Starting phenix.real_space_refine
on Fri Oct 10 13:14:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qq0_18571/10_2025/8qq0_18571.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qq0_18571/10_2025/8qq0_18571.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qq0_18571/10_2025/8qq0_18571.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qq0_18571/10_2025/8qq0_18571.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qq0_18571/10_2025/8qq0_18571.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qq0_18571/10_2025/8qq0_18571.cif"
  }
  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=  -0.000 sd=   1.000
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      23      5.16       5
     C    3632      2.51       5
     N     920      2.21       5
     O    1102      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5677
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 484, 3751
          Classifications: {'peptide': 484}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 28, 'TRANS': 455}
          Chain breaks: 8
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 118
          Unresolved non-hydrogen angles: 139
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 70
    Chain: "D"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 814
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "E"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 928
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "a"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "c"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "e"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "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
  Time building chain proxies: 1.63, per 1000 atoms: 0.29
  Number of scatterers: 5677
  At special positions: 0
  Unit cell: (62.4, 88.14, 150.54, 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      23     16.00
     O    1102      8.00
     N     920      7.00
     C    3632      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  90 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG a   1 " - " NAG a   2 "
      " NAG c   1 " - " NAG c   2 "
      " NAG e   1 " - " NAG e   2 "
    BETA1-6
      " NAG F   1 " - " FUC F   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
      " NAG c   1 " - " FUC c   3 "
      " NAG e   1 " - " FUC e   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 122 "
      " NAG F   1 " - " ASN A 331 "
      " NAG a   1 " - " ASN A 282 "
      " NAG c   1 " - " ASN A 343 "
      " NAG e   1 " - " ASN E  59 "
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 225.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1320

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 15 sheets defined
      5.3% alpha, 32.2% 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 294 through 304
      removed outlier: 3.539A  pdb=" N   GLU A 298 " --> pdb=" O   ASP A 294 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR A 299 " --> pdb=" O   PRO A 295 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
      removed outlier: 3.563A  pdb=" N   PHE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ASN A 343 " --> pdb=" O   GLY A 339 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 338 through 343'
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 4.105A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 5.276A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.636A  pdb=" N   ASP E  31 " --> pdb=" O   THR E  28 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   HIS E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 28 through 32'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.720A  pdb=" N   ASP E  90 " --> pdb=" O   ARG E  87 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 91'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31
      removed outlier: 4.222A  pdb=" N   ALA A  27 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   TRP A  64 " --> pdb=" O   ALA A  27 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER A  31 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   SER A  60 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
      removed outlier: 9.541A  pdb=" N   HIS A 207 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
      removed outlier: 9.801A  pdb=" N   LEU A 223 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55
      removed outlier: 4.049A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.963A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   VAL A 130 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   PHE A 168 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135
      removed outlier: 7.044A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326
      removed outlier: 3.508A  pdb=" N   ILE A 326 " --> pdb=" O   ASN A 540 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   PHE A 543 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 355
      removed outlier: 4.116A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER A 514 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392
    Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453
    Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 12
      removed outlier: 3.770A  pdb=" N   ALA D  86 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE D  50 " --> pdb=" O   TRP D  37 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   GLN D  39 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   LEU D  48 " --> pdb=" O   GLN D  39 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 9 through 12
      removed outlier: 3.770A  pdb=" N   ALA D  86 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 17 through 18
    Processing sheet with id=AB4, first strand: chain 'D' and resid 17 through 18
    Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 6
    Processing sheet with id=AB6, first strand: chain 'E' and resid 58 through 60
      removed outlier: 3.601A  pdb=" N   ASN E  59 " --> pdb=" O   TRP E  50 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   TRP E  36 " --> pdb=" O   MET E  48 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   TRP E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ILE E  34 " --> pdb=" O   TRP E  50 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL E  37 " --> pdb=" O   TYR E  95 " (cutoff:3.500A)

    156 hydrogen bonds defined for protein.
    390 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: 0.82

