_NAG-ASN         : bond        0.00254 (    2)
  link_NAG-ASN         : angle       1.66305 (    6)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 98
  time to evaluate  : 0.128 
Fit side-chains
REVERT: B  487 SER cc_start: 0.9253 (OUTLIER) cc_final: 0.8936 (p)
REVERT: C   65 GLN cc_start: 0.8311 (tp40) cc_final: 0.7654 (tt0)
REVERT: C   78 THR cc_start: 0.8126 (p) cc_final: 0.7787 (p)
REVERT: D  125 LEU cc_start: 0.7767 (mp) cc_final: 0.7408 (mt)
REVERT: E   19 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8006 (ttm-80)
REVERT: E   65 GLN cc_start: 0.8332 (tp-100) cc_final: 0.8103 (tp-100)
REVERT: E   78 THR cc_start: 0.8061 (p) cc_final: 0.7790 (p)
REVERT: E   89 ASP cc_start: 0.8130 (t0) cc_final: 0.7925 (t0)
REVERT: F  204 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8743 (tm-30)
  outliers start: 31
  outliers final: 18
  residues processed: 122
  average time/residue: 0.0684
  time to fit residues: 10.8365
Evaluate side-chains
  107 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  563 THR
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  162 ILE
Chi-restraints excluded: chain F residue  204 GLN
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 68 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 602 HIS
B 530 GLN
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 204 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.116383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.091518 restraints weight = 8318.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.094874 restraints weight = 4213.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.097059 restraints weight = 2843.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.098513 restraints weight = 2228.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.099312 restraints weight = 1903.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   5680  Z= 0.251
  Angle     :  0.677   8.432   7769  Z= 0.362
  Chirality :  0.048   0.154    897
  Planarity :  0.005   0.051    974
  Dihedral  :  7.532  83.133    852
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 12.18 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.30), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.50 (0.26), residues: 365
  loop : -1.39 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  77 
 TYR   0.020   0.002   TYR A 561 
 PHE   0.019   0.002   PHE B 500 
 TRP   0.012   0.002   TRP E  50 
 HIS   0.008   0.003   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 5674)
  covalent geometry    : angle       0.67482 ( 7755)
  SS BOND              : bond        0.01009 (    4)
  SS BOND              : angle       1.67034 (    8)
  hydrogen bonds       : bond        0.04804 (  173)
  hydrogen bonds       : angle       6.32161 (  459)
  link_NAG-ASN         : bond        0.00731 (    2)
  link_NAG-ASN         : angle       1.09287 (    6)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 82
  time to evaluate  : 0.212 
Fit side-chains
REVERT: C  109 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8185 (m-30)
REVERT: D  159 LYS cc_start: 0.8533 (tttt) cc_final: 0.8086 (ttpt)
REVERT: F  175 ARG cc_start: 0.7349 (ptt-90) cc_final: 0.6978 (ptt-90)
REVERT: F  204 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8757 (tm-30)
  outliers start: 32
  outliers final: 21
  residues processed: 107
  average time/residue: 0.0833
  time to fit residues: 11.4080
Evaluate side-chains
  98 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  520 THR
Chi-restraints excluded: chain B residue  563 THR
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  109 ASP
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  162 ILE
Chi-restraints excluded: chain F residue  204 GLN
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 49 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0570
   chunk 26 optimal weight:    2.9990
   chunk 39 optimal weight:    0.3980
   overall best weight:    0.5100

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN
E  65 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.123083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.097694 restraints weight = 8311.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.101283 restraints weight = 4178.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.103615 restraints weight = 2781.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.105151 restraints weight = 2152.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.106177 restraints weight = 1831.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5680  Z= 0.088
  Angle     :  0.499   8.554   7769  Z= 0.261
  Chirality :  0.043   0.166    897
  Planarity :  0.004   0.045    974
  Dihedral  :  6.184  83.648    849
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.72 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.30), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.21 (0.26), residues: 360
  loop : -1.26 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 175 
 TYR   0.016   0.001   TYR E  54 
 PHE   0.012   0.001   PHE B 547 
 TRP   0.016   0.001   TRP E 100 
 HIS   0.003   0.001   HIS A 577 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 5674)
