Starting phenix.real_space_refine
on Thu Jun  5 10:25:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qpr_18560/06_2025/8qpr_18560.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qpr_18560/06_2025/8qpr_18560.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qpr_18560/06_2025/8qpr_18560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qpr_18560/06_2025/8qpr_18560.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qpr_18560/06_2025/8qpr_18560.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qpr_18560/06_2025/8qpr_18560.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.027
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      22      5.16       5
     C    3691      2.51       5
     N     945      2.21       5
     O    1129      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5787
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 491, 3844
          Classifications: {'peptide': 491}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 28, 'TRANS': 462}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 42
    Chain: "D"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 803
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 7, 'TRANS': 101}
    Chain: "E"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 942
          Classifications: {'peptide': 123}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117}
    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: "F"
      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: "G"
      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
  Time building chain proxies: 8.38, per 1000 atoms: 1.45
  Number of scatterers: 5787
  At special positions: 0
  Unit cell: (81.12, 75.66, 149.76, 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      22     16.00
     O    1129      8.00
     N     945      7.00
     C    3691      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.04
    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=2.03
    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=2.04

  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 G   1 " - " NAG G   2 "
      " NAG a   1 " - " NAG a   2 "
      " NAG c   1 " - " NAG c   2 "
      " NAG e   1 " - " NAG e   2 "
    BETA1-6
      " NAG G   1 " - " FUC G   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  61 "
      " NAG G   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: 1.72
  Conformation dependent library (CDL) restraints added in 935.1 milliseconds
  

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1332

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 11 sheets defined
      4.8% alpha, 27.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 3.611A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASN A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 365 through 370'
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 4.049A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 410
      removed outlier: 3.797A  pdb=" N   GLU A 406 " --> pdb=" O   ARG A 403 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL A 407 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE A 410 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.959A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
      removed outlier: 8.166A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55
      removed outlier: 3.843A  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: 7.340A  pdb=" N   ARG A 237 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   PHE A 106 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   GLN A 239 " --> pdb=" O   TRP A 104 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   TRP A 104 " --> pdb=" O   GLN A 239 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU A 241 " --> pdb=" O   ARG A 102 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ASN A 121 " --> pdb=" O   ARG A 102 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   VAL A 126 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   VAL A 171 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ILE A 128 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   GLU A 169 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   VAL A 130 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328
      removed outlier: 3.984A  pdb=" N   PHE A 543 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 356 through 358
      removed outlier: 3.622A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 12
    Processing sheet with id=AA8, first strand: chain 'D' and resid 19 through 23
      removed outlier: 3.884A  pdb=" N   SER D  67 " --> pdb=" O   SER D  74 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 47 through 51
      removed outlier: 6.362A  pdb=" N   TRP D  37 " --> pdb=" O   MET D  49 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASP D  87 " --> pdb=" O   HIS D  40 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   TYR D  93 " --> pdb=" O   VAL D 100 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   VAL D 100 " --> pdb=" O   TYR D  93 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6
      removed outlier: 3.606A  pdb=" N   THR E  78 " --> pdb=" O   ASP E  73 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.833A  pdb=" N   ALA E  92 " --> pdb=" O   VAL E 118 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLY E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)

    140 hydrogen bonds defined for protein.