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1757
        1.34 -     1.46: 1555
        1.46 -     1.58: 2482
        1.58 -     1.70: 0
        1.70 -     1.82: 26
  Bond restraints: 5820
  Sorted by residual:
  bond pdb=" C5  FUC F   3 "
       pdb=" O5  FUC F   3 "
    ideal  model  delta    sigma   weight residual
    1.423  1.459 -0.036 2.00e-02 2.50e+03 3.20e+00
  bond pdb=" C1  NAG c   2 "
       pdb=" O5  NAG c   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.00e+00
  bond pdb=" C1  NAG a   2 "
       pdb=" O5  NAG a   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.54e+00
  bond pdb=" C1  FUC F   3 "
       pdb=" O5  FUC F   3 "
    ideal  model  delta    sigma   weight residual
    1.400  1.431 -0.031 2.00e-02 2.50e+03 2.36e+00
  bond pdb=" CG  LEU A 223 "
       pdb=" CD2 LEU A 223 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.17e+00
  ... (remaining 5815 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 7443
        1.44 -     2.87: 387
        2.87 -     4.31: 74
        4.31 -     5.75: 25
        5.75 -     7.19: 6
  Bond angle restraints: 7935
  Sorted by residual:
  angle pdb=" CB  LYS E  13 "
        pdb=" CG  LYS E  13 "
        pdb=" CD  LYS E  13 "
      ideal   model   delta    sigma   weight residual
     111.30  118.49   -7.19 2.30e+00 1.89e-01 9.76e+00
  angle pdb=" N   VAL D  53 "
        pdb=" CA  VAL D  53 "
        pdb=" C   VAL D  53 "
      ideal   model   delta    sigma   weight residual
     109.34  115.48   -6.14 2.08e+00 2.31e-01 8.71e+00
  angle pdb=" C   GLU D  52 "
        pdb=" N   VAL D  53 "
        pdb=" CA  VAL D  53 "
      ideal   model   delta    sigma   weight residual
     121.97  127.14   -5.17 1.80e+00 3.09e-01 8.24e+00
  angle pdb=" C   VAL D  53 "
        pdb=" N   THR D  54 "
        pdb=" CA  THR D  54 "
      ideal   model   delta    sigma   weight residual
     122.26  117.72    4.54 1.59e+00 3.96e-01 8.15e+00
  angle pdb=" C   GLY A  89 "
        pdb=" N   VAL A  90 "
        pdb=" CA  VAL A  90 "
      ideal   model   delta    sigma   weight residual
     122.25  118.03    4.22 1.57e+00 4.06e-01 7.22e+00
  ... (remaining 7930 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.88: 3285
       23.88 -    47.76: 183
       47.76 -    71.64: 44
       71.64 -    95.52: 31
       95.52 -   119.40: 20
  Dihedral angle restraints: 3563
    sinusoidal: 1498
      harmonic: 2065
  Sorted by residual:
  dihedral pdb=" CA  GLU D  52 "
           pdb=" C   GLU D  52 "
           pdb=" N   VAL D  53 "
           pdb=" CA  VAL D  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -132.68  -47.32     0      5.00e+00 4.00e-02 8.96e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.03   85.03     1      1.00e+01 1.00e-02 8.77e+01
  dihedral pdb=" CB  CYS A 291 "
           pdb=" SG  CYS A 291 "
           pdb=" SG  CYS A 301 "
           pdb=" CB  CYS A 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.71  -65.71     1      1.00e+01 1.00e-02 5.65e+01
  ... (remaining 3560 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 603
       0.042 -    0.084: 217
       0.084 -    0.126: 82
       0.126 -    0.168: 16
       0.168 -    0.210: 5
  Chirality restraints: 923
  Sorted by residual:
  chirality pdb=" C4  NAG e   2 "
            pdb=" C3  NAG e   2 "
            pdb=" C5  NAG e   2 "
            pdb=" O4  NAG e   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.32   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CB  THR E 119 "
            pdb=" CA  THR E 119 "
            pdb=" OG1 THR E 119 "
            pdb=" CG2 THR E 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 9.73e-01
  chirality pdb=" C4  NAG A1301 "
            pdb=" C3  NAG A1301 "
            pdb=" C5  NAG A1301 "
            pdb=" O4  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.34   -0.20 2.00e-01 2.50e+01 9.58e-01
  ... (remaining 920 not shown)

