Starting phenix.real_space_refine
on Thu May 15 08:59:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tgz_41247/05_2025/8tgz_41247_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tgz_41247/05_2025/8tgz_41247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tgz_41247/05_2025/8tgz_41247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tgz_41247/05_2025/8tgz_41247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tgz_41247/05_2025/8tgz_41247_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tgz_41247/05_2025/8tgz_41247_trim.cif"
  }
  resolution = 3.78
  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=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4195      2.51       5
     N    1125      2.21       5
     O    1339      1.98       5
     H    6122      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12820
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 3395
          Classifications: {'peptide': 234}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 90
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 56
    Chain: "E"
      Number of atoms: 3129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 3129
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 199}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 4
    Chain: "F"
      Number of atoms: 3104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 3104
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "M"
      Number of atoms: 1531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 1531
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "N"
      Number of atoms: 1480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 1480
          Classifications: {'peptide': 104}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 8
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 3, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    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: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 2, '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: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 6.19, per 1000 atoms: 0.48
  Number of scatterers: 12820
  At special positions: 0
  Unit cell: (108.587, 102.637, 136.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      39     16.00
     O    1339      8.00
     N    1125      7.00
     C    4195      6.00
     H    6122      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 429 " - pdb=" SG  CYS A 503 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 452 " - pdb=" SG  CYS A 620 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 486 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 494 " - pdb=" SG  CYS A 564 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 508 " - pdb=" SG  CYS A 552 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 569 " - pdb=" SG  CYS A 597 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 581 " - pdb=" SG  CYS A 585 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 607 " - pdb=" SG  CYS A 644 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 145 " - pdb=" SG  CYS E 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 133 " - pdb=" SG  CYS F 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 133 " - pdb=" SG  CYS M 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 145 " - pdb=" SG  CYS N 201 " 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
    BETA1-3
      " BMA B   3 " - " BMA B   4 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " BMA D   3 " - " BMA D   4 "
    BETA1-6
      " BMA B   3 " - " BMA B   5 "
    NAG-ASN
      " NAG A 701 " - " ASN A 448 "
      " NAG A 702 " - " ASN A 532 "
      " NAG A 703 " - " ASN A 430 "
      " NAG B   1 " - " ASN A 423 "
      " NAG C   1 " - " ASN A 540 "
      " NAG D   1 " - " ASN A 556 "
  Time building additional restraints: 3.18
  Conformation dependent library (CDL) restraints added in 951.6 milliseconds
  

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1604

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 19 sheets defined
      9.9% alpha, 40.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 437 through 442
      removed outlier: 4.230A  pdb=" N   PHE A 442 " --> pdb=" O   ALA A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 457
      removed outlier: 4.053A  pdb=" N   ARG A 455 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 547
    Processing helix  chain 'A' and resid 593 through 598
    Processing helix  chain 'A' and resid 613 through 618
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.964A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 161 through 163
      No H-bonds generated for 'chain 'E' and resid 161 through 163'
    Processing helix  chain 'E' and resid 192 through 194
      No H-bonds generated for 'chain 'E' and resid 192 through 194'
    Processing helix  chain 'E' and resid 206 through 209
    Processing helix  chain 'F' and resid 26 through 30
    Processing helix  chain 'F' and resid 78 through 82
      removed outlier: 4.056A  pdb=" N   GLU F  82 " --> pdb=" O   ALA F  79 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 120 through 126
      removed outlier: 3.658A  pdb=" N   SER F 126 " --> pdb=" O   GLU F 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 182 through 187
    Processing helix  chain 'M' and resid 122 through 127
    Processing helix  chain 'N' and resid 159 through 163
    Processing helix  chain 'N' and resid 190 through 196