    348 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1802
        1.35 -     1.47: 1626
        1.47 -     1.59: 2481
        1.59 -     1.71: 0
        1.71 -     1.83: 25
  Bond restraints: 5934
  Sorted by residual:
  bond pdb=" C   PHE A 559 "
       pdb=" N   LEU A 560 "
    ideal  model  delta    sigma   weight residual
    1.329  1.257  0.072 1.86e-02 2.89e+03 1.48e+01
  bond pdb=" C1  FUC G   3 "
       pdb=" C2  FUC G   3 "
    ideal  model  delta    sigma   weight residual
    1.528  1.571 -0.043 2.00e-02 2.50e+03 4.67e+00
  bond pdb=" C5  FUC G   3 "
       pdb=" O5  FUC G   3 "
    ideal  model  delta    sigma   weight residual
    1.423  1.465 -0.042 2.00e-02 2.50e+03 4.49e+00
  bond pdb=" C1  FUC G   3 "
       pdb=" O5  FUC G   3 "
    ideal  model  delta    sigma   weight residual
    1.400  1.437 -0.037 2.00e-02 2.50e+03 3.49e+00
  bond pdb=" C5  FUC e   3 "
       pdb=" O5  FUC e   3 "
    ideal  model  delta    sigma   weight residual
    1.423  1.457 -0.034 2.00e-02 2.50e+03 2.92e+00
  ... (remaining 5929 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 7893
        2.44 -     4.88: 172
        4.88 -     7.31: 18
        7.31 -     9.75: 5
        9.75 -    12.19: 2
  Bond angle restraints: 8090
  Sorted by residual:
  angle pdb=" C   TYR D  51 "
        pdb=" N   GLU D  52 "
        pdb=" CA  GLU D  52 "
      ideal   model   delta    sigma   weight residual
     121.54  132.03  -10.49 1.91e+00 2.74e-01 3.01e+01
  angle pdb=" C   PHE A 559 "
        pdb=" N   LEU A 560 "
        pdb=" CA  LEU A 560 "
      ideal   model   delta    sigma   weight residual
     121.48  112.16    9.32 2.04e+00 2.40e-01 2.09e+01
  angle pdb=" C   GLY A 416 "
        pdb=" N   LYS A 417 "
        pdb=" CA  LYS A 417 "
      ideal   model   delta    sigma   weight residual
     121.54  129.43   -7.89 1.91e+00 2.74e-01 1.71e+01
  angle pdb=" N   GLU D  52 "
        pdb=" CA  GLU D  52 "
        pdb=" C   GLU D  52 "
      ideal   model   delta    sigma   weight residual
     110.80  119.44   -8.64 2.13e+00 2.20e-01 1.65e+01
  angle pdb=" CA  LEU A 212 "
        pdb=" CB  LEU A 212 "
        pdb=" CG  LEU A 212 "
      ideal   model   delta    sigma   weight residual
     116.30  128.49  -12.19 3.50e+00 8.16e-02 1.21e+01
  ... (remaining 8085 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.53: 3424
       24.53 -    49.07: 163
       49.07 -    73.60: 34
       73.60 -    98.13: 23
       98.13 -   122.67: 9
  Dihedral angle restraints: 3653
    sinusoidal: 1564
      harmonic: 2089
  Sorted by residual:
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   35.85   57.15     1      1.00e+01 1.00e-02 4.39e+01
  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  149.51   30.49     0      5.00e+00 4.00e-02 3.72e+01
  dihedral pdb=" CA  TRP A 436 "
           pdb=" C   TRP A 436 "
           pdb=" N   ASN A 437 "
           pdb=" CA  ASN A 437 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.85   30.15     0      5.00e+00 4.00e-02 3.64e+01
  ... (remaining 3650 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 862
       0.092 -    0.185: 76
       0.185 -    0.277: 3
       0.277 -    0.369: 0
       0.369 -    0.462: 1
  Chirality restraints: 942
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 122 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-01 2.50e+01 5.33e+00
  chirality pdb=" C1  NAG c   1 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG c   1 "
            pdb=" O5  NAG c   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  THR A  95 "
            pdb=" CA  THR A  95 "
            pdb=" OG1 THR A  95 "
            pdb=" CG2 THR A  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 939 not shown)

  Planarity restraints: 1027
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 417 "    0.020 2.00e-02 2.50e+03   3.90e-02 1.52e+01
        pdb=" C   LYS A 417 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   LYS A 417 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ILE A 418 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E  52 "   -0.041 5.00e-02 4.00e+02   6.17e-02 6.10e+00
        pdb=" N   PRO E  53 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO E  53 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E  53 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 294 "   -0.032 5.00e-02 4.00e+02   4.97e-02 3.94e+00
        pdb=" N   PRO A 295 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 295 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 295 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1024 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1236
        2.78 -     3.31: 5083
        3.31 -     3.84: 8392
        3.84 -     4.37: 9195
        4.37 -     4.90: 16937
  Nonbonded interactions: 40843
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG E  23 "
            pdb=" O   ILE E  76 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" O   PRO D   7 "
            pdb=" OG1 THR D 105 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" NE  ARG A 357 "
