Starting phenix.real_space_refine
on Thu Jun 12 20:10:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z27_39743/06_2025/8z27_39743.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z27_39743/06_2025/8z27_39743.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z27_39743/06_2025/8z27_39743.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z27_39743/06_2025/8z27_39743.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z27_39743/06_2025/8z27_39743.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z27_39743/06_2025/8z27_39743.cif"
  }
  resolution = 2.86
  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=   0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6946 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    5481      2.51       5
     N    1418      2.21       5
     O    1666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8596
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "a"
      Number of atoms: 1118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1118
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 4, 'TRANS': 137}
          Chain breaks: 2
    Chain: "b"
      Number of atoms: 7292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 905, 7292
          Classifications: {'peptide': 905}
          Link IDs: {'PTRANS': 43, 'TRANS': 861}
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "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: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      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: "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: 6.72, per 1000 atoms: 0.78
  Number of scatterers: 8596
  At special positions: 0
  Unit cell: (97.98, 124.2, 92.46, 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      31     16.00
     O    1666      8.00
     N    1418      7.00
     C    5481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS a  72 " - pdb=" SG  CYS a 131 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a  86 " - pdb=" SG  CYS a  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 114 " - pdb=" SG  CYS a 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 769 " - pdb=" SG  CYS b 776 " distance=2.04
    Simple disulfide: pdb=" SG  CYS b 806 " - pdb=" SG  CYS b 842 " 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 A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    BETA1-6
      " NAG D   1 " - " FUC D   4 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A   1 " - " ASN a  58 "
      " NAG B   1 " - " ASN b 533 "
      " NAG C   1 " - " ASN b 633 "
      " NAG D   1 " - " ASN b 747 "
      " NAG E   1 " - " ASN b 689 "
      " NAG a 201 " - " ASN a  98 "
  Time building additional restraints: 2.69
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2004

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 12 sheets defined
      45.0% alpha, 14.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'a' and resid 100 through 104
    Processing helix  chain 'b' and resid 220 through 227
      removed outlier: 4.490A  pdb=" N   ARG b 224 " --> pdb=" O   ALA b 220 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 311 through 318
    Processing helix  chain 'b' and resid 320 through 339
      removed outlier: 4.037A  pdb=" N   GLY b 328 " --> pdb=" O   LEU b 324 " (cutoff:3.500A)
      Proline residue:  b 329  - end of helix
    Processing helix  chain 'b' and resid 370 through 374
    Processing helix  chain 'b' and resid 381 through 400
      removed outlier: 3.783A  pdb=" N   TRP b 400 " --> pdb=" O   LEU b 396 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 409 through 411
      No H-bonds generated for 'chain 'b' and resid 409 through 411'
    Processing helix  chain 'b' and resid 412 through 432
    Processing helix  chain 'b' and resid 436 through 445
      removed outlier: 4.275A  pdb=" N   VAL b 442 " --> pdb=" O   LYS b 438 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   LEU b 443 " --> pdb=" O   ASP b 439 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 445 through 455
      removed outlier: 3.507A  pdb=" N   ALA b 451 " --> pdb=" O   TYR b 447 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL b 452 " --> pdb=" O   ARG b 448 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 470 through 478
      removed outlier: 3.907A  pdb=" N   PHE b 478 " --> pdb=" O   ILE b 474 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 479 through 497
      removed outlier: 3.559A  pdb=" N   GLY b 486 " --> pdb=" O   SER b 482 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 499 through 513
    Processing helix  chain 'b' and resid 519 through 534
      removed outlier: 3.817A  pdb=" N   LEU b 523 " --> pdb=" O   ILE b 519 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 542 through 553
      removed outlier: 3.568A  pdb=" N   ARG b 549 " --> pdb=" O   ALA b 545 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TRP b 550 " --> pdb=" O   ILE b 546 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLN b 553 " --> pdb=" O   ARG b 549 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 631 through 635
      removed outlier: 3.867A  pdb=" N   THR b 635 " --> pdb=" O   LEU b 632 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 643 through 657
    Processing helix  chain 'b' and resid 662 through 679
    Processing helix  chain 'b' and resid 683 through 693
      removed outlier: 3.559A  pdb=" N   ALA b 687 " --> pdb=" O   PRO b 683 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   PHE b 693 " --> pdb=" O   ASN b 689 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 694 through 696
      No H-bonds generated for 'chain 'b' and resid 694 through 696'
    Processing helix  chain 'b' and resid 699 through 718
      removed outlier: 3.632A  pdb=" N   TRP b 703 " --> pdb=" O   GLU b 699 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   TYR b 712 " --> pdb=" O   SER b 708 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   PHE b 713 " --> pdb=" O   SER b 709 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 722 through 745
      Proline residue:  b 736  - end of helix
    Processing helix  chain 'b' and resid 754 through 771
    Processing helix  chain 'b' and resid 773 through 789
      removed outlier: 3.673A  pdb=" N   LYS b 777 " --> pdb=" O   VAL b 773 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 800 through 812
    Processing helix  chain 'b' and resid 813 through 827
      removed outlier: 3.546A  pdb=" N   TRP b 817 " --> pdb=" O   GLY b 813 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 829 through 841
      removed outlier: 4.024A  pdb=" N   ALA b 841 " --> pdb=" O   ARG b 837 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 845 through 858
      removed outlier: 4.198A  pdb=" N   LEU b 857 " --> pdb=" O   LEU b 853 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ASN b 858 " --> pdb=" O   SER b 854 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 863 through 877
      removed outlier: 4.145A  pdb=" N   ILE b 868 " --> pdb=" O   LYS b 864 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   SER b 869 " --> pdb=" O   GLN b 865 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 877 through 891
      removed outlier: 4.497A  pdb=" N   SER b 882 " --> pdb=" O   VAL b 878 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   LEU b 883 " --> pdb=" O   ILE b 879 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 891 through 900
    Processing helix  chain 'b' and resid 905 through 913
    Processing helix  chain 'b' and resid 919 through 933
    Processing helix  chain 'b' and resid 940 through 962
      removed outlier: 4.675A  pdb=" N   ALA b 944 " --> pdb=" O   SER b 940 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 962 through 977
    Processing sheet with id=AA1, first strand: chain 'a' and resid 51 through 53
      removed outlier: 3.882A  pdb=" N   ILE a  52 " --> pdb=" O   LYS a  44 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   THR a  38 " --> pdb=" O   THR a  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'a' and resid 51 through 53
      removed outlier: 3.882A  pdb=" N   ILE a  52 " --> pdb=" O   LYS a  44 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ARG a  97 " --> pdb=" O   SER a  88 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'a' and resid 106 through 109
      removed outlier: 3.516A  pdb=" N   THR a 106 " --> pdb=" O   ARG a 148 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ALA a 147 " --> pdb=" O   VAL a 155 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   VAL a 155 " --> pdb=" O   ALA a 147 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'b' and resid 143 through 146