      removed outlier: 3.563A  pdb=" N   GLY N 195 " --> pdb=" O   SER N 192 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR N 196 " --> pdb=" O   SER N 193 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 416
      removed outlier: 3.597A  pdb=" N   VAL A 516 " --> pdb=" O   VAL A 506 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   VAL A 506 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLY A 551 " --> pdb=" O   PHE A 509 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE A 560 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 498
    Processing sheet with id=AA3, first strand: chain 'A' and resid 602 through 604
      removed outlier: 7.517A  pdb=" N   TRP A 602 " --> pdb=" O   VAL A 609 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   VAL A 609 " --> pdb=" O   TRP A 602 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR A 604 " --> pdb=" O   CYS A 607 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 17 through 23
    Processing sheet with id=AA5, first strand: chain 'E' and resid 58 through 60
      removed outlier: 6.864A  pdb=" N   TRP E  36 " --> pdb=" O   MET E  48 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLY E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ILE E  34 " --> pdb=" O   GLY E  50 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   CYS E  96 " --> pdb=" O   TRP E 109 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   TRP E 109 " --> pdb=" O   CYS E  96 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG E  98 " --> pdb=" O   ASP E 107 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASP E 107 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 58 through 60
      removed outlier: 6.864A  pdb=" N   TRP E  36 " --> pdb=" O   MET E  48 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLY E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ILE E  34 " --> pdb=" O   GLY E  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 125 through 129
      removed outlier: 4.128A  pdb=" N   GLY E 144 " --> pdb=" O   LEU E 129 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   TYR E 181 " --> pdb=" O   ASP E 149 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 125 through 129
      removed outlier: 4.128A  pdb=" N   GLY E 144 " --> pdb=" O   LEU E 129 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   TYR E 181 " --> pdb=" O   ASP E 149 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 156 through 159
    Processing sheet with id=AB1, first strand: chain 'F' and resid 9 through 12
      removed outlier: 5.775A  pdb=" N   GLN F  36 " --> pdb=" O   LEU F  45 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   LEU F  45 " --> pdb=" O   GLN F  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 12
    Processing sheet with id=AB3, first strand: chain 'F' and resid 18 through 23
    Processing sheet with id=AB4, first strand: chain 'F' and resid 113 through 117
      removed outlier: 6.281A  pdb=" N   TYR F 172 " --> pdb=" O   ASN F 137 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 152 through 153
    Processing sheet with id=AB6, first strand: chain 'M' and resid 114 through 117
      removed outlier: 3.714A  pdb=" N   VAL M 132 " --> pdb=" O   PHE M 117 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASN M 137 " --> pdb=" O   TYR M 172 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   TYR M 172 " --> pdb=" O   ASN M 137 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'M' and resid 144 through 147
      removed outlier: 3.673A  pdb=" N   LYS M 144 " --> pdb=" O   THR M 196 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'N' and resid 125 through 129
    Processing sheet with id=AB9, first strand: chain 'N' and resid 125 through 129
    Processing sheet with id=AC1, first strand: chain 'N' and resid 155 through 158

    274 hydrogen bonds defined for protein.
    669 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: 4.09

  Time building geometry restraints manager: 3.85 seconds

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

  Histogram of bond lengths:
        0.84 -     1.05: 6118
        1.05 -     1.26: 1065
        1.26 -     1.47: 2881
        1.47 -     1.68: 2885
        1.68 -     1.89: 46
  Bond restraints: 12995
  Sorted by residual:
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.510 -0.104 2.00e-02 2.50e+03 2.68e+01
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.476 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" CB  CYS A 552 "
       pdb=" SG  CYS A 552 "
    ideal  model  delta    sigma   weight residual
    1.808  1.727  0.081 3.30e-02 9.18e+02 6.07e+00
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.357  0.049 2.00e-02 2.50e+03 6.04e+00
  bond pdb=" CB  CYS A 508 "
       pdb=" SG  CYS A 508 "
    ideal  model  delta    sigma   weight residual
    1.808  1.889 -0.081 3.30e-02 9.18e+02 5.95e+00
  ... (remaining 12990 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 23122
        2.72 -     5.44: 150
        5.44 -     8.16: 19
        8.16 -    10.88: 3
       10.88 -    13.59: 2
  Bond angle restraints: 23296
  Sorted by residual:
  angle pdb=" CA  CYS A 552 "
        pdb=" CB  CYS A 552 "
        pdb=" SG  CYS A 552 "
      ideal   model   delta    sigma   weight residual
     114.40  126.37  -11.97 2.30e+00 1.89e-01 2.71e+01
  angle pdb=" CG  ASN A 556 "
        pdb=" ND2 ASN A 556 "
        pdb="HD21 ASN A 556 "
      ideal   model   delta    sigma   weight residual
     120.00  106.41   13.59 3.00e+00 1.11e-01 2.05e+01