  Planarity restraints: 1004
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 216 "    0.038 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO A 217 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 217 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 217 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "   -0.030 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO A 463 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D  45 "   -0.028 5.00e-02 4.00e+02   4.25e-02 2.89e+00
        pdb=" N   PRO D  46 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO D  46 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D  46 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1001 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 237
        2.71 -     3.26: 5083
        3.26 -     3.80: 7599
        3.80 -     4.35: 9611
        4.35 -     4.90: 17645
  Nonbonded interactions: 40175
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  11 "
            pdb=" OG1 THR D 108 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" O   CYS A 291 "
            pdb=" N   ALA A 292 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" NH1 ARG A 457 "
            pdb=" O   SER A 459 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" NH1 ARG D  56 "
            pdb=" O   VAL D  60 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   SER D  65 "
            pdb=" OG1 THR D  76 "
     model   vdw
     2.258 3.040
  ... (remaining 40170 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 'B'
  selection = chain 'a'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'c'
  selection = chain 'e'
}

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:             12.490
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.210
  Find NCS groups from input model:        0.020
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5841  Z= 0.234
  Angle     :  0.803   7.187   7990  Z= 0.407
  Chirality :  0.051   0.210    923
  Planarity :  0.005   0.058    999
  Dihedral  : 20.439 119.400   2219
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.67 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -3.12 (0.28), residues: 693
  helix: -4.03 (0.73), residues: 26
  sheet: -0.62 (0.35), residues: 233
  loop : -2.97 (0.23), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 355 
 TYR   0.022   0.002   TYR A 266 
 PHE   0.015   0.002   PHE A 238 
 TRP   0.014   0.002   TRP E  50 
 HIS   0.005   0.002   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 ( 5820)
  covalent geometry    : angle       0.78612 ( 7935)
  SS BOND              : bond        0.00408 (    8)
  SS BOND              : angle       1.63575 (   16)
  hydrogen bonds       : bond        0.17364 (  148)
  hydrogen bonds       : angle       6.97682 (  390)
  link_BETA1-4         : bond        0.00839 (    5)
  link_BETA1-4         : angle       2.21944 (   15)
  link_BETA1-6         : bond        0.00623 (    3)
  link_BETA1-6         : angle       1.70455 (    9)
  link_NAG-ASN         : bond        0.00198 (    5)
  link_NAG-ASN         : angle       2.63049 (   15)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.146 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0784
  time to fit residues: 7.0117
Evaluate side-chains
  55 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    0.0570
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0000
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.2902