      removed outlier: 3.870A  pdb=" N   GLU b 183 " --> pdb=" O   ARG b 146 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   THR b 118 " --> pdb=" O   PRO b  88 " (cutoff:3.500A)
      removed outlier: 9.148A  pdb=" N   THR b 238 " --> pdb=" O   ILE b  87 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   SER b  89 " --> pdb=" O   THR b 238 " (cutoff:3.500A)
      removed outlier: 8.306A  pdb=" N   ASN b 240 " --> pdb=" O   SER b  89 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   TYR b  91 " --> pdb=" O   ASN b 240 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   THR b 242 " --> pdb=" O   TYR b  91 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   VAL b  93 " --> pdb=" O   THR b 242 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ILE b 244 " --> pdb=" O   VAL b  93 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   LEU b  95 " --> pdb=" O   ILE b 244 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'b' and resid 125 through 128
    Processing sheet with id=AA6, first strand: chain 'b' and resid 199 through 206
    Processing sheet with id=AA7, first strand: chain 'b' and resid 250 through 253
    Processing sheet with id=AA8, first strand: chain 'b' and resid 294 through 295
      removed outlier: 6.877A  pdb=" N   TRP b 309 " --> pdb=" O   ALA b 351 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   ASP b 348 " --> pdb=" O   VAL b 366 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   TYR b 368 " --> pdb=" O   ASP b 348 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   ILE b 350 " --> pdb=" O   TYR b 368 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'b' and resid 401 through 402
    Processing sheet with id=AB1, first strand: chain 'b' and resid 614 through 616
      removed outlier: 7.576A  pdb=" N   ASN b 641 " --> pdb=" O   PRO b 557 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   VAL b 559 " --> pdb=" O   ASN b 641 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'b' and resid 593 through 595
    Processing sheet with id=AB3, first strand: chain 'b' and resid 602 through 603

    380 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.19

  Time building geometry restraints manager: 3.16 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2033
        1.33 -     1.45: 2000
        1.45 -     1.57: 4727
        1.57 -     1.69: 1
        1.69 -     1.81: 50
  Bond restraints: 8811
  Sorted by residual:
  bond pdb=" C   THR b 216 "
       pdb=" N   GLN b 217 "
    ideal  model  delta    sigma   weight residual
    1.330  1.394 -0.064 1.39e-02 5.18e+03 2.13e+01
  bond pdb=" CA  GLN a  64 "
       pdb=" C   GLN a  64 "
    ideal  model  delta    sigma   weight residual
    1.525  1.486  0.038 1.28e-02 6.10e+03 8.96e+00
  bond pdb=" C   TRP b 958 "
       pdb=" O   TRP b 958 "
    ideal  model  delta    sigma   weight residual
    1.237  1.205  0.031 1.17e-02 7.31e+03 7.18e+00
  bond pdb=" CA  ASN a 128 "
       pdb=" C   ASN a 128 "
    ideal  model  delta    sigma   weight residual
    1.523  1.488  0.036 1.34e-02 5.57e+03 7.03e+00
  bond pdb=" CA  MET b 609 "
       pdb=" C   MET b 609 "
    ideal  model  delta    sigma   weight residual
    1.528  1.500  0.028 1.08e-02 8.57e+03 6.64e+00
  ... (remaining 8806 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 11066
        2.49 -     4.98: 775
        4.98 -     7.47: 132
        7.47 -     9.95: 26
        9.95 -    12.44: 9
  Bond angle restraints: 12008
  Sorted by residual:
  angle pdb=" N   TYR a  48 "
        pdb=" CA  TYR a  48 "
        pdb=" C   TYR a  48 "
      ideal   model   delta    sigma   weight residual
     113.17  101.60   11.57 1.26e+00 6.30e-01 8.43e+01
  angle pdb=" N   TRP b 748 "
        pdb=" CA  TRP b 748 "
        pdb=" C   TRP b 748 "
      ideal   model   delta    sigma   weight residual
     112.24  122.09   -9.85 1.28e+00 6.10e-01 5.92e+01
  angle pdb=" N   ASN a  67 "
        pdb=" CA  ASN a  67 "
        pdb=" C   ASN a  67 "
      ideal   model   delta    sigma   weight residual
     108.73  120.84  -12.11 1.63e+00 3.76e-01 5.52e+01
  angle pdb=" N   GLY a  47 "
        pdb=" CA  GLY a  47 "
        pdb=" C   GLY a  47 "
      ideal   model   delta    sigma   weight residual
     114.92  105.55    9.37 1.30e+00 5.92e-01 5.20e+01
  angle pdb=" N   THR b 844 "
        pdb=" CA  THR b 844 "
        pdb=" C   THR b 844 "
      ideal   model   delta    sigma   weight residual
     111.36  119.15   -7.79 1.09e+00 8.42e-01 5.11e+01
  ... (remaining 12003 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.37: 4394
       21.37 -    42.74: 606
       42.74 -    64.10: 345
       64.10 -    85.47: 44
       85.47 -   106.84: 12
  Dihedral angle restraints: 5401
    sinusoidal: 2306
      harmonic: 3095
  Sorted by residual:
  dihedral pdb=" N   ARG b 307 "
           pdb=" C   ARG b 307 "
           pdb=" CA  ARG b 307 "
           pdb=" CB  ARG b 307 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  141.91  -19.11     0      2.50e+00 1.60e-01 5.84e+01
  dihedral pdb=" C   ARG b 307 "
           pdb=" N   ARG b 307 "
           pdb=" CA  ARG b 307 "
           pdb=" CB  ARG b 307 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.56   18.96     0      2.50e+00 1.60e-01 5.75e+01
  dihedral pdb=" C   VAL a  80 "
           pdb=" N   VAL a  80 "
           pdb=" CA  VAL a  80 "
           pdb=" CB  VAL a  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -139.81   17.81     0      2.50e+00 1.60e-01 5.07e+01
  ... (remaining 5398 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.160: 1210
       0.160 -    0.319: 147
       0.319 -    0.479: 16
       0.479 -    0.639: 5
       0.639 -    0.798: 1
  Chirality restraints: 1379
  Sorted by residual:
  chirality pdb=" C1  BMA A   3 "
            pdb=" O4  NAG A   2 "
            pdb=" C2  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-02 2.50e+03 1.10e+02
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-02 2.50e+03 9.25e+01
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-02 2.50e+03 9.12e+01
  ... (remaining 1376 not shown)

  Planarity restraints: 1521
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   2 "    0.358 2.00e-02 2.50e+03   3.08e-01 1.18e+03
        pdb=" C7  NAG B   2 "   -0.087 2.00e-02 2.50e+03
        pdb=" C8  NAG B   2 "    0.124 2.00e-02 2.50e+03
        pdb=" N2  NAG B   2 "   -0.547 2.00e-02 2.50e+03
        pdb=" O7  NAG B   2 "    0.152 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG a 201 "   -0.309 2.00e-02 2.50e+03   2.60e-01 8.44e+02
        pdb=" C7  NAG a 201 "    0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG a 201 "   -0.191 2.00e-02 2.50e+03
        pdb=" N2  NAG a 201 "    0.446 2.00e-02 2.50e+03
        pdb=" O7  NAG a 201 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "    0.196 2.00e-02 2.50e+03   1.62e-01 3.27e+02
        pdb=" C7  NAG D   1 "   -0.054 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "    0.143 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "   -0.261 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1518 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2515
        2.81 -     3.33: 8038
        3.33 -     3.86: 16703
        3.86 -     4.38: 19679
        4.38 -     4.90: 30103
  Nonbonded interactions: 77038
  Sorted by model distance:
  nonbonded pdb=" CG1 VAL b 262 "
            pdb=" OG1 THR b 265 "
     model   vdw
     2.290 3.460
  nonbonded pdb=" CD1 ILE a  59 "
            pdb=" CD2 LEU a  61 "
     model   vdw
     2.312 3.880
  nonbonded pdb=" CB  VAL b 262 "
            pdb=" OG1 THR b 265 "
     model   vdw
     2.383 3.470
  nonbonded pdb=" N   TYR a  48 "
            pdb=" N   GLY a  49 "
     model   vdw
     2.399 2.560
  nonbonded pdb=" N   LEU a  56 "
            pdb=" NH2 ARG a 157 "
     model   vdw
     2.419 3.200
  ... (remaining 77033 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 '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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     26.160
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4785
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      :  0.007   0.064   8830  Z= 0.534
  Angle     :  1.413  12.443  12060  Z= 0.942
  Chirality :  0.109   0.798   1379
  Planarity :  0.016   0.308   1515
  Dihedral  : 24.392 106.837   3382
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  1.44 %
    Favored  : 98.17 %
  Rotamer:
    Outliers : 32.69 %
    Allowed  : 18.16 %
    Favored  : 49.15 %
  Cbeta Deviations :  0.90 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.16 (0.25), residues: 1039