  angle pdb=" N   CYS A 552 "
        pdb=" CA  CYS A 552 "
        pdb=" C   CYS A 552 "
      ideal   model   delta    sigma   weight residual
     107.88  114.01   -6.13 1.41e+00 5.03e-01 1.89e+01
  angle pdb=" CB  ASN A 556 "
        pdb=" CG  ASN A 556 "
        pdb=" ND2 ASN A 556 "
      ideal   model   delta    sigma   weight residual
     116.40  122.25   -5.85 1.50e+00 4.44e-01 1.52e+01
  angle pdb=" CB  LYS A 596 "
        pdb=" CG  LYS A 596 "
        pdb=" CD  LYS A 596 "
      ideal   model   delta    sigma   weight residual
     111.30  118.49   -7.19 2.30e+00 1.89e-01 9.76e+00
  ... (remaining 23291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.85: 5924
       24.85 -    49.70: 424
       49.70 -    74.56: 117
       74.56 -    99.41: 58
       99.41 -   124.26: 28
  Dihedral angle restraints: 6551
    sinusoidal: 3578
      harmonic: 2973
  Sorted by residual:
  dihedral pdb=" CB  CYS A 459 "
           pdb=" SG  CYS A 459 "
           pdb=" SG  CYS A 486 "
           pdb=" CB  CYS A 486 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -152.43   66.43     1      1.00e+01 1.00e-02 5.76e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.89  -64.89     1      1.00e+01 1.00e-02 5.53e+01
  dihedral pdb=" CB  CYS A 452 "
           pdb=" SG  CYS A 452 "
           pdb=" SG  CYS A 620 "
           pdb=" CB  CYS A 620 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  149.25  -56.25     1      1.00e+01 1.00e-02 4.27e+01
  ... (remaining 6548 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.198: 1086
       0.198 -    0.397: 7
       0.397 -    0.595: 1
       0.595 -    0.794: 0
       0.794 -    0.992: 2
  Chirality restraints: 1096
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 556 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.41   -0.99 2.00e-01 2.50e+01 2.46e+01
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 430 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.56   -0.84 2.00e-01 2.50e+01 1.74e+01
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 540 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.96   -0.44 2.00e-01 2.50e+01 4.81e+00
  ... (remaining 1093 not shown)

  Planarity restraints: 2004
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 452 "    0.053 5.00e-02 4.00e+02   7.98e-02 1.02e+01
        pdb=" N   PRO A 453 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO A 453 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 453 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS N 206 "    0.047 5.00e-02 4.00e+02   7.05e-02 7.94e+00
        pdb=" N   PRO N 207 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO N 207 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO N 207 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 460 "    0.042 5.00e-02 4.00e+02   6.27e-02 6.29e+00
        pdb=" N   PRO A 461 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 461 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 461 "    0.035 5.00e-02 4.00e+02
  ... (remaining 2001 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 530
        2.16 -     2.77: 22891
        2.77 -     3.38: 31861
        3.38 -     3.99: 41744
        3.99 -     4.60: 63350
  Nonbonded interactions: 160376
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN E  62 "
            pdb=" H   GLN E  62 "
     model   vdw
     1.546 2.450
  nonbonded pdb=" OE2 GLU M 142 "
            pdb="HE21 GLN M 198 "
     model   vdw
     1.553 2.450
  nonbonded pdb=" OD1 ASP A 520 "
            pdb=" H   ARG A 521 "
     model   vdw
     1.567 2.450
  nonbonded pdb="HE21 GLN F   6 "
            pdb=" O   GLY F  99 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" OE1 GLU N 153 "
            pdb=" H   GLU N 153 "
     model   vdw
     1.581 2.450
  ... (remaining 160371 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.240
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.050
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
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      :  0.004   0.104   6901  Z= 0.203
  Angle     :  0.978  24.722   9464  Z= 0.424
  Chirality :  0.066   0.992   1096
  Planarity :  0.006   0.080   1193
  Dihedral  : 24.265 124.259   2612
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 22.44 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.95 (0.28), residues: 857
  helix: -1.27 (1.01), residues: 32
  sheet:  0.81 (0.29), residues: 322
  loop : -1.67 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 469 
 HIS   0.003   0.001   HIS A 421 
 PHE   0.012   0.001   PHE A 509 
 TYR   0.021   0.001   TYR N 150 
 ARG   0.004   0.000   ARG F 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01991 (    6)
  link_NAG-ASN         : angle      10.51128 (   18)
  link_BETA1-4         : bond        0.02635 (    6)
  link_BETA1-4         : angle       7.93821 (   18)
  hydrogen bonds       : bond        0.12382 (  226)
  hydrogen bonds       : angle       6.39144 (  669)
  link_BETA1-6         : bond        0.00294 (    1)
  link_BETA1-6         : angle       2.50983 (    3)
  SS BOND              : bond        0.00503 (   14)
  SS BOND              : angle       2.08204 (   28)
  link_BETA1-3         : bond        0.00274 (    1)
  link_BETA1-3         : angle       1.23582 (    3)
  covalent geometry    : bond        0.00437 ( 6873)
  covalent geometry    : angle       0.78484 ( 9394)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  413 is missing expected H atoms. Skipping.