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

Flipped N/Q/H residues before XYZ refinement:
A 125 ASN
E 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.162280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.139668 restraints weight = 7510.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.138873 restraints weight = 10258.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.139699 restraints weight = 10540.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.139717 restraints weight = 7795.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.139271 restraints weight = 8702.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.0875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5841  Z= 0.124
  Angle     :  0.708   7.959   7990  Z= 0.335
  Chirality :  0.047   0.206    923
  Planarity :  0.004   0.043    999
  Dihedral  : 16.351 102.785   1052
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.20 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  7.82 %
    Favored  : 91.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.82 (0.28), residues: 693
  helix: -3.49 (0.71), residues: 28
  sheet: -0.32 (0.35), residues: 224
  loop : -2.80 (0.23), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.011   0.001   TYR A 204 
 PHE   0.010   0.001   PHE A 192 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 5820)
  covalent geometry    : angle       0.69584 ( 7935)
  SS BOND              : bond        0.00263 (    8)
  SS BOND              : angle       1.08137 (   16)
  hydrogen bonds       : bond        0.03988 (  148)
  hydrogen bonds       : angle       5.61520 (  390)
  link_BETA1-4         : bond        0.00479 (    5)
  link_BETA1-4         : angle       2.02193 (   15)
  link_BETA1-6         : bond        0.01365 (    3)
  link_BETA1-6         : angle       2.33152 (    9)
  link_NAG-ASN         : bond        0.00295 (    5)
  link_NAG-ASN         : angle       1.41912 (   15)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 5
  residues processed: 63
  average time/residue: 0.0659
  time to fit residues: 5.7203
Evaluate side-chains
  57 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  119 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.157974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.134759 restraints weight = 7448.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.134002 restraints weight = 10201.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.135160 restraints weight = 10531.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.135231 restraints weight = 7713.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.135073 restraints weight = 8379.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5841  Z= 0.176
  Angle     :  0.730   9.130   7990  Z= 0.350
  Chirality :  0.047   0.161    923
  Planarity :  0.005   0.043    999
  Dihedral  : 11.690  88.559   1052
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.24 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.59 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.91 (0.28), residues: 693
  helix: -3.20 (0.79), residues: 28
  sheet: -0.52 (0.34), residues: 246
  loop : -2.90 (0.23), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.014   0.002   TYR A 204 
 PHE   0.013   0.001   PHE A 400 
 TRP   0.013   0.002   TRP E  50 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 5820)
  covalent geometry    : angle       0.71840 ( 7935)
  SS BOND              : bond        0.00330 (    8)
  SS BOND              : angle       0.93188 (   16)
  hydrogen bonds       : bond        0.04789 (  148)
  hydrogen bonds       : angle       5.42134 (  390)
  link_BETA1-4         : bond        0.00481 (    5)
  link_BETA1-4         : angle       1.95167 (   15)
  link_BETA1-6         : bond        0.01535 (    3)
  link_BETA1-6         : angle       2.62616 (    9)
  link_NAG-ASN         : bond        0.00250 (    5)
  link_NAG-ASN         : angle       1.27897 (   15)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 11
  residues processed: 60
  average time/residue: 0.0844
  time to fit residues: 6.8604
Evaluate side-chains
  63 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   23 THR
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue  119 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 5 optimal weight:    0.0670
   chunk 35 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 33 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   overall best weight:    0.5496

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

Flipped N/Q/H residues before XYZ refinement:
D  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.163311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.140295 restraints weight = 7383.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.139204 restraints weight = 9864.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.139659 restraints weight = 10403.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.139808 restraints weight = 8359.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.140024 restraints weight = 7882.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5841  Z= 0.126
  Angle     :  0.655   8.915   7990  Z= 0.311
  Chirality :  0.044   0.189    923
  Planarity :  0.004   0.042    999
  Dihedral  :  9.296  68.188   1052
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.77 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.27 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.71 (0.28), residues: 693
  helix: -3.14 (0.82), residues: 28
  sheet: -0.29 (0.35), residues: 235
  loop : -2.77 (0.24), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.009   0.001   TYR D  32 
 PHE   0.009   0.001   PHE A 400 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5820)
  covalent geometry    : angle       0.64294 ( 7935)
  SS BOND              : bond        0.00265 (    8)
  SS BOND              : angle       0.79580 (   16)
  hydrogen bonds       : bond        0.03658 (  148)
  hydrogen bonds       : angle       5.17222 (  390)
  link_BETA1-4         : bond        0.00519 (    5)
  link_BETA1-4         : angle       2.16246 (   15)
  link_BETA1-6         : bond        0.01606 (    3)
  link_BETA1-6         : angle       2.29175 (    9)
  link_NAG-ASN         : bond        0.00298 (    5)
  link_NAG-ASN         : angle       1.16189 (   15)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 10
  residues processed: 62
  average time/residue: 0.0779
  time to fit residues: 6.5654
Evaluate side-chains
  61 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain E residue  119 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0870
   chunk 36 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8362