  helix:  3.98 (0.22), residues: 426
  sheet:  1.25 (0.37), residues: 186
  loop :  0.52 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP b 969 
 HIS   0.005   0.001   HIS b 394 
 PHE   0.032   0.003   PHE b 496 
 TYR   0.022   0.002   TYR b 368 
 ARG   0.005   0.001   ARG b 142 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00501 (    6)
  link_NAG-ASN         : angle       2.80140 (   18)
  link_BETA1-4         : bond        0.00293 (    7)
  link_BETA1-4         : angle       1.19858 (   21)
  hydrogen bonds       : bond        0.21957 (  379)
  hydrogen bonds       : angle       7.64993 ( 1101)
  link_BETA1-6         : bond        0.00104 (    1)
  link_BETA1-6         : angle       0.82342 (    3)
  SS BOND              : bond        0.00452 (    5)
  SS BOND              : angle       0.79232 (   10)
  covalent geometry    : bond        0.00732 ( 8811)
  covalent geometry    : angle       1.41071 (12008)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  474 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 306
    poor density    : 168
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: b  479 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5298 (p0)
  outliers start: 306
  outliers final: 43
  residues processed: 415
  average time/residue: 0.9213
  time to fit residues: 412.4283
Evaluate side-chains
  121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 77
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   59 ILE
Chi-restraints excluded: chain a residue   79 SER
Chi-restraints excluded: chain a residue  101 ASP
Chi-restraints excluded: chain a residue  111 THR
Chi-restraints excluded: chain a residue  120 LYS
Chi-restraints excluded: chain a residue  121 LEU
Chi-restraints excluded: chain a residue  129 LYS
Chi-restraints excluded: chain a residue  132 LEU
Chi-restraints excluded: chain a residue  137 VAL
Chi-restraints excluded: chain a residue  148 ARG
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  159 LEU
Chi-restraints excluded: chain a residue  165 GLU
Chi-restraints excluded: chain a residue  170 VAL
Chi-restraints excluded: chain b residue   85 THR
Chi-restraints excluded: chain b residue  104 ASN
Chi-restraints excluded: chain b residue  143 VAL
Chi-restraints excluded: chain b residue  164 VAL
Chi-restraints excluded: chain b residue  168 LEU
Chi-restraints excluded: chain b residue  169 VAL
Chi-restraints excluded: chain b residue  182 TYR
Chi-restraints excluded: chain b residue  187 LYS
Chi-restraints excluded: chain b residue  250 VAL
Chi-restraints excluded: chain b residue  253 SER
Chi-restraints excluded: chain b residue  258 ARG
Chi-restraints excluded: chain b residue  265 THR
Chi-restraints excluded: chain b residue  273 THR
Chi-restraints excluded: chain b residue  326 VAL
Chi-restraints excluded: chain b residue  442 VAL
Chi-restraints excluded: chain b residue  479 ASP
Chi-restraints excluded: chain b residue  483 TYR
Chi-restraints excluded: chain b residue  544 ASN
Chi-restraints excluded: chain b residue  561 VAL
Chi-restraints excluded: chain b residue  591 TRP
Chi-restraints excluded: chain b residue  690 SER
Chi-restraints excluded: chain b residue  756 THR
Chi-restraints excluded: chain b residue  789 LYS
Chi-restraints excluded: chain b residue  802 SER
Chi-restraints excluded: chain b residue  838 SER
Chi-restraints excluded: chain b residue  864 LYS
Chi-restraints excluded: chain b residue  876 SER
Chi-restraints excluded: chain b residue  910 ILE
Chi-restraints excluded: chain b residue  958 TRP
Chi-restraints excluded: chain b residue  961 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 60 optimal weight:   20.0000
   chunk 94 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
a  93 ASN
a 154 GLN
b 104 ASN
** b 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 171 HIS
b 179 ASN
b 295 ASN
b 356 ASN
b 399 GLN
b 403 ASN
b 733 GLN
** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 889 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.103096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.077348 restraints weight = 34809.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 4.81
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   8830  Z= 0.262
  Angle     :  0.878  13.137  12060  Z= 0.463
  Chirality :  0.052   0.264   1379
  Planarity :  0.007   0.058   1515
  Dihedral  : 11.989  66.891   1499
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 19.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.41 %
    Favored  : 97.50 %
  Rotamer:
    Outliers : 11.00 %
    Allowed  : 28.85 %
    Favored  : 60.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.25), residues: 1039
  helix:  1.88 (0.23), residues: 441
  sheet:  0.68 (0.37), residues: 183
  loop : -0.10 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP b 892 
 HIS   0.009   0.002   HIS a  83 
 PHE   0.028   0.003   PHE b 784 
 TYR   0.026   0.002   TYR a  71 
 ARG   0.007   0.001   ARG b 549 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00534 (    6)
  link_NAG-ASN         : angle       2.64993 (   18)
  link_BETA1-4         : bond        0.00392 (    7)
  link_BETA1-4         : angle       1.69186 (   21)
  hydrogen bonds       : bond        0.08157 (  379)
  hydrogen bonds       : angle       6.51617 ( 1101)
  link_BETA1-6         : bond        0.00239 (    1)
  link_BETA1-6         : angle       1.49475 (    3)
  SS BOND              : bond        0.00689 (    5)
  SS BOND              : angle       1.48519 (   10)
  covalent geometry    : bond        0.00573 ( 8811)
  covalent geometry    : angle       0.86938 (12008)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 103
    poor density    : 85
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a  118 PHE cc_start: 0.8812 (m-80) cc_final: 0.8467 (m-80)
REVERT: a  128 ASN cc_start: 0.9418 (t0) cc_final: 0.9178 (m-40)
REVERT: b  146 ARG cc_start: 0.1099 (OUTLIER) cc_final: 0.0865 (pmt170)
REVERT: b  157 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7482 (m-30)
REVERT: b  200 TYR cc_start: 0.8320 (p90) cc_final: 0.7897 (p90)
REVERT: b  315 MET cc_start: 0.6916 (mmm) cc_final: 0.6684 (mmp)
REVERT: b  449 VAL cc_start: 0.9603 (t) cc_final: 0.9389 (p)
REVERT: b  675 ASP cc_start: 0.8598 (m-30) cc_final: 0.8271 (t70)
REVERT: b  775 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6121 (mtpp)
REVERT: b  916 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7933 (ttp-170)
REVERT: b  958 TRP cc_start: 0.4738 (OUTLIER) cc_final: 0.3491 (t-100)
  outliers start: 103
  outliers final: 40
  residues processed: 171
  average time/residue: 0.8412
  time to fit residues: 157.6158
Evaluate side-chains
  111 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 66
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   31 THR
Chi-restraints excluded: chain a residue   55 THR
Chi-restraints excluded: chain a residue   78 PHE
Chi-restraints excluded: chain a residue   79 SER
Chi-restraints excluded: chain a residue   97 ARG
Chi-restraints excluded: chain a residue  111 THR
Chi-restraints excluded: chain a residue  119 ASP
Chi-restraints excluded: chain a residue  121 LEU
Chi-restraints excluded: chain a residue  132 LEU
Chi-restraints excluded: chain a residue  137 VAL
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  165 GLU
Chi-restraints excluded: chain b residue   85 THR
Chi-restraints excluded: chain b residue   89 SER
Chi-restraints excluded: chain b residue  108 THR
Chi-restraints excluded: chain b residue  130 SER
Chi-restraints excluded: chain b residue  146 ARG
Chi-restraints excluded: chain b residue  157 ASP
Chi-restraints excluded: chain b residue  164 VAL
Chi-restraints excluded: chain b residue  168 LEU
Chi-restraints excluded: chain b residue  181 GLN
Chi-restraints excluded: chain b residue  187 LYS
Chi-restraints excluded: chain b residue  205 THR
Chi-restraints excluded: chain b residue  215 THR
Chi-restraints excluded: chain b residue  236 LYS
Chi-restraints excluded: chain b residue  250 VAL
Chi-restraints excluded: chain b residue  273 THR
Chi-restraints excluded: chain b residue  326 VAL
Chi-restraints excluded: chain b residue  479 ASP
Chi-restraints excluded: chain b residue  544 ASN
Chi-restraints excluded: chain b residue  561 VAL
Chi-restraints excluded: chain b residue  591 TRP
Chi-restraints excluded: chain b residue  623 THR
Chi-restraints excluded: chain b residue  649 LYS
Chi-restraints excluded: chain b residue  682 VAL
Chi-restraints excluded: chain b residue  775 LYS
Chi-restraints excluded: chain b residue  809 ILE
Chi-restraints excluded: chain b residue  831 ASN
Chi-restraints excluded: chain b residue  844 THR