            pdb=" OD1 ASN A 394 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" OG  SER E  17 "
            pdb=" OE2 GLU E  82 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" NH2 ARG A 454 "
            pdb=" O   ASP A 467 "
     model   vdw
     2.302 3.120
  ... (remaining 40838 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 'F'
  selection = chain 'a'
}
ncs_group {
  reference = chain 'G'
  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:             14.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     22.960
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   5956  Z= 0.278
  Angle     :  0.920  12.191   8149  Z= 0.468
  Chirality :  0.054   0.462    942
  Planarity :  0.006   0.062   1021
  Dihedral  : 17.697 122.667   2300
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.55 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.99 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.29), residues: 709
  helix: -3.62 (0.69), residues: 31
  sheet: -0.44 (0.35), residues: 227
  loop : -3.35 (0.24), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP D  99 
 HIS   0.005   0.002   HIS A  66 
 PHE   0.027   0.002   PHE A 377 
 TYR   0.023   0.002   TYR E  60 
 ARG   0.008   0.001   ARG A 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00883 (    6)
  link_NAG-ASN         : angle       4.57307 (   18)
  link_BETA1-4         : bond        0.00605 (    6)
  link_BETA1-4         : angle       1.44812 (   18)
  hydrogen bonds       : bond        0.14945 (  140)
  hydrogen bonds       : angle       6.57727 (  348)
  link_BETA1-6         : bond        0.01363 (    3)
  link_BETA1-6         : angle       2.41052 (    9)
  SS BOND              : bond        0.00517 (    7)
  SS BOND              : angle       1.58192 (   14)
  covalent geometry    : bond        0.00625 ( 5934)
  covalent geometry    : angle       0.88949 ( 8090)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.608 
Fit side-chains
REVERT: D   56 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8468 (ttt-90)
REVERT: D  107 LEU cc_start: 0.8378 (tp) cc_final: 0.7813 (tp)
REVERT: E   63 LYS cc_start: 0.9265 (ttpp) cc_final: 0.9032 (ttpp)
  outliers start: 1
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1760
  time to fit residues: 19.7962
Evaluate side-chains
  58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0970
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0870
   overall best weight:    0.5560

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
A 207 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.149899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.124978 restraints weight = 9376.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.122457 restraints weight = 14348.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.121086 restraints weight = 15479.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5956  Z= 0.151
  Angle     :  0.803  12.096   8149  Z= 0.386
  Chirality :  0.050   0.305    942
  Planarity :  0.005   0.049   1021
  Dihedral  : 15.349 111.040   1087
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.16 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.05 %
    Favored  : 89.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.10 (0.29), residues: 709
  helix: -3.56 (0.63), residues: 35
  sheet: -0.13 (0.35), residues: 221
  loop : -3.18 (0.25), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  50 
 HIS   0.004   0.001   HIS A  69 
 PHE   0.018   0.001   PHE A 168 
 TYR   0.014   0.001   TYR D  51 
 ARG   0.004   0.001   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00926 (    6)
  link_NAG-ASN         : angle       4.54464 (   18)
  link_BETA1-4         : bond        0.00580 (    6)
  link_BETA1-4         : angle       1.40209 (   18)
  hydrogen bonds       : bond        0.04400 (  140)
  hydrogen bonds       : angle       5.65506 (  348)
  link_BETA1-6         : bond        0.01972 (    3)
  link_BETA1-6         : angle       2.75892 (    9)
  SS BOND              : bond        0.00485 (    7)
  SS BOND              : angle       1.24911 (   14)
  covalent geometry    : bond        0.00339 ( 5934)
  covalent geometry    : angle       0.76684 ( 8090)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 5
  residues processed: 72
  average time/residue: 0.2026
  time to fit residues: 20.1452
Evaluate side-chains
  69 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain D residue   41 HIS
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   84 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0270
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 46 optimal weight:    0.3980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.149418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 121)---------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.112835 restraints weight = 9822.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 85)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.105374 restraints weight = 13188.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.106063 restraints weight = 11359.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5956  Z= 0.156