  covalent geometry    : angle       0.49878 ( 7755)
  SS BOND              : bond        0.00480 (    4)
  SS BOND              : angle       0.72186 (    8)
  hydrogen bonds       : bond        0.02998 (  173)
  hydrogen bonds       : angle       5.64334 (  459)
  link_NAG-ASN         : bond        0.00088 (    2)
  link_NAG-ASN         : angle       0.71697 (    6)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.126 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8444 (tttt) cc_final: 0.7994 (ttpt)
REVERT: E   60 TYR cc_start: 0.8969 (m-80) cc_final: 0.8712 (m-80)
  outliers start: 22
  outliers final: 17
  residues processed: 102
  average time/residue: 0.0794
  time to fit residues: 10.3188
Evaluate side-chains
  92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 39 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 25 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN
E  65 GLN
F 204 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.118426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.093091 restraints weight = 8567.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.096562 restraints weight = 4250.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.098847 restraints weight = 2826.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.100254 restraints weight = 2197.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.101185 restraints weight = 1875.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5680  Z= 0.164
  Angle     :  0.554   8.253   7769  Z= 0.295
  Chirality :  0.044   0.145    897
  Planarity :  0.004   0.044    974
  Dihedral  :  5.311  45.950    842
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 16.24 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.30), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.24 (0.27), residues: 367
  loop : -1.34 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 175 
 TYR   0.014   0.002   TYR B 537 
 PHE   0.015   0.002   PHE B 547 
 TRP   0.011   0.001   TRP C 100 
 HIS   0.003   0.001   HIS F 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 5674)
  covalent geometry    : angle       0.55249 ( 7755)
  SS BOND              : bond        0.00740 (    4)
  SS BOND              : angle       1.33268 (    8)
  hydrogen bonds       : bond        0.03767 (  173)
  hydrogen bonds       : angle       5.68521 (  459)
  link_NAG-ASN         : bond        0.00340 (    2)
  link_NAG-ASN         : angle       0.75975 (    6)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.193 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8469 (tttt) cc_final: 0.7972 (ttpt)
  outliers start: 26
  outliers final: 21
  residues processed: 94
  average time/residue: 0.0775
  time to fit residues: 9.2731
Evaluate side-chains
  96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 69 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
E  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.118421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.093191 restraints weight = 8393.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.096608 restraints weight = 4211.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.098840 restraints weight = 2815.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.100259 restraints weight = 2195.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.101213 restraints weight = 1874.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5680  Z= 0.151
  Angle     :  0.537   8.025   7769  Z= 0.286
  Chirality :  0.044   0.150    897
  Planarity :  0.004   0.043    974
  Dihedral  :  5.144  43.056    841
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 16.92 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.30), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.17 (0.27), residues: 369
  loop : -1.42 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 175 
 TYR   0.014   0.001   TYR E  54 
 PHE   0.015   0.002   PHE B 547 
 TRP   0.011   0.001   TRP E 100 
 HIS   0.004   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5674)
  covalent geometry    : angle       0.53628 ( 7755)
  SS BOND              : bond        0.00691 (    4)
  SS BOND              : angle       1.16470 (    8)
  hydrogen bonds       : bond        0.03558 (  173)
  hydrogen bonds       : angle       5.62613 (  459)
  link_NAG-ASN         : bond        0.00250 (    2)
  link_NAG-ASN         : angle       0.73008 (    6)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 72
  time to evaluate  : 0.149 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8508 (tttt) cc_final: 0.8009 (ttpt)
  outliers start: 31
  outliers final: 25
  residues processed: 96
  average time/residue: 0.0711
  time to fit residues: 8.8248
Evaluate side-chains
  96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0020
   chunk 1 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.121456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.096299 restraints weight = 8509.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.099734 restraints weight = 4274.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.101828 restraints weight = 2858.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.103451 restraints weight = 2246.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.104343 restraints weight = 1904.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5680  Z= 0.098