Chi-restraints excluded: chain b residue  864 LYS
Chi-restraints excluded: chain b residue  876 SER
Chi-restraints excluded: chain b residue  907 SER
Chi-restraints excluded: chain b residue  913 VAL
Chi-restraints excluded: chain b residue  916 ARG
Chi-restraints excluded: chain b residue  958 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   chunk 23 optimal weight:   30.0000
   chunk 37 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 4 optimal weight:    8.9990
   chunk 63 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** a  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 758 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.102462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.076893 restraints weight = 35189.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 4.69
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.5167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8830  Z= 0.198
  Angle     :  0.749   9.712  12060  Z= 0.393
  Chirality :  0.047   0.216   1379
  Planarity :  0.005   0.048   1515
  Dihedral  :  8.934  58.217   1452
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.69 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  7.91 %
    Allowed  : 29.49 %
    Favored  : 62.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.74 (0.25), residues: 1039
  helix:  1.40 (0.23), residues: 441
  sheet:  0.05 (0.35), residues: 216
  loop : -0.20 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP b 892 
 HIS   0.008   0.001   HIS a  83 
 PHE   0.022   0.002   PHE a 143 
 TYR   0.020   0.002   TYR b 284 
 ARG   0.007   0.001   ARG b 201 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00331 (    6)
  link_NAG-ASN         : angle       2.02017 (   18)
  link_BETA1-4         : bond        0.00364 (    7)
  link_BETA1-4         : angle       1.63480 (   21)
  hydrogen bonds       : bond        0.06570 (  379)
  hydrogen bonds       : angle       6.09312 ( 1101)
  link_BETA1-6         : bond        0.00475 (    1)
  link_BETA1-6         : angle       1.05638 (    3)
  SS BOND              : bond        0.00491 (    5)
  SS BOND              : angle       1.16559 (   10)
  covalent geometry    : bond        0.00436 ( 8811)
  covalent geometry    : angle       0.74198 (12008)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 74
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a  118 PHE cc_start: 0.8701 (m-80) cc_final: 0.8467 (m-80)
REVERT: a  128 ASN cc_start: 0.9373 (t0) cc_final: 0.9128 (m-40)
REVERT: b  200 TYR cc_start: 0.8180 (p90) cc_final: 0.7874 (p90)
REVERT: b  252 LEU cc_start: 0.6879 (mt) cc_final: 0.6586 (mt)
REVERT: b  450 MET cc_start: 0.8668 (mmt) cc_final: 0.8446 (mmt)
REVERT: b  479 ASP cc_start: 0.6460 (OUTLIER) cc_final: 0.5606 (p0)
REVERT: b  490 LEU cc_start: 0.8793 (tp) cc_final: 0.8432 (mp)
REVERT: b  675 ASP cc_start: 0.8613 (m-30) cc_final: 0.8326 (t70)
  outliers start: 74
  outliers final: 36
  residues processed: 137
  average time/residue: 0.8448
  time to fit residues: 127.1258
Evaluate side-chains
  97 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 60
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   55 THR
Chi-restraints excluded: chain a residue   78 PHE
Chi-restraints excluded: chain a residue   79 SER
Chi-restraints excluded: chain a residue  111 THR
Chi-restraints excluded: chain a residue  113 THR
Chi-restraints excluded: chain a residue  119 ASP
Chi-restraints excluded: chain a residue  121 LEU
Chi-restraints excluded: chain a residue  137 VAL
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  159 LEU
Chi-restraints excluded: chain a residue  165 GLU
Chi-restraints excluded: chain b residue   85 THR
Chi-restraints excluded: chain b residue   89 SER
Chi-restraints excluded: chain b residue  108 THR
Chi-restraints excluded: chain b residue  130 SER
Chi-restraints excluded: chain b residue  164 VAL
Chi-restraints excluded: chain b residue  169 VAL
Chi-restraints excluded: chain b residue  181 GLN
Chi-restraints excluded: chain b residue  187 LYS
Chi-restraints excluded: chain b residue  205 THR
Chi-restraints excluded: chain b residue  215 THR
Chi-restraints excluded: chain b residue  308 ILE
Chi-restraints excluded: chain b residue  326 VAL
Chi-restraints excluded: chain b residue  479 ASP
Chi-restraints excluded: chain b residue  494 SER
Chi-restraints excluded: chain b residue  554 MET
Chi-restraints excluded: chain b residue  561 VAL
Chi-restraints excluded: chain b residue  575 LEU
Chi-restraints excluded: chain b residue  591 TRP
Chi-restraints excluded: chain b residue  649 LYS
Chi-restraints excluded: chain b residue  682 VAL
Chi-restraints excluded: chain b residue  766 SER
Chi-restraints excluded: chain b residue  803 THR
Chi-restraints excluded: chain b residue  809 ILE
Chi-restraints excluded: chain b residue  831 ASN
Chi-restraints excluded: chain b residue  869 SER
Chi-restraints excluded: chain b residue  876 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 28 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   chunk 15 optimal weight:   30.0000
   chunk 1 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** a  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 207 ASN
** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 793 ASN
** b 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.100360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.074750 restraints weight = 35287.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 4.62
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.5702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8830  Z= 0.220
  Angle     :  0.730  10.084  12060  Z= 0.384
  Chirality :  0.046   0.201   1379
  Planarity :  0.005   0.046   1515
  Dihedral  :  7.457  57.394   1438
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 17.83
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.98 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 31.62 %
    Favored  : 61.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.40 (0.25), residues: 1039
  helix:  1.11 (0.24), residues: 441
  sheet: -0.04 (0.36), residues: 204
  loop : -0.40 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP b  77 
 HIS   0.006   0.001   HIS b 671 
 PHE   0.018   0.002   PHE b 496 
 TYR   0.017   0.002   TYR b 712 
 ARG   0.006   0.001   ARG a 157 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00450 (    6)
  link_NAG-ASN         : angle       1.98596 (   18)
  link_BETA1-4         : bond        0.00312 (    7)
  link_BETA1-4         : angle       1.44044 (   21)
  hydrogen bonds       : bond        0.06730 (  379)
  hydrogen bonds       : angle       5.96940 ( 1101)
  link_BETA1-6         : bond        0.01029 (    1)
  link_BETA1-6         : angle       0.86982 (    3)
  SS BOND              : bond        0.00413 (    5)
  SS BOND              : angle       1.55479 (   10)
  covalent geometry    : bond        0.00495 ( 8811)
  covalent geometry    : angle       0.72311 (12008)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 66
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a  118 PHE cc_start: 0.8646 (m-80) cc_final: 0.8428 (m-80)
REVERT: a  128 ASN cc_start: 0.9342 (t0) cc_final: 0.9042 (m-40)
REVERT: b  200 TYR cc_start: 0.8147 (p90) cc_final: 0.7872 (p90)
REVERT: b  252 LEU cc_start: 0.7050 (mt) cc_final: 0.6685 (mt)
REVERT: b  281 MET cc_start: 0.6542 (ptp) cc_final: 0.5995 (tmm)
REVERT: b  315 MET cc_start: 0.7307 (mmm) cc_final: 0.7066 (mmp)
REVERT: b  479 ASP cc_start: 0.6466 (OUTLIER) cc_final: 0.5654 (p0)
REVERT: b  490 LEU cc_start: 0.8805 (tp) cc_final: 0.8478 (mp)
REVERT: b  675 ASP cc_start: 0.8619 (m-30) cc_final: 0.8369 (t70)
REVERT: b  681 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8604 (tp)
  outliers start: 60
  outliers final: 33
  residues processed: 118
  average time/residue: 0.7433
  time to fit residues: 97.3189
Evaluate side-chains
  92 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 57
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   55 THR
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   78 PHE
Chi-restraints excluded: chain a residue   79 SER
Chi-restraints excluded: chain a residue   97 ARG
Chi-restraints excluded: chain a residue  113 THR
Chi-restraints excluded: chain a residue  121 LEU
Chi-restraints excluded: chain a residue  137 VAL
Chi-restraints excluded: chain a residue  141 CYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  159 LEU
Chi-restraints excluded: chain a residue  165 GLU
Chi-restraints excluded: chain b residue  108 THR
Chi-restraints excluded: chain b residue  130 SER