  Angle     :  0.773  11.889   8149  Z= 0.369
  Chirality :  0.048   0.300    942
  Planarity :  0.005   0.048   1021
  Dihedral  : 12.714 103.023   1087
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.44 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 11.02 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.97 (0.29), residues: 709
  helix: -3.72 (0.59), residues: 37
  sheet: -0.07 (0.35), residues: 227
  loop : -3.07 (0.25), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.003   0.001   HIS A 207 
 PHE   0.016   0.001   PHE A  86 
 TYR   0.015   0.001   TYR D  51 
 ARG   0.003   0.000   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00851 (    6)
  link_NAG-ASN         : angle       4.34890 (   18)
  link_BETA1-4         : bond        0.00504 (    6)
  link_BETA1-4         : angle       1.49049 (   18)
  hydrogen bonds       : bond        0.04112 (  140)
  hydrogen bonds       : angle       5.37203 (  348)
  link_BETA1-6         : bond        0.02115 (    3)
  link_BETA1-6         : angle       3.01729 (    9)
  SS BOND              : bond        0.00432 (    7)
  SS BOND              : angle       1.09040 (   14)
  covalent geometry    : bond        0.00357 ( 5934)
  covalent geometry    : angle       0.73664 ( 8090)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.635 
Fit side-chains
REVERT: D   56 ARG cc_start: 0.8543 (ttt-90) cc_final: 0.8292 (ttt-90)
  outliers start: 15
  outliers final: 9
  residues processed: 77
  average time/residue: 0.2029
  time to fit residues: 21.1202
Evaluate side-chains
  67 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain E residue    4 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 65 optimal weight:    0.2980
   chunk 0 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0670
   chunk 44 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.150102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.125097 restraints weight = 9616.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.122498 restraints weight = 15277.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.119966 restraints weight = 16170.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5956  Z= 0.145
  Angle     :  0.763  14.783   8149  Z= 0.362
  Chirality :  0.047   0.299    942
  Planarity :  0.005   0.049   1021
  Dihedral  : 11.159  98.341   1087
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.16 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 12.66 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.30), residues: 709
  helix: -3.67 (0.63), residues: 37
  sheet:  0.03 (0.36), residues: 225
  loop : -2.97 (0.26), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  50 
 HIS   0.003   0.001   HIS A 207 
 PHE   0.015   0.001   PHE A  86 
 TYR   0.014   0.001   TYR D  51 
 ARG   0.002   0.000   ARG A 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00834 (    6)
  link_NAG-ASN         : angle       4.35761 (   18)
  link_BETA1-4         : bond        0.00513 (    6)
  link_BETA1-4         : angle       1.53569 (   18)
  hydrogen bonds       : bond        0.03879 (  140)
  hydrogen bonds       : angle       5.25690 (  348)
  link_BETA1-6         : bond        0.01825 (    3)
  link_BETA1-6         : angle       2.63685 (    9)
  SS BOND              : bond        0.00386 (    7)
  SS BOND              : angle       1.05569 (   14)
  covalent geometry    : bond        0.00335 ( 5934)
  covalent geometry    : angle       0.72743 ( 8090)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: A  415 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8142 (p)
  outliers start: 20
  outliers final: 13
  residues processed: 77
  average time/residue: 0.1704
  time to fit residues: 17.5324
Evaluate side-chains
  78 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  436 TRP
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain D residue   41 HIS
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain E residue    4 LEU
Chi-restraints excluded: chain E residue  116 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0980
   chunk 16 optimal weight:    0.0020
   chunk 33 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
A 540 ASN
D  27 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.150850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.128005 restraints weight = 9461.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.123515 restraints weight = 15234.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.121378 restraints weight = 16732.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5956  Z= 0.130
  Angle     :  0.725  11.943   8149  Z= 0.347
  Chirality :  0.047   0.300    942
  Planarity :  0.005   0.048   1021
  Dihedral  : 10.088  94.030   1087