Residue SER  419 is missing expected H atoms. Skipping.
Residue ILE  472 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it.
Residue SER  135 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LYS  187 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue SER  167 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue SER  181 is missing expected H atoms. Skipping.
Residue LYS  182 is missing expected H atoms. Skipping.
Residue LYS  134 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it.
Evaluate side-chains
  139 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.4063
  time to fit residues: 73.2073
Evaluate side-chains
  133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0570
   chunk 34 optimal weight:    0.5980
   chunk 66 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
M 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.163584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.132763 restraints weight = 30997.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.138418 restraints weight = 16431.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.142134 restraints weight = 11005.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.0648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   6901  Z= 0.147
  Angle     :  0.811  18.937   9464  Z= 0.367
  Chirality :  0.057   0.720   1096
  Planarity :  0.006   0.063   1193
  Dihedral  : 21.999 115.192   1216
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 20.90 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.98 (0.28), residues: 857
  helix: -1.56 (0.94), residues: 32
  sheet:  0.75 (0.30), residues: 317
  loop : -1.61 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 554 
 HIS   0.003   0.001   HIS A 649 
 PHE   0.009   0.001   PHE F  97 
 TYR   0.012   0.001   TYR F  35 
 ARG   0.003   0.000   ARG E  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01385 (    6)
  link_NAG-ASN         : angle       6.62432 (   18)
  link_BETA1-4         : bond        0.01213 (    6)
  link_BETA1-4         : angle       4.33035 (   18)
  hydrogen bonds       : bond        0.03767 (  226)
  hydrogen bonds       : angle       5.82585 (  669)
  link_BETA1-6         : bond        0.00366 (    1)
  link_BETA1-6         : angle       3.01784 (    3)
  SS BOND              : bond        0.00450 (   14)
  SS BOND              : angle       1.87487 (   28)
  link_BETA1-3         : bond        0.00081 (    1)
  link_BETA1-3         : angle       2.52021 (    3)
  covalent geometry    : bond        0.00346 ( 6873)
  covalent geometry    : angle       0.72555 ( 9394)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  413 is missing expected H atoms. Skipping.
Residue SER  419 is missing expected H atoms. Skipping.
Residue ILE  472 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it.
Residue SER  135 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LYS  187 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue SER  167 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue SER  181 is missing expected H atoms. Skipping.
Residue LYS  182 is missing expected H atoms. Skipping.
Residue LYS  134 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it.
Evaluate side-chains
  143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.948 
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
  outliers start: 9
  outliers final: 5
  residues processed: 138
  average time/residue: 0.4213
  time to fit residues: 75.1308
Evaluate side-chains
  134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain E residue  166 SER
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain N residue  155 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 14 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 649 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.163339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.132565 restraints weight = 30887.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.138179 restraints weight = 16541.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.141883 restraints weight = 11121.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   6901  Z= 0.152
  Angle     :  0.789  15.208   9464  Z= 0.354
  Chirality :  0.055   0.710   1096
  Planarity :  0.005   0.061   1193
  Dihedral  : 18.254 109.787   1216
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.93 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 20.90 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.97 (0.28), residues: 857
  helix: -1.60 (0.92), residues: 32
  sheet:  0.73 (0.29), residues: 324
  loop : -1.61 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 109 
 HIS   0.003   0.001   HIS A 649 
 PHE   0.008   0.001   PHE F  97 
 TYR   0.016   0.001   TYR N 150 
 ARG   0.002   0.000   ARG F 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01706 (    6)
  link_NAG-ASN         : angle       6.39845 (   18)
  link_BETA1-4         : bond        0.01084 (    6)
  link_BETA1-4         : angle       3.96922 (   18)
  hydrogen bonds       : bond        0.03643 (  226)
  hydrogen bonds       : angle       5.65382 (  669)
  link_BETA1-6         : bond        0.00103 (    1)
  link_BETA1-6         : angle       2.13968 (    3)
  SS BOND              : bond        0.00439 (   14)
  SS BOND              : angle       1.82098 (   28)
  link_BETA1-3         : bond        0.00123 (    1)
  link_BETA1-3         : angle       2.95910 (    3)
  covalent geometry    : bond        0.00361 ( 6873)
  covalent geometry    : angle       0.71067 ( 9394)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  413 is missing expected H atoms. Skipping.