Chi-restraints excluded: chain b residue  164 VAL
Chi-restraints excluded: chain b residue  186 SER
Chi-restraints excluded: chain b residue  215 THR
Chi-restraints excluded: chain b residue  308 ILE
Chi-restraints excluded: chain b residue  326 VAL
Chi-restraints excluded: chain b residue  479 ASP
Chi-restraints excluded: chain b residue  497 LEU
Chi-restraints excluded: chain b residue  554 MET
Chi-restraints excluded: chain b residue  561 VAL
Chi-restraints excluded: chain b residue  575 LEU
Chi-restraints excluded: chain b residue  591 TRP
Chi-restraints excluded: chain b residue  681 ILE
Chi-restraints excluded: chain b residue  682 VAL
Chi-restraints excluded: chain b residue  766 SER
Chi-restraints excluded: chain b residue  803 THR
Chi-restraints excluded: chain b residue  809 ILE
Chi-restraints excluded: chain b residue  831 ASN
Chi-restraints excluded: chain b residue  844 THR
Chi-restraints excluded: chain b residue  869 SER
Chi-restraints excluded: chain b residue  876 SER
Chi-restraints excluded: chain b residue  926 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 43 optimal weight:    9.9990
   chunk 96 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:   30.0000
   chunk 5 optimal weight:   20.0000
   chunk 83 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 644 GLN
** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.100376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.075036 restraints weight = 35581.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 4.61
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.6038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8830  Z= 0.185
  Angle     :  0.692  10.510  12060  Z= 0.362
  Chirality :  0.045   0.201   1379
  Planarity :  0.005   0.045   1515
  Dihedral  :  6.771  59.811   1432
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 16.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.27 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 31.41 %
    Favored  : 62.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.36 (0.26), residues: 1039
  helix:  1.12 (0.24), residues: 441
  sheet: -0.06 (0.36), residues: 199
  loop : -0.48 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP b  77 
 HIS   0.005   0.001   HIS b 671 
 PHE   0.020   0.002   PHE a 143 
 TYR   0.020   0.002   TYR a 163 
 ARG   0.010   0.001   ARG a 148 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00304 (    6)
  link_NAG-ASN         : angle       1.68526 (   18)
  link_BETA1-4         : bond        0.00362 (    7)
  link_BETA1-4         : angle       1.30806 (   21)
  hydrogen bonds       : bond        0.05987 (  379)
  hydrogen bonds       : angle       5.78796 ( 1101)
  link_BETA1-6         : bond        0.00743 (    1)
  link_BETA1-6         : angle       0.76700 (    3)
  SS BOND              : bond        0.00331 (    5)
  SS BOND              : angle       1.41860 (   10)
  covalent geometry    : bond        0.00415 ( 8811)
  covalent geometry    : angle       0.68703 (12008)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 65
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   81 TYR cc_start: 0.7932 (m-10) cc_final: 0.7705 (m-10)
REVERT: a  118 PHE cc_start: 0.8599 (m-80) cc_final: 0.8383 (m-80)
REVERT: a  148 ARG cc_start: 0.7544 (ptm160) cc_final: 0.6157 (ppt170)
REVERT: b  200 TYR cc_start: 0.8179 (p90) cc_final: 0.7910 (p90)
REVERT: b  252 LEU cc_start: 0.7177 (mt) cc_final: 0.6746 (mt)
REVERT: b  479 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.5718 (p0)
REVERT: b  490 LEU cc_start: 0.8785 (tp) cc_final: 0.8499 (mp)
REVERT: b  675 ASP cc_start: 0.8618 (m-30) cc_final: 0.8364 (t70)
REVERT: b  793 ASN cc_start: 0.6859 (OUTLIER) cc_final: 0.6645 (p0)
  outliers start: 61
  outliers final: 38
  residues processed: 119
  average time/residue: 0.7129
  time to fit residues: 94.3909
Evaluate side-chains
  97 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 57
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   55 THR
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   78 PHE
Chi-restraints excluded: chain a residue   79 SER
Chi-restraints excluded: chain a residue  113 THR
Chi-restraints excluded: chain a residue  119 ASP
Chi-restraints excluded: chain a residue  121 LEU
Chi-restraints excluded: chain a residue  137 VAL
Chi-restraints excluded: chain a residue  141 CYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  159 LEU
Chi-restraints excluded: chain a residue  165 GLU
Chi-restraints excluded: chain b residue  108 THR
Chi-restraints excluded: chain b residue  130 SER
Chi-restraints excluded: chain b residue  164 VAL
Chi-restraints excluded: chain b residue  169 VAL
Chi-restraints excluded: chain b residue  181 GLN
Chi-restraints excluded: chain b residue  186 SER
Chi-restraints excluded: chain b residue  205 THR
Chi-restraints excluded: chain b residue  213 LEU
Chi-restraints excluded: chain b residue  215 THR
Chi-restraints excluded: chain b residue  308 ILE
Chi-restraints excluded: chain b residue  326 VAL
Chi-restraints excluded: chain b residue  479 ASP
Chi-restraints excluded: chain b residue  497 LEU
Chi-restraints excluded: chain b residue  554 MET
Chi-restraints excluded: chain b residue  561 VAL
Chi-restraints excluded: chain b residue  575 LEU
Chi-restraints excluded: chain b residue  591 TRP
Chi-restraints excluded: chain b residue  628 VAL
Chi-restraints excluded: chain b residue  681 ILE
Chi-restraints excluded: chain b residue  682 VAL
Chi-restraints excluded: chain b residue  793 ASN
Chi-restraints excluded: chain b residue  803 THR
Chi-restraints excluded: chain b residue  809 ILE
Chi-restraints excluded: chain b residue  831 ASN
Chi-restraints excluded: chain b residue  844 THR
Chi-restraints excluded: chain b residue  869 SER
Chi-restraints excluded: chain b residue  876 SER
Chi-restraints excluded: chain b residue  926 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 46 optimal weight:   20.0000
   chunk 42 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 86 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** a  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 399 GLN
** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 889 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.097718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.072054 restraints weight = 36435.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 4.65
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.6440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   8830  Z= 0.255
  Angle     :  0.764  11.044  12060  Z= 0.400
  Chirality :  0.046   0.209   1379
  Planarity :  0.006   0.069   1515
  Dihedral  :  6.953  57.443   1432
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 18.78
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.04 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 31.84 %
    Favored  : 61.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.08 (0.25), residues: 1039
  helix:  0.74 (0.24), residues: 440
  sheet: -0.24 (0.36), residues: 204
  loop : -0.73 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP b  77 
 HIS   0.007   0.002   HIS b 671 
 PHE   0.028   0.003   PHE a 127 
 TYR   0.017   0.002   TYR b 899 
 ARG   0.007   0.001   ARG a 148 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00517 (    6)
  link_NAG-ASN         : angle       1.90382 (   18)
  link_BETA1-4         : bond        0.00220 (    7)
  link_BETA1-4         : angle       1.38637 (   21)
  hydrogen bonds       : bond        0.07283 (  379)
  hydrogen bonds       : angle       5.94259 ( 1101)
  link_BETA1-6         : bond        0.00588 (    1)
  link_BETA1-6         : angle       0.77085 (    3)
  SS BOND              : bond        0.00415 (    5)
  SS BOND              : angle       1.65444 (   10)
  covalent geometry    : bond        0.00575 ( 8811)
  covalent geometry    : angle       0.75785 (12008)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 64
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   81 TYR cc_start: 0.7750 (m-10) cc_final: 0.7441 (m-10)
REVERT: a  120 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7530 (mmpt)
REVERT: a  127 PHE cc_start: 0.7362 (t80) cc_final: 0.7101 (t80)
REVERT: b  200 TYR cc_start: 0.8160 (p90) cc_final: 0.7934 (p90)
REVERT: b  252 LEU cc_start: 0.7256 (mt) cc_final: 0.6794 (mt)
REVERT: b  281 MET cc_start: 0.6579 (ptp) cc_final: 0.5773 (tmm)
REVERT: b  479 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6176 (p0)
REVERT: b  490 LEU cc_start: 0.8834 (tp) cc_final: 0.8501 (mp)
REVERT: b  592 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7338 (pp)