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.87 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.47 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.30), residues: 709
  helix: -3.39 (0.77), residues: 31
  sheet: -0.45 (0.35), residues: 244
  loop : -2.78 (0.26), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  50 
 HIS   0.004   0.001   HIS A 207 
 PHE   0.012   0.001   PHE A  86 
 TYR   0.013   0.001   TYR D  51 
 ARG   0.005   0.000   ARG D  56 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00779 (    6)
  link_NAG-ASN         : angle       4.34115 (   18)
  link_BETA1-4         : bond        0.00491 (    6)
  link_BETA1-4         : angle       1.63082 (   18)
  hydrogen bonds       : bond        0.03545 (  140)
  hydrogen bonds       : angle       5.09416 (  348)
  link_BETA1-6         : bond        0.01424 (    3)
  link_BETA1-6         : angle       1.44019 (    9)
  SS BOND              : bond        0.00378 (    7)
  SS BOND              : angle       0.95827 (   14)
  covalent geometry    : bond        0.00300 ( 5934)
  covalent geometry    : angle       0.69145 ( 8090)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.629 
Fit side-chains
REVERT: A  415 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8273 (p)
REVERT: D   41 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.7505 (t-90)
REVERT: D  107 LEU cc_start: 0.8065 (tp) cc_final: 0.7793 (tp)
  outliers start: 21
  outliers final: 14
  residues processed: 83
  average time/residue: 0.1741
  time to fit residues: 19.3456
Evaluate side-chains
  84 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain D residue   41 HIS
Chi-restraints excluded: chain D residue   48 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue    4 LEU
Chi-restraints excluded: chain E residue  116 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.149578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.125587 restraints weight = 9440.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.121528 restraints weight = 15041.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.120631 restraints weight = 16079.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5956  Z= 0.166
  Angle     :  0.749  11.811   8149  Z= 0.362
  Chirality :  0.047   0.293    942
  Planarity :  0.005   0.048   1021
  Dihedral  :  9.715  88.796   1087
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.14 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.46 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.30), residues: 709
  helix: -2.97 (0.92), residues: 25
  sheet: -0.26 (0.36), residues: 232
  loop : -2.83 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  37 
 HIS   0.003   0.001   HIS A 207 
 PHE   0.022   0.001   PHE A  86 
 TYR   0.016   0.001   TYR D  51 
 ARG   0.006   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00796 (    6)
  link_NAG-ASN         : angle       4.31746 (   18)
  link_BETA1-4         : bond        0.00476 (    6)
  link_BETA1-4         : angle       1.74157 (   18)
  hydrogen bonds       : bond        0.04090 (  140)
  hydrogen bonds       : angle       5.11992 (  348)
  link_BETA1-6         : bond        0.01424 (    3)
  link_BETA1-6         : angle       1.51644 (    9)
  SS BOND              : bond        0.00396 (    7)
  SS BOND              : angle       1.00805 (   14)
  covalent geometry    : bond        0.00390 ( 5934)
  covalent geometry    : angle       0.71554 ( 8090)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.752 
Fit side-chains
REVERT: A  394 ASN cc_start: 0.7446 (m-40) cc_final: 0.7036 (m-40)
REVERT: A  415 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8396 (p)
REVERT: D   41 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7520 (t-90)
  outliers start: 23
  outliers final: 17
  residues processed: 81
  average time/residue: 0.1938
  time to fit residues: 21.0924
Evaluate side-chains
  84 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain D residue   41 HIS
Chi-restraints excluded: chain D residue   48 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   52 GLU
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue    4 LEU
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue  116 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0470
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6882

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
D  27 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.163518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.122499 restraints weight = 9663.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.124212 restraints weight = 7902.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.125096 restraints weight = 6847.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5956  Z= 0.150
  Angle     :  0.752  11.896   8149  Z= 0.361
  Chirality :  0.047   0.299    942
  Planarity :  0.005   0.049   1021
  Dihedral  :  9.254  78.855   1087
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.44 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 15.95 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.30), residues: 709