Residue SER  419 is missing expected H atoms. Skipping.
Residue ILE  472 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it.
Residue SER  135 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LYS  187 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue SER  167 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue SER  181 is missing expected H atoms. Skipping.
Residue LYS  182 is missing expected H atoms. Skipping.
Residue LYS  134 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it.
Evaluate side-chains
  149 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 1.015 
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: A  454 GLU cc_start: 0.8265 (tp30) cc_final: 0.8001 (mp0)
REVERT: F   93 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8496 (p)
REVERT: M  149 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8032 (p)
  outliers start: 15
  outliers final: 10
  residues processed: 143
  average time/residue: 0.4392
  time to fit residues: 80.9899
Evaluate side-chains
  143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain E residue  166 SER
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain N residue  196 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
M 159 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.161131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.129903 restraints weight = 30912.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.135606 restraints weight = 16607.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.139140 restraints weight = 11108.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   6901  Z= 0.158
  Angle     :  0.754  13.788   9464  Z= 0.346
  Chirality :  0.054   0.689   1096
  Planarity :  0.005   0.060   1193
  Dihedral  : 16.907 107.652   1216
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.28 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 20.48 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.98 (0.28), residues: 857
  helix: -1.62 (0.91), residues: 32
  sheet:  0.70 (0.29), residues: 324
  loop : -1.60 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 109 
 HIS   0.004   0.001   HIS A 649 
 PHE   0.009   0.001   PHE F  97 
 TYR   0.015   0.001   TYR N 150 
 ARG   0.007   0.000   ARG A 543 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00960 (    6)
  link_NAG-ASN         : angle       5.51069 (   18)
  link_BETA1-4         : bond        0.00863 (    6)
  link_BETA1-4         : angle       3.72121 (   18)
  hydrogen bonds       : bond        0.03474 (  226)
  hydrogen bonds       : angle       5.59325 (  669)
  link_BETA1-6         : bond        0.00282 (    1)
  link_BETA1-6         : angle       1.90755 (    3)
  SS BOND              : bond        0.00449 (   14)
  SS BOND              : angle       1.83631 (   28)
  link_BETA1-3         : bond        0.00037 (    1)
  link_BETA1-3         : angle       3.17673 (    3)
  covalent geometry    : bond        0.00385 ( 6873)
  covalent geometry    : angle       0.68783 ( 9394)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  413 is missing expected H atoms. Skipping.
Residue SER  419 is missing expected H atoms. Skipping.
Residue ILE  472 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it.
Residue SER  135 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LYS  187 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue SER  167 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue SER  181 is missing expected H atoms. Skipping.
Residue LYS  182 is missing expected H atoms. Skipping.
Residue LYS  134 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it.
Evaluate side-chains
  148 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.954 
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: A  454 GLU cc_start: 0.8263 (tp30) cc_final: 0.7936 (mp0)
REVERT: F   93 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8513 (p)
REVERT: M  149 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8142 (p)
REVERT: M  150 ASP cc_start: 0.8572 (t0) cc_final: 0.8346 (t0)
REVERT: N  209 ASN cc_start: 0.7845 (m-40) cc_final: 0.7050 (p0)
  outliers start: 18
  outliers final: 12
  residues processed: 139
  average time/residue: 0.4130
  time to fit residues: 74.8030
Evaluate side-chains
  141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain E residue   80 TYR
Chi-restraints excluded: chain E residue  166 SER
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain N residue  196 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 48 optimal weight:    0.4980
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0770
   chunk 73 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
M 159 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.162803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.132185 restraints weight = 30799.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.137734 restraints weight = 16632.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.141368 restraints weight = 11213.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   6901  Z= 0.132
  Angle     :  0.729  12.866   9464  Z= 0.334
  Chirality :  0.053   0.668   1096
  Planarity :  0.005   0.060   1193
  Dihedral  : 16.271 106.481   1216
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.05 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 21.04 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.89 (0.28), residues: 857
  helix: -1.51 (0.94), residues: 32
  sheet:  0.78 (0.29), residues: 316
  loop : -1.52 (0.26), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 109 
 HIS   0.003   0.001   HIS A 649 
 PHE   0.009   0.001   PHE F  97 
 TYR   0.018   0.001   TYR N 150 
 ARG   0.003   0.000   ARG A 543 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00931 (    6)
  link_NAG-ASN         : angle       4.98847 (   18)
  link_BETA1-4         : bond        0.00873 (    6)
  link_BETA1-4         : angle       3.71719 (   18)
  hydrogen bonds       : bond        0.03295 (  226)
  hydrogen bonds       : angle       5.46292 (  669)
  link_BETA1-6         : bond        0.00386 (    1)
  link_BETA1-6         : angle       1.81598 (    3)
  SS BOND              : bond        0.00430 (   14)
  SS BOND              : angle       1.79804 (   28)
  link_BETA1-3         : bond        0.00071 (    1)
  link_BETA1-3         : angle       3.31962 (    3)
  covalent geometry    : bond        0.00326 ( 6873)
  covalent geometry    : angle       0.66809 ( 9394)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  413 is missing expected H atoms. Skipping.