REVERT: b  649 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8820 (ttpp)
REVERT: b  675 ASP cc_start: 0.8625 (m-30) cc_final: 0.8397 (t70)
REVERT: b  681 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8727 (tp)
REVERT: b  775 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.7042 (mmmm)
REVERT: b  793 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7418 (p0)
  outliers start: 61
  outliers final: 37
  residues processed: 119
  average time/residue: 0.6688
  time to fit residues: 89.1132
Evaluate side-chains
  102 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 58
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   55 THR
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   78 PHE
Chi-restraints excluded: chain a residue   79 SER
Chi-restraints excluded: chain a residue   89 SER
Chi-restraints excluded: chain a residue  113 THR
Chi-restraints excluded: chain a residue  119 ASP
Chi-restraints excluded: chain a residue  120 LYS
Chi-restraints excluded: chain a residue  121 LEU
Chi-restraints excluded: chain a residue  137 VAL
Chi-restraints excluded: chain a residue  141 CYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  165 GLU
Chi-restraints excluded: chain b residue  108 THR
Chi-restraints excluded: chain b residue  130 SER
Chi-restraints excluded: chain b residue  164 VAL
Chi-restraints excluded: chain b residue  169 VAL
Chi-restraints excluded: chain b residue  181 GLN
Chi-restraints excluded: chain b residue  205 THR
Chi-restraints excluded: chain b residue  215 THR
Chi-restraints excluded: chain b residue  242 THR
Chi-restraints excluded: chain b residue  308 ILE
Chi-restraints excluded: chain b residue  326 VAL
Chi-restraints excluded: chain b residue  446 VAL
Chi-restraints excluded: chain b residue  479 ASP
Chi-restraints excluded: chain b residue  494 SER
Chi-restraints excluded: chain b residue  561 VAL
Chi-restraints excluded: chain b residue  575 LEU
Chi-restraints excluded: chain b residue  591 TRP
Chi-restraints excluded: chain b residue  592 ILE
Chi-restraints excluded: chain b residue  628 VAL
Chi-restraints excluded: chain b residue  649 LYS
Chi-restraints excluded: chain b residue  681 ILE
Chi-restraints excluded: chain b residue  682 VAL
Chi-restraints excluded: chain b residue  766 SER
Chi-restraints excluded: chain b residue  775 LYS
Chi-restraints excluded: chain b residue  793 ASN
Chi-restraints excluded: chain b residue  803 THR
Chi-restraints excluded: chain b residue  809 ILE
Chi-restraints excluded: chain b residue  831 ASN
Chi-restraints excluded: chain b residue  844 THR
Chi-restraints excluded: chain b residue  869 SER
Chi-restraints excluded: chain b residue  876 SER
Chi-restraints excluded: chain b residue  926 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 68 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 46 optimal weight:   20.0000
   chunk 40 optimal weight:    5.9990
   chunk 18 optimal weight:   40.0000
   overall best weight:    3.7786

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

Flipped N/Q/H residues before XYZ refinement:
a 168 ASN
b 181 GLN
** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 973 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.097861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.072237 restraints weight = 36798.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 4.65
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.6778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8830  Z= 0.227
  Angle     :  0.739  11.148  12060  Z= 0.384
  Chirality :  0.045   0.234   1379
  Planarity :  0.006   0.064   1515
  Dihedral  :  6.922  56.835   1432
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.85 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 32.48 %
    Favored  : 61.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.17 (0.25), residues: 1039
  helix:  0.80 (0.24), residues: 434
  sheet: -0.25 (0.37), residues: 200
  loop : -0.95 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP b  77 
 HIS   0.014   0.002   HIS b 740 
 PHE   0.022   0.002   PHE b 496 
 TYR   0.023   0.002   TYR a 163 
 ARG   0.012   0.001   ARG a 148 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00349 (    6)
  link_NAG-ASN         : angle       1.70762 (   18)
  link_BETA1-4         : bond        0.00313 (    7)
  link_BETA1-4         : angle       1.35569 (   21)
  hydrogen bonds       : bond        0.06522 (  379)
  hydrogen bonds       : angle       5.91299 ( 1101)
  link_BETA1-6         : bond        0.00545 (    1)
  link_BETA1-6         : angle       0.79394 (    3)
  SS BOND              : bond        0.00386 (    5)
  SS BOND              : angle       1.94345 (   10)
  covalent geometry    : bond        0.00513 ( 8811)
  covalent geometry    : angle       0.73274 (12008)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 60
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: a   81 TYR cc_start: 0.7893 (m-10) cc_final: 0.7567 (m-10)
REVERT: a  120 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7197 (mmpt)
REVERT: a  127 PHE cc_start: 0.7044 (t80) cc_final: 0.6517 (t80)
REVERT: a  148 ARG cc_start: 0.7586 (mtp-110) cc_final: 0.7345 (ptm160)
REVERT: a  163 TYR cc_start: 0.7908 (t80) cc_final: 0.7702 (t80)
REVERT: b  181 GLN cc_start: 0.1476 (OUTLIER) cc_final: 0.1020 (tm-30)
REVERT: b  200 TYR cc_start: 0.8078 (p90) cc_final: 0.7876 (p90)
REVERT: b  252 LEU cc_start: 0.7355 (mt) cc_final: 0.6903 (mt)
REVERT: b  281 MET cc_start: 0.6708 (ptp) cc_final: 0.5883 (tmm)
REVERT: b  479 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6242 (p0)
REVERT: b  490 LEU cc_start: 0.8837 (tp) cc_final: 0.8525 (mp)
REVERT: b  675 ASP cc_start: 0.8617 (m-30) cc_final: 0.8407 (t70)
REVERT: b  681 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8719 (tp)
REVERT: b  775 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.7028 (mmmm)
REVERT: b  793 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7728 (p0)
REVERT: b  916 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8213 (ttp-170)
  outliers start: 59
  outliers final: 34
  residues processed: 113
  average time/residue: 0.7443
  time to fit residues: 93.6714
Evaluate side-chains
  92 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 51
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   55 THR
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   78 PHE
Chi-restraints excluded: chain a residue   79 SER
Chi-restraints excluded: chain a residue  119 ASP
Chi-restraints excluded: chain a residue  120 LYS
Chi-restraints excluded: chain a residue  121 LEU
Chi-restraints excluded: chain a residue  141 CYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  159 LEU
Chi-restraints excluded: chain a residue  165 GLU
Chi-restraints excluded: chain b residue  108 THR
Chi-restraints excluded: chain b residue  130 SER
Chi-restraints excluded: chain b residue  164 VAL
Chi-restraints excluded: chain b residue  168 LEU
Chi-restraints excluded: chain b residue  169 VAL
Chi-restraints excluded: chain b residue  181 GLN
Chi-restraints excluded: chain b residue  186 SER
Chi-restraints excluded: chain b residue  213 LEU
Chi-restraints excluded: chain b residue  215 THR
Chi-restraints excluded: chain b residue  242 THR
Chi-restraints excluded: chain b residue  308 ILE
Chi-restraints excluded: chain b residue  326 VAL
Chi-restraints excluded: chain b residue  446 VAL
Chi-restraints excluded: chain b residue  479 ASP
Chi-restraints excluded: chain b residue  494 SER
Chi-restraints excluded: chain b residue  561 VAL
Chi-restraints excluded: chain b residue  575 LEU
Chi-restraints excluded: chain b residue  591 TRP
Chi-restraints excluded: chain b residue  628 VAL
Chi-restraints excluded: chain b residue  681 ILE
Chi-restraints excluded: chain b residue  682 VAL
Chi-restraints excluded: chain b residue  775 LYS
Chi-restraints excluded: chain b residue  793 ASN
Chi-restraints excluded: chain b residue  803 THR
Chi-restraints excluded: chain b residue  809 ILE
Chi-restraints excluded: chain b residue  831 ASN
Chi-restraints excluded: chain b residue  844 THR
Chi-restraints excluded: chain b residue  869 SER
Chi-restraints excluded: chain b residue  876 SER
Chi-restraints excluded: chain b residue  916 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 102 optimal weight:    0.6980
   chunk 90 optimal weight:    0.7980
   chunk 18 optimal weight:   40.0000
   chunk 27 optimal weight:    9.9990
   chunk 101 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 57 optimal weight:   20.0000
   chunk 9 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   overall best weight:    2.2984