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

Flipped N/Q/H residues before XYZ refinement:
D  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.161182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.138715 restraints weight = 7481.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.138099 restraints weight = 10443.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.139397 restraints weight = 11093.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.139084 restraints weight = 7947.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.139325 restraints weight = 8871.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5841  Z= 0.162
  Angle     :  0.674   8.667   7990  Z= 0.324
  Chirality :  0.045   0.155    923
  Planarity :  0.004   0.042    999
  Dihedral  :  8.123  56.935   1052
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.95 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 12.41 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.75 (0.29), residues: 693
  helix: -3.07 (0.84), residues: 28
  sheet: -0.38 (0.34), residues: 245
  loop : -2.81 (0.24), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  56 
 TYR   0.011   0.001   TYR A 204 
 PHE   0.012   0.001   PHE A 400 
 TRP   0.012   0.002   TRP E  50 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 5820)
  covalent geometry    : angle       0.66059 ( 7935)
  SS BOND              : bond        0.00304 (    8)
  SS BOND              : angle       0.79058 (   16)
  hydrogen bonds       : bond        0.04325 (  148)
  hydrogen bonds       : angle       5.20307 (  390)
  link_BETA1-4         : bond        0.00411 (    5)
  link_BETA1-4         : angle       2.46534 (   15)
  link_BETA1-6         : bond        0.01757 (    3)
  link_BETA1-6         : angle       2.23480 (    9)
  link_NAG-ASN         : bond        0.00243 (    5)
  link_NAG-ASN         : angle       1.29758 (   15)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 53
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
  outliers start: 23
  outliers final: 20
  residues processed: 70
  average time/residue: 0.0752
  time to fit residues: 7.3022
Evaluate side-chains
  72 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   23 THR
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue   81 GLN
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  119 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 38 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 28 optimal weight:    0.1980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
D  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.162697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.140813 restraints weight = 7407.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.139917 restraints weight = 9668.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.140088 restraints weight = 10087.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.140303 restraints weight = 8324.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.140348 restraints weight = 8483.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5841  Z= 0.125
  Angle     :  0.642   8.325   7990  Z= 0.307
  Chirality :  0.044   0.226    923
  Planarity :  0.004   0.041    999
  Dihedral  :  7.443  55.781   1052
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.20 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 12.93 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.63 (0.29), residues: 693
  helix: -3.06 (0.84), residues: 28
  sheet: -0.23 (0.35), residues: 236
  loop : -2.73 (0.24), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.009   0.001   TYR A 204 
 PHE   0.009   0.001   PHE A  92 
 TRP   0.010   0.001   TRP E  50 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5820)
  covalent geometry    : angle       0.62817 ( 7935)
  SS BOND              : bond        0.00251 (    8)
  SS BOND              : angle       0.70698 (   16)
  hydrogen bonds       : bond        0.03734 (  148)
  hydrogen bonds       : angle       5.11171 (  390)
  link_BETA1-4         : bond        0.00456 (    5)
  link_BETA1-4         : angle       2.50465 (   15)
  link_BETA1-6         : bond        0.01793 (    3)
  link_BETA1-6         : angle       2.13189 (    9)
  link_NAG-ASN         : bond        0.00269 (    5)
  link_NAG-ASN         : angle       1.14640 (   15)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: E   60 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6417 (m-80)
  outliers start: 23
  outliers final: 21
  residues processed: 70
  average time/residue: 0.0770
  time to fit residues: 7.4952
Evaluate side-chains
  73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 51
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  136 CYS
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue   81 GLN
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  114 GLN
Chi-restraints excluded: chain E residue  119 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0070
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 39 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
D  71 ASN
D  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.160725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.137336 restraints weight = 7436.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.136594 restraints weight = 9966.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.137751 restraints weight = 9550.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.137659 restraints weight = 7257.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.138063 restraints weight = 6996.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5841  Z= 0.117
  Angle     :  0.632   8.357   7990  Z= 0.302
  Chirality :  0.043   0.151    923
  Planarity :  0.004   0.041    999
  Dihedral  :  6.966  55.506   1052
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 13.10 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.58 (0.29), residues: 693
  helix: -3.04 (0.85), residues: 28
  sheet: -0.17 (0.35), residues: 236
  loop : -2.70 (0.24), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 466 
 TYR   0.010   0.001   TYR A 204 
 PHE   0.009   0.001   PHE A  92 
 TRP   0.010   0.001   TRP E  47 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 5820)
  covalent geometry    : angle       0.61736 ( 7935)
  SS BOND              : bond        0.00235 (    8)
  SS BOND              : angle       0.65172 (   16)
  hydrogen bonds       : bond        0.03530 (  148)
  hydrogen bonds       : angle       5.02685 (  390)
  link_BETA1-4         : bond        0.00447 (    5)
  link_BETA1-4         : angle       2.54677 (   15)
  link_BETA1-6         : bond        0.01825 (    3)
  link_BETA1-6         : angle       2.09110 (    9)
  link_NAG-ASN         : bond        0.00267 (    5)
  link_NAG-ASN         : angle       1.11609 (   15)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 55
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
  outliers start: 26
  outliers final: 25
  residues processed: 72
  average time/residue: 0.0760
  time to fit residues: 7.4462
Evaluate side-chains
  80 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 55
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  136 CYS
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue   71 ASN
Chi-restraints excluded: chain D residue   81 GLN
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  114 GLN
Chi-restraints excluded: chain E residue  119 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0050
   chunk 4 optimal weight:    0.0980
   chunk 39 optimal weight:    0.0670
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.3132