  helix: -2.96 (0.92), residues: 25
  sheet: -0.27 (0.36), residues: 233
  loop : -2.76 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  37 
 HIS   0.003   0.001   HIS A 207 
 PHE   0.017   0.001   PHE A  86 
 TYR   0.014   0.001   TYR D  51 
 ARG   0.010   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00781 (    6)
  link_NAG-ASN         : angle       4.33548 (   18)
  link_BETA1-4         : bond        0.00483 (    6)
  link_BETA1-4         : angle       1.76214 (   18)
  hydrogen bonds       : bond        0.03891 (  140)
  hydrogen bonds       : angle       5.10476 (  348)
  link_BETA1-6         : bond        0.01449 (    3)
  link_BETA1-6         : angle       1.60619 (    9)
  SS BOND              : bond        0.00373 (    7)
  SS BOND              : angle       0.94227 (   14)
  covalent geometry    : bond        0.00350 ( 5934)
  covalent geometry    : angle       0.71905 ( 8090)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.552 
Fit side-chains
REVERT: D   41 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7367 (t-90)
  outliers start: 24
  outliers final: 16
  residues processed: 82
  average time/residue: 0.1565
  time to fit residues: 17.5307
Evaluate side-chains
  85 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   41 HIS
Chi-restraints excluded: chain D residue   48 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue    4 LEU
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue  116 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 7 optimal weight:    0.2980
   chunk 20 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
D  27 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.151276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.123979 restraints weight = 9377.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.122109 restraints weight = 16969.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.120680 restraints weight = 16942.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5956  Z= 0.142
  Angle     :  0.750  11.870   8149  Z= 0.360
  Chirality :  0.046   0.301    942
  Planarity :  0.005   0.048   1021
  Dihedral  :  8.408  54.465   1087
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.72 %
    Favored  : 89.28 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 16.28 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.30), residues: 709
  helix: -2.93 (0.92), residues: 25
  sheet: -0.24 (0.36), residues: 233
  loop : -2.70 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  37 
 HIS   0.003   0.001   HIS A 207 
 PHE   0.014   0.001   PHE A  86 
 TYR   0.014   0.001   TYR D  51 
 ARG   0.009   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00789 (    6)
  link_NAG-ASN         : angle       4.34265 (   18)
  link_BETA1-4         : bond        0.00480 (    6)
  link_BETA1-4         : angle       1.81126 (   18)
  hydrogen bonds       : bond        0.03804 (  140)
  hydrogen bonds       : angle       5.00069 (  348)
  link_BETA1-6         : bond        0.01687 (    3)
  link_BETA1-6         : angle       1.96978 (    9)
  SS BOND              : bond        0.00360 (    7)
  SS BOND              : angle       0.91036 (   14)
  covalent geometry    : bond        0.00332 ( 5934)
  covalent geometry    : angle       0.71562 ( 8090)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.669 
Fit side-chains
REVERT: D   56 ARG cc_start: 0.8302 (ttt-90) cc_final: 0.8085 (ttt-90)
  outliers start: 22
  outliers final: 18
  residues processed: 83
  average time/residue: 0.1738
  time to fit residues: 19.2798
Evaluate side-chains
  87 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue    4 LEU
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  116 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 46 optimal weight:    0.0980
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0970
   chunk 4 optimal weight:    0.0670
   chunk 68 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
D  27 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.152265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.126884 restraints weight = 9450.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.123223 restraints weight = 13757.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.121747 restraints weight = 14515.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5956  Z= 0.127
  Angle     :  0.740  11.905   8149  Z= 0.352
  Chirality :  0.046   0.305    942
  Planarity :  0.005   0.046   1021
  Dihedral  :  7.940  53.922   1087
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.45 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.27 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.31), residues: 709
  helix: -2.85 (0.94), residues: 25
  sheet: -0.12 (0.37), residues: 227
  loop : -2.65 (0.26), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  37 
 HIS   0.003   0.001   HIS A 207 
 PHE   0.010   0.001   PHE A  86 
 TYR   0.011   0.001   TYR D  51 