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

Flipped N/Q/H residues before XYZ refinement:
b 181 GLN
** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 297 GLN
** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.099004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.073356 restraints weight = 36863.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 4.71
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.6935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8830  Z= 0.171
  Angle     :  0.718  12.075  12060  Z= 0.366
  Chirality :  0.045   0.293   1379
  Planarity :  0.005   0.060   1515
  Dihedral  :  6.628  58.007   1431
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.33 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 33.33 %
    Favored  : 61.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.05 (0.25), residues: 1039
  helix:  0.94 (0.24), residues: 440
  sheet: -0.26 (0.37), residues: 199
  loop : -0.92 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP b  77 
 HIS   0.012   0.001   HIS b 740 
 PHE   0.020   0.002   PHE b 496 
 TYR   0.022   0.002   TYR a 163 
 ARG   0.009   0.001   ARG a 148 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00244 (    6)
  link_NAG-ASN         : angle       1.50677 (   18)
  link_BETA1-4         : bond        0.00297 (    7)
  link_BETA1-4         : angle       1.35275 (   21)
  hydrogen bonds       : bond        0.05745 (  379)
  hydrogen bonds       : angle       5.75764 ( 1101)
  link_BETA1-6         : bond        0.00456 (    1)
  link_BETA1-6         : angle       0.80215 (    3)
  SS BOND              : bond        0.00314 (    5)
  SS BOND              : angle       1.62408 (   10)
  covalent geometry    : bond        0.00382 ( 8811)
  covalent geometry    : angle       0.71332 (12008)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 65
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
REVERT: a   76 ASP cc_start: 0.2784 (OUTLIER) cc_final: 0.0833 (p0)
REVERT: a   81 TYR cc_start: 0.7847 (m-10) cc_final: 0.7555 (m-10)
REVERT: a  120 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7409 (mmpt)
REVERT: b  200 TYR cc_start: 0.8102 (p90) cc_final: 0.7822 (p90)
REVERT: b  217 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8152 (pp30)
REVERT: b  252 LEU cc_start: 0.7356 (mt) cc_final: 0.6884 (mt)
REVERT: b  281 MET cc_start: 0.6728 (ptp) cc_final: 0.5958 (tmm)
REVERT: b  479 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6236 (p0)
REVERT: b  490 LEU cc_start: 0.8827 (tp) cc_final: 0.8545 (mp)
REVERT: b  649 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8835 (ttpp)
REVERT: b  675 ASP cc_start: 0.8609 (m-30) cc_final: 0.8405 (t70)
REVERT: b  681 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8710 (tp)
REVERT: b  775 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6843 (mmmm)
REVERT: b  793 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7770 (p0)
REVERT: b  916 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8078 (ttp-170)
  outliers start: 50
  outliers final: 30
  residues processed: 111
  average time/residue: 0.7131
  time to fit residues: 88.1021
Evaluate side-chains
  94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 56
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   55 THR
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   76 ASP
Chi-restraints excluded: chain a residue   78 PHE
Chi-restraints excluded: chain a residue   79 SER
Chi-restraints excluded: chain a residue  113 THR
Chi-restraints excluded: chain a residue  119 ASP
Chi-restraints excluded: chain a residue  120 LYS
Chi-restraints excluded: chain a residue  121 LEU
Chi-restraints excluded: chain a residue  141 CYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  159 LEU
Chi-restraints excluded: chain a residue  165 GLU
Chi-restraints excluded: chain b residue  130 SER
Chi-restraints excluded: chain b residue  164 VAL
Chi-restraints excluded: chain b residue  168 LEU
Chi-restraints excluded: chain b residue  169 VAL
Chi-restraints excluded: chain b residue  186 SER
Chi-restraints excluded: chain b residue  213 LEU
Chi-restraints excluded: chain b residue  215 THR
Chi-restraints excluded: chain b residue  242 THR
Chi-restraints excluded: chain b residue  308 ILE
Chi-restraints excluded: chain b residue  326 VAL
Chi-restraints excluded: chain b residue  479 ASP
Chi-restraints excluded: chain b residue  561 VAL
Chi-restraints excluded: chain b residue  575 LEU
Chi-restraints excluded: chain b residue  591 TRP
Chi-restraints excluded: chain b residue  649 LYS
Chi-restraints excluded: chain b residue  681 ILE
Chi-restraints excluded: chain b residue  682 VAL
Chi-restraints excluded: chain b residue  775 LYS
Chi-restraints excluded: chain b residue  793 ASN
Chi-restraints excluded: chain b residue  803 THR
Chi-restraints excluded: chain b residue  809 ILE
Chi-restraints excluded: chain b residue  831 ASN
Chi-restraints excluded: chain b residue  844 THR
Chi-restraints excluded: chain b residue  869 SER
Chi-restraints excluded: chain b residue  916 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0670
   chunk 64 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    2.1724

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

Flipped N/Q/H residues before XYZ refinement:
** a  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 889 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.099248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.073684 restraints weight = 36313.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 4.64
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.7124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8830  Z= 0.168
  Angle     :  0.718  12.718  12060  Z= 0.365
  Chirality :  0.044   0.285   1379
  Planarity :  0.005   0.059   1515
  Dihedral  :  6.427  57.209   1430
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.33 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 33.87 %
    Favored  : 61.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.03 (0.26), residues: 1039
  helix:  1.01 (0.24), residues: 439
  sheet: -0.39 (0.36), residues: 204
  loop : -0.90 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP b  77 
 HIS   0.011   0.001   HIS b 740 
 PHE   0.022   0.002   PHE a 118 
 TYR   0.015   0.002   TYR b 284 
 ARG   0.013   0.001   ARG a 148 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00225 (    6)
  link_NAG-ASN         : angle       1.44686 (   18)
  link_BETA1-4         : bond        0.00333 (    7)
  link_BETA1-4         : angle       1.38420 (   21)
  hydrogen bonds       : bond        0.05536 (  379)
  hydrogen bonds       : angle       5.69384 ( 1101)
  link_BETA1-6         : bond        0.00508 (    1)
  link_BETA1-6         : angle       0.86172 (    3)
  SS BOND              : bond        0.00311 (    5)
  SS BOND              : angle       1.73966 (   10)
  covalent geometry    : bond        0.00379 ( 8811)
  covalent geometry    : angle       0.71347 (12008)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 58
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: a   81 TYR cc_start: 0.7828 (m-10) cc_final: 0.7587 (m-10)
REVERT: a  120 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7197 (mmpt)
REVERT: b  252 LEU cc_start: 0.7397 (mt) cc_final: 0.6910 (mt)
REVERT: b  281 MET cc_start: 0.7040 (ptp) cc_final: 0.6395 (ppp)
REVERT: b  479 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6250 (p0)
REVERT: b  490 LEU cc_start: 0.8859 (tp) cc_final: 0.8587 (mp)
REVERT: b  509 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.6935 (t80)
REVERT: b  649 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8839 (ttpp)
REVERT: b  681 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8710 (tp)
REVERT: b  775 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6783 (mmmm)
REVERT: b  793 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7808 (p0)
REVERT: b  916 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8067 (ttp-170)
  outliers start: 46
  outliers final: 30
  residues processed: 100
  average time/residue: 0.7367
  time to fit residues: 81.9522
Evaluate side-chains
  94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 56
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   55 THR
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   79 SER
Chi-restraints excluded: chain a residue  113 THR
Chi-restraints excluded: chain a residue  119 ASP
Chi-restraints excluded: chain a residue  120 LYS
Chi-restraints excluded: chain a residue  121 LEU
Chi-restraints excluded: chain a residue  141 CYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  159 LEU