  Angle     :  0.482   8.246   7769  Z= 0.252
  Chirality :  0.042   0.148    897
  Planarity :  0.004   0.042    974
  Dihedral  :  4.738  38.422    841
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.38 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.78 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.30), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.03 (0.27), residues: 365
  loop : -1.35 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 175 
 TYR   0.013   0.001   TYR E  54 
 PHE   0.012   0.001   PHE B 547 
 TRP   0.014   0.001   TRP E 100 
 HIS   0.004   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 5674)
  covalent geometry    : angle       0.48098 ( 7755)
  SS BOND              : bond        0.00511 (    4)
  SS BOND              : angle       0.79401 (    8)
  hydrogen bonds       : bond        0.02924 (  173)
  hydrogen bonds       : angle       5.30184 (  459)
  link_NAG-ASN         : bond        0.00078 (    2)
  link_NAG-ASN         : angle       0.73585 (    6)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.207 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8507 (tttt) cc_final: 0.8017 (ttpt)
  outliers start: 21
  outliers final: 19
  residues processed: 92
  average time/residue: 0.0863
  time to fit residues: 10.1585
Evaluate side-chains
  92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0980
   chunk 56 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN
C 113 GLN
** D 163 HIS ** 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 = 0.3311 r_free = 0.3311 target = 0.121551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.096302 restraints weight = 8389.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.099732 restraints weight = 4195.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.102036 restraints weight = 2809.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.103400 restraints weight = 2186.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.104498 restraints weight = 1872.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5680  Z= 0.097
  Angle     :  0.485   8.359   7769  Z= 0.255
  Chirality :  0.042   0.146    897
  Planarity :  0.004   0.042    974
  Dihedral  :  4.659  35.284    841
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.66 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 17.94 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.31), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.09 (0.27), residues: 369
  loop : -1.25 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 175 
 TYR   0.013   0.001   TYR E  54 
 PHE   0.011   0.001   PHE B 547 
 TRP   0.009   0.001   TRP E 100 
 HIS   0.003   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 5674)
  covalent geometry    : angle       0.48439 ( 7755)
  SS BOND              : bond        0.00527 (    4)
  SS BOND              : angle       0.83963 (    8)
  hydrogen bonds       : bond        0.02875 (  173)
  hydrogen bonds       : angle       5.23053 (  459)
  link_NAG-ASN         : bond        0.00055 (    2)
  link_NAG-ASN         : angle       0.74948 (    6)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  554 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8322 (mtmm)
REVERT: C  109 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.7994 (m-30)
REVERT: D  159 LYS cc_start: 0.8537 (tttt) cc_final: 0.8037 (ttpt)
  outliers start: 28
  outliers final: 25
  residues processed: 94
  average time/residue: 0.0780
  time to fit residues: 9.3518
Evaluate side-chains
  99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  109 ASP
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:    0.0040
   chunk 49 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.1798

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

Flipped N/Q/H residues before XYZ refinement:
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.119242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.094016 restraints weight = 8501.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.097440 restraints weight = 4251.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.099510 restraints weight = 2837.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.101085 restraints weight = 2226.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.101966 restraints weight = 1893.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5680  Z= 0.136
  Angle     :  0.522   8.095   7769  Z= 0.276
  Chirality :  0.043   0.147    897
  Planarity :  0.004   0.041    974
  Dihedral  :  4.817  34.739    841
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.22 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 18.78 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.31), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.26 (0.28), residues: 355
  loop : -1.40 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 175 
 TYR   0.014   0.001   TYR E  60 