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

Flipped N/Q/H residues before XYZ refinement:
D  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.164339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.140341 restraints weight = 7417.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.139345 restraints weight = 10228.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.139666 restraints weight = 11029.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.139868 restraints weight = 9241.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.141117 restraints weight = 8156.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5841  Z= 0.107
  Angle     :  0.616   8.437   7990  Z= 0.295
  Chirality :  0.044   0.265    923
  Planarity :  0.004   0.041    999
  Dihedral  :  6.652  55.076   1052
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 13.78 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.47 (0.29), residues: 693
  helix: -3.03 (0.85), residues: 28
  sheet:  0.02 (0.36), residues: 224
  loop : -2.63 (0.24), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 466 
 TYR   0.009   0.001   TYR A 204 
 PHE   0.008   0.001   PHE A  92 
 TRP   0.010   0.001   TRP E  47 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 5820)
  covalent geometry    : angle       0.60212 ( 7935)
  SS BOND              : bond        0.00212 (    8)
  SS BOND              : angle       0.61230 (   16)
  hydrogen bonds       : bond        0.03240 (  148)
  hydrogen bonds       : angle       4.96046 (  390)
  link_BETA1-4         : bond        0.00455 (    5)
  link_BETA1-4         : angle       2.54272 (   15)
  link_BETA1-6         : bond        0.01888 (    3)
  link_BETA1-6         : angle       2.04670 (    9)
  link_NAG-ASN         : bond        0.00279 (    5)
  link_NAG-ASN         : angle       1.05461 (   15)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 58
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 25
  outliers final: 22
  residues processed: 74
  average time/residue: 0.0731
  time to fit residues: 7.3446
Evaluate side-chains
  76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 54
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  136 CYS
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  114 GLN
Chi-restraints excluded: chain E residue  119 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0470
   chunk 45 optimal weight:    0.0070
   chunk 31 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    0.1980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.3296