Chi-restraints excluded: chain a residue  165 GLU
Chi-restraints excluded: chain b residue  130 SER
Chi-restraints excluded: chain b residue  164 VAL
Chi-restraints excluded: chain b residue  168 LEU
Chi-restraints excluded: chain b residue  169 VAL
Chi-restraints excluded: chain b residue  205 THR
Chi-restraints excluded: chain b residue  213 LEU
Chi-restraints excluded: chain b residue  215 THR
Chi-restraints excluded: chain b residue  242 THR
Chi-restraints excluded: chain b residue  308 ILE
Chi-restraints excluded: chain b residue  446 VAL
Chi-restraints excluded: chain b residue  479 ASP
Chi-restraints excluded: chain b residue  509 TYR
Chi-restraints excluded: chain b residue  561 VAL
Chi-restraints excluded: chain b residue  575 LEU
Chi-restraints excluded: chain b residue  591 TRP
Chi-restraints excluded: chain b residue  649 LYS
Chi-restraints excluded: chain b residue  681 ILE
Chi-restraints excluded: chain b residue  682 VAL
Chi-restraints excluded: chain b residue  755 LEU
Chi-restraints excluded: chain b residue  775 LYS
Chi-restraints excluded: chain b residue  793 ASN
Chi-restraints excluded: chain b residue  803 THR
Chi-restraints excluded: chain b residue  809 ILE
Chi-restraints excluded: chain b residue  831 ASN
Chi-restraints excluded: chain b residue  844 THR
Chi-restraints excluded: chain b residue  869 SER
Chi-restraints excluded: chain b residue  916 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 58 optimal weight:   20.0000
   chunk 56 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 23 optimal weight:   30.0000
   chunk 79 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 86 optimal weight:    0.0060
   chunk 52 optimal weight:    9.9990
   overall best weight:    3.0004

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

Flipped N/Q/H residues before XYZ refinement:
** a  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 181 GLN
** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 889 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.098350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.072417 restraints weight = 35969.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 4.73
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.7269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8830  Z= 0.198
  Angle     :  0.742  13.806  12060  Z= 0.376
  Chirality :  0.045   0.271   1379
  Planarity :  0.006   0.076   1515
  Dihedral  :  6.308  56.233   1429
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.52 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 34.29 %
    Favored  : 61.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.14 (0.25), residues: 1039
  helix:  0.90 (0.24), residues: 438
  sheet: -0.29 (0.37), residues: 199
  loop : -1.01 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP b 524 
 HIS   0.010   0.001   HIS b 740 
 PHE   0.022   0.002   PHE b 573 
 TYR   0.031   0.002   TYR a 163 
 ARG   0.013   0.001   ARG a 148 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00250 (    6)
  link_NAG-ASN         : angle       1.55672 (   18)
  link_BETA1-4         : bond        0.00325 (    7)
  link_BETA1-4         : angle       1.44804 (   21)
  hydrogen bonds       : bond        0.06017 (  379)
  hydrogen bonds       : angle       5.75643 ( 1101)
  link_BETA1-6         : bond        0.00530 (    1)
  link_BETA1-6         : angle       0.83072 (    3)
  SS BOND              : bond        0.00379 (    5)
  SS BOND              : angle       1.98954 (   10)
  covalent geometry    : bond        0.00450 ( 8811)
  covalent geometry    : angle       0.73673 (12008)

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 56
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
REVERT: a   81 TYR cc_start: 0.7867 (m-10) cc_final: 0.7603 (m-10)
REVERT: a  127 PHE cc_start: 0.7442 (t80) cc_final: 0.7206 (t80)
REVERT: a  148 ARG cc_start: 0.7629 (mtp-110) cc_final: 0.7408 (ptm160)
REVERT: b  252 LEU cc_start: 0.7383 (mt) cc_final: 0.6911 (mt)
REVERT: b  281 MET cc_start: 0.6950 (ptp) cc_final: 0.6355 (ppp)
REVERT: b  479 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6316 (p0)
REVERT: b  490 LEU cc_start: 0.8866 (tp) cc_final: 0.8565 (mp)
REVERT: b  509 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.6861 (t80)
REVERT: b  649 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8861 (ttpp)
REVERT: b  681 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8719 (tp)
REVERT: b  793 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7944 (p0)
REVERT: b  916 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8001 (ttp-170)
  outliers start: 42
  outliers final: 28
  residues processed: 96
  average time/residue: 0.7637
  time to fit residues: 81.1228
Evaluate side-chains
  89 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 55
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   55 THR
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   79 SER
Chi-restraints excluded: chain a residue  113 THR
Chi-restraints excluded: chain a residue  119 ASP
Chi-restraints excluded: chain a residue  121 LEU
Chi-restraints excluded: chain a residue  141 CYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain b residue  130 SER
Chi-restraints excluded: chain b residue  164 VAL
Chi-restraints excluded: chain b residue  168 LEU
Chi-restraints excluded: chain b residue  169 VAL
Chi-restraints excluded: chain b residue  186 SER
Chi-restraints excluded: chain b residue  205 THR
Chi-restraints excluded: chain b residue  213 LEU
Chi-restraints excluded: chain b residue  215 THR
Chi-restraints excluded: chain b residue  242 THR
Chi-restraints excluded: chain b residue  308 ILE
Chi-restraints excluded: chain b residue  446 VAL
Chi-restraints excluded: chain b residue  479 ASP
Chi-restraints excluded: chain b residue  509 TYR
Chi-restraints excluded: chain b residue  561 VAL
Chi-restraints excluded: chain b residue  575 LEU
Chi-restraints excluded: chain b residue  591 TRP
Chi-restraints excluded: chain b residue  649 LYS
Chi-restraints excluded: chain b residue  681 ILE
Chi-restraints excluded: chain b residue  682 VAL
Chi-restraints excluded: chain b residue  793 ASN
Chi-restraints excluded: chain b residue  803 THR
Chi-restraints excluded: chain b residue  809 ILE
Chi-restraints excluded: chain b residue  831 ASN
Chi-restraints excluded: chain b residue  844 THR
Chi-restraints excluded: chain b residue  869 SER
Chi-restraints excluded: chain b residue  916 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 23 optimal weight:   40.0000
   chunk 79 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 59 optimal weight:   10.0000
   chunk 37 optimal weight:   20.0000
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
a  36 ASN
** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 646 ASN
** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 889 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.100357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.074788 restraints weight = 36016.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 4.84
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.7410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8830  Z= 0.141
  Angle     :  0.717  13.820  12060  Z= 0.359
  Chirality :  0.044   0.267   1379
  Planarity :  0.005   0.061   1515
  Dihedral  :  5.707  45.684   1426
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.23 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 35.15 %
    Favored  : 60.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.04 (0.26), residues: 1039
  helix:  1.09 (0.25), residues: 439
  sheet: -0.25 (0.37), residues: 199
  loop : -0.95 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP b 524 
 HIS   0.011   0.001   HIS b 740 
 PHE   0.019   0.002   PHE b 573 
 TYR   0.016   0.001   TYR b 284 
 ARG   0.014   0.001   ARG a 148 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00275 (    6)
  link_NAG-ASN         : angle       1.26059 (   18)
  link_BETA1-4         : bond        0.00346 (    7)
  link_BETA1-4         : angle       1.34976 (   21)
  hydrogen bonds       : bond        0.04811 (  379)
  hydrogen bonds       : angle       5.53401 ( 1101)
  link_BETA1-6         : bond        0.00687 (    1)
  link_BETA1-6         : angle       0.76131 (    3)
  SS BOND              : bond        0.00285 (    5)
  SS BOND              : angle       1.70623 (   10)
  covalent geometry    : bond        0.00316 ( 8811)
  covalent geometry    : angle       0.71267 (12008)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6739.60 seconds
wall clock time: 115 minutes 49.33 seconds (6949.33 seconds total)