 PHE   0.014   0.002   PHE B 547 
 TRP   0.009   0.001   TRP E 100 
 HIS   0.004   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 5674)
  covalent geometry    : angle       0.52059 ( 7755)
  SS BOND              : bond        0.00646 (    4)
  SS BOND              : angle       1.09976 (    8)
  hydrogen bonds       : bond        0.03307 (  173)
  hydrogen bonds       : angle       5.34579 (  459)
  link_NAG-ASN         : bond        0.00209 (    2)
  link_NAG-ASN         : angle       0.73203 (    6)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 73
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  554 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8345 (mtmm)
REVERT: D  159 LYS cc_start: 0.8545 (tttt) cc_final: 0.8017 (ttpt)
REVERT: D  175 ARG cc_start: 0.7349 (ptt-90) cc_final: 0.7068 (ptt-90)
  outliers start: 29
  outliers final: 23
  residues processed: 95
  average time/residue: 0.0772
  time to fit residues: 9.4911
Evaluate side-chains
  93 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   chunk 47 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN
C 106 ASN
** D 163 HIS ** 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 = 0.3306 r_free = 0.3306 target = 0.121230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.096213 restraints weight = 8493.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.099637 restraints weight = 4275.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.101831 restraints weight = 2861.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.103320 restraints weight = 2232.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.104242 restraints weight = 1901.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5680  Z= 0.098
  Angle     :  0.487   8.198   7769  Z= 0.256
  Chirality :  0.042   0.146    897
  Planarity :  0.004   0.041    974
  Dihedral  :  4.620  32.580    841
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.80 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 19.97 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.31), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.33 (0.28), residues: 355
  loop : -1.38 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 175 
 TYR   0.012   0.001   TYR E  54 
 PHE   0.012   0.001   PHE B 547 
 TRP   0.013   0.001   TRP E 100 
 HIS   0.004   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 5674)
  covalent geometry    : angle       0.48636 ( 7755)
  SS BOND              : bond        0.00508 (    4)
  SS BOND              : angle       0.80450 (    8)
  hydrogen bonds       : bond        0.02866 (  173)
  hydrogen bonds       : angle       5.22490 (  459)
  link_NAG-ASN         : bond        0.00062 (    2)
  link_NAG-ASN         : angle       0.74411 (    6)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  554 LYS cc_start: 0.8547 (mtmt) cc_final: 0.8318 (mtmm)
REVERT: C  109 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8005 (m-30)
REVERT: D  159 LYS cc_start: 0.8524 (tttt) cc_final: 0.7990 (ttpt)
REVERT: D  175 ARG cc_start: 0.7316 (ptt-90) cc_final: 0.7029 (ptt-90)
  outliers start: 24
  outliers final: 21
  residues processed: 92
  average time/residue: 0.0854
  time to fit residues: 9.9614
Evaluate side-chains
  95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  109 ASP
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 45 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 7 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.119656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.094512 restraints weight = 8452.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.097869 restraints weight = 4221.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.100116 restraints weight = 2829.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.101430 restraints weight = 2202.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.102360 restraints weight = 1892.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5680  Z= 0.124
  Angle     :  0.514   8.072   7769  Z= 0.272
  Chirality :  0.043   0.149    897
  Planarity :  0.004   0.041    974
  Dihedral  :  4.513  32.509    838
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.92 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 20.14 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.77 (0.31), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.33 (0.28), residues: 355
  loop : -1.41 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 175 
 TYR   0.012   0.001   TYR E  60 
 PHE   0.013   0.001   PHE B 547 
 TRP   0.010   0.001   TRP E 100 
 HIS   0.004   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5674)
  covalent geometry    : angle       0.51325 ( 7755)
  SS BOND              : bond        0.00625 (    4)
  SS BOND              : angle       1.05224 (    8)
  hydrogen bonds       : bond        0.03203 (  173)
  hydrogen bonds       : angle       5.32740 (  459)
  link_NAG-ASN         : bond        0.00148 (    2)
  link_NAG-ASN         : angle       0.75031 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 997.30 seconds
wall clock time: 17 minutes 46.91 seconds (1066.91 seconds total)