 ARG   0.008   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00768 (    6)
  link_NAG-ASN         : angle       4.33336 (   18)
  link_BETA1-4         : bond        0.00496 (    6)
  link_BETA1-4         : angle       1.83917 (   18)
  hydrogen bonds       : bond        0.03430 (  140)
  hydrogen bonds       : angle       4.95198 (  348)
  link_BETA1-6         : bond        0.01804 (    3)
  link_BETA1-6         : angle       2.14677 (    9)
  SS BOND              : bond        0.00329 (    7)
  SS BOND              : angle       0.85274 (   14)
  covalent geometry    : bond        0.00292 ( 5934)
  covalent geometry    : angle       0.70444 ( 8090)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.658 
Fit side-chains
  outliers start: 18
  outliers final: 14
  residues processed: 83
  average time/residue: 0.1762
  time to fit residues: 19.4757
Evaluate side-chains
  85 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue  116 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0670
   chunk 53 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0570
   chunk 32 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5236

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.150759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.125258 restraints weight = 9582.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.123161 restraints weight = 15047.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120213 restraints weight = 15909.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5956  Z= 0.134
  Angle     :  0.747  11.864   8149  Z= 0.357
  Chirality :  0.046   0.300    942
  Planarity :  0.005   0.047   1021
  Dihedral  :  7.801  53.617   1087
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.44 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.61 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.31), residues: 709
  helix: -2.84 (0.94), residues: 25
  sheet: -0.14 (0.37), residues: 227
  loop : -2.61 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  37 
 HIS   0.004   0.001   HIS A 207 
 PHE   0.013   0.001   PHE A  86 
 TYR   0.013   0.001   TYR D  51 
 ARG   0.007   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00791 (    6)
  link_NAG-ASN         : angle       4.32587 (   18)
  link_BETA1-4         : bond        0.00483 (    6)
  link_BETA1-4         : angle       1.85414 (   18)
  hydrogen bonds       : bond        0.03616 (  140)
  hydrogen bonds       : angle       4.96611 (  348)
  link_BETA1-6         : bond        0.01813 (    3)
  link_BETA1-6         : angle       2.22806 (    9)
  SS BOND              : bond        0.00349 (    7)
  SS BOND              : angle       0.89101 (   14)
  covalent geometry    : bond        0.00311 ( 5934)
  covalent geometry    : angle       0.71144 ( 8090)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.600 
Fit side-chains
  outliers start: 17
  outliers final: 16
  residues processed: 79
  average time/residue: 0.1665
  time to fit residues: 17.7911
Evaluate side-chains
  86 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  116 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 57 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.149931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 153)---------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.120624 restraints weight = 9667.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 136)---------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.110765 restraints weight = 14749.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.110189 restraints weight = 14743.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5956  Z= 0.156
  Angle     :  0.759  11.893   8149  Z= 0.365
  Chirality :  0.047   0.299    942
  Planarity :  0.005   0.049   1021
  Dihedral  :  7.873  53.039   1087
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.16 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 16.28 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.31), residues: 709
  helix: -2.94 (0.92), residues: 25
  sheet: -0.24 (0.36), residues: 233
  loop : -2.65 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  37 
 HIS   0.004   0.001   HIS A 207 
 PHE   0.018   0.001   PHE A  86 
 TYR   0.014   0.001   TYR D  51 
 ARG   0.009   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00778 (    6)
  link_NAG-ASN         : angle       4.34758 (   18)
  link_BETA1-4         : bond        0.00461 (    6)
  link_BETA1-4         : angle       1.87888 (   18)
  hydrogen bonds       : bond        0.04029 (  140)
  hydrogen bonds       : angle       5.06169 (  348)
  link_BETA1-6         : bond        0.01797 (    3)
  link_BETA1-6         : angle       2.26548 (    9)
  SS BOND              : bond        0.00369 (    7)
  SS BOND              : angle       0.91359 (   14)
  covalent geometry    : bond        0.00364 ( 5934)
  covalent geometry    : angle       0.72359 ( 8090)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2938.33 seconds
wall clock time: 52 minutes 13.25 seconds (3133.25 seconds total)