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

Flipped N/Q/H residues before XYZ refinement:
D  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.165035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.140387 restraints weight = 7405.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.139398 restraints weight = 10090.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.139986 restraints weight = 10184.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.140256 restraints weight = 8565.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.140660 restraints weight = 7396.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5841  Z= 0.104
  Angle     :  0.603   8.543   7990  Z= 0.289
  Chirality :  0.043   0.146    923
  Planarity :  0.004   0.040    999
  Dihedral  :  6.205  53.973   1052
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 14.97 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.31 (0.29), residues: 693
  helix: -2.84 (0.84), residues: 29
  sheet:  0.13 (0.36), residues: 224
  loop : -2.52 (0.24), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  63 
 TYR   0.009   0.001   TYR A 204 
 PHE   0.008   0.001   PHE A  92 
 TRP   0.010   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 5820)
  covalent geometry    : angle       0.58858 ( 7935)
  SS BOND              : bond        0.00207 (    8)
  SS BOND              : angle       0.59173 (   16)
  hydrogen bonds       : bond        0.03069 (  148)
  hydrogen bonds       : angle       4.82691 (  390)
  link_BETA1-4         : bond        0.00445 (    5)
  link_BETA1-4         : angle       2.54080 (   15)
  link_BETA1-6         : bond        0.01754 (    3)
  link_BETA1-6         : angle       2.03006 (    9)
  link_NAG-ASN         : bond        0.00260 (    5)
  link_NAG-ASN         : angle       1.01691 (   15)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 53
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 20
  residues processed: 69
  average time/residue: 0.0710
  time to fit residues: 6.8898
Evaluate side-chains
  73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  136 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  114 GLN
Chi-restraints excluded: chain E residue  119 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 20 optimal weight:    0.4980
   chunk 11 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 65 optimal weight:    0.4980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
D  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.163200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.139664 restraints weight = 7506.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.138412 restraints weight = 10739.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.139381 restraints weight = 12414.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.139527 restraints weight = 8956.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.140116 restraints weight = 8008.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5841  Z= 0.129
  Angle     :  0.626   8.494   7990  Z= 0.302
  Chirality :  0.044   0.260    923
  Planarity :  0.004   0.040    999
  Dihedral  :  6.239  54.877   1052
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 14.97 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.33 (0.29), residues: 693
  helix: -2.76 (0.86), residues: 29
  sheet:  0.12 (0.36), residues: 224
  loop : -2.55 (0.24), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 466 
 TYR   0.010   0.001   TYR A 265 
 PHE   0.011   0.001   PHE A  92 
 TRP   0.010   0.001   TRP E  50 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 5820)
  covalent geometry    : angle       0.61105 ( 7935)
  SS BOND              : bond        0.00255 (    8)
  SS BOND              : angle       0.64312 (   16)
  hydrogen bonds       : bond        0.03703 (  148)
  hydrogen bonds       : angle       4.90152 (  390)
  link_BETA1-4         : bond        0.00411 (    5)
  link_BETA1-4         : angle       2.57742 (   15)
  link_BETA1-6         : bond        0.01725 (    3)
  link_BETA1-6         : angle       2.05612 (    9)
  link_NAG-ASN         : bond        0.00229 (    5)
  link_NAG-ASN         : angle       1.12855 (   15)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 55
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
  outliers start: 24
  outliers final: 23
  residues processed: 70
  average time/residue: 0.0650
  time to fit residues: 6.5816
Evaluate side-chains
  75 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 52
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  136 CYS
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue   81 GLN
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  114 GLN
Chi-restraints excluded: chain E residue  119 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 46 optimal weight:    0.0060
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0970
   chunk 5 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0030
   chunk 23 optimal weight:    6.9990
   chunk 2 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.3004

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

Flipped N/Q/H residues before XYZ refinement:
D  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.162231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.138674 restraints weight = 7294.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.139761 restraints weight = 8697.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.139921 restraints weight = 9030.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140000 restraints weight = 6973.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140158 restraints weight = 6487.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5841  Z= 0.104
  Angle     :  0.612   9.358   7990  Z= 0.293
  Chirality :  0.043   0.151    923
  Planarity :  0.004   0.040    999
  Dihedral  :  6.072  54.353   1052
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 15.14 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.24 (0.29), residues: 693
  helix: -2.85 (0.84), residues: 29
  sheet:  0.18 (0.36), residues: 224
  loop : -2.47 (0.25), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 466 
 TYR   0.008   0.001   TYR A 204 
 PHE   0.019   0.001   PHE A 133 
 TRP   0.010   0.001   TRP E  47 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 5820)
  covalent geometry    : angle       0.59771 ( 7935)
  SS BOND              : bond        0.00221 (    8)
  SS BOND              : angle       0.61747 (   16)
  hydrogen bonds       : bond        0.03211 (  148)
  hydrogen bonds       : angle       4.83853 (  390)
  link_BETA1-4         : bond        0.00452 (    5)
  link_BETA1-4         : angle       2.52603 (   15)
  link_BETA1-6         : bond        0.01710 (    3)
  link_BETA1-6         : angle       2.03067 (    9)
  link_NAG-ASN         : bond        0.00269 (    5)
  link_NAG-ASN         : angle       1.06505 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1384.28 seconds
wall clock time: 24 minutes 36.41 seconds (1476.41 seconds total)