Residue SER  419 is missing expected H atoms. Skipping.
Residue ILE  472 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it.
Residue SER  135 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LYS  187 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue SER  167 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue SER  181 is missing expected H atoms. Skipping.
Residue LYS  182 is missing expected H atoms. Skipping.
Residue LYS  134 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it.
Evaluate side-chains
  148 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.941 
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: A  454 GLU cc_start: 0.8349 (tp30) cc_final: 0.8054 (mp0)
REVERT: F   34 TRP cc_start: 0.8928 (m100) cc_final: 0.8353 (m-90)
REVERT: F   93 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8550 (p)
REVERT: M  149 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8152 (p)
REVERT: M  150 ASP cc_start: 0.8544 (t0) cc_final: 0.8339 (t0)
REVERT: N  209 ASN cc_start: 0.7819 (m-40) cc_final: 0.7022 (p0)
  outliers start: 15
  outliers final: 11
  residues processed: 143
  average time/residue: 0.3949
  time to fit residues: 73.7877
Evaluate side-chains
  142 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  548 ASN
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain E residue   80 TYR
Chi-restraints excluded: chain E residue  166 SER
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0970
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 649 HIS
** E  43 GLN ** 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 = 0.3970 r_free = 0.3970 target = 0.162109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.131312 restraints weight = 31446.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.136905 restraints weight = 16983.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.140575 restraints weight = 11435.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   6901  Z= 0.146
  Angle     :  0.728  12.930   9464  Z= 0.335
  Chirality :  0.053   0.666   1096
  Planarity :  0.005   0.059   1193
  Dihedral  : 15.858 106.068   1216
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.98 %
    Favored  : 90.90 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.32 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.93 (0.28), residues: 857
  helix: -1.54 (0.92), residues: 32
  sheet:  0.77 (0.29), residues: 317
  loop : -1.56 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 487 
 HIS   0.002   0.001   HIS M 197 
 PHE   0.009   0.001   PHE F  97 
 TYR   0.015   0.001   TYR N 150 
 ARG   0.003   0.000   ARG A 543 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00864 (    6)
  link_NAG-ASN         : angle       4.80977 (   18)
  link_BETA1-4         : bond        0.00840 (    6)
  link_BETA1-4         : angle       3.64771 (   18)
  hydrogen bonds       : bond        0.03316 (  226)
  hydrogen bonds       : angle       5.45198 (  669)
  link_BETA1-6         : bond        0.00343 (    1)
  link_BETA1-6         : angle       1.76630 (    3)
  SS BOND              : bond        0.00427 (   14)
  SS BOND              : angle       1.82982 (   28)
  link_BETA1-3         : bond        0.00127 (    1)
  link_BETA1-3         : angle       3.32997 (    3)
  covalent geometry    : bond        0.00360 ( 6873)
  covalent geometry    : angle       0.67064 ( 9394)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  413 is missing expected H atoms. Skipping.
Residue SER  419 is missing expected H atoms. Skipping.
Residue ILE  472 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it.
Residue SER  135 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LYS  187 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue SER  167 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue SER  181 is missing expected H atoms. Skipping.
Residue LYS  182 is missing expected H atoms. Skipping.
Residue LYS  134 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it.
Evaluate side-chains
  149 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 1.120 
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: A  454 GLU cc_start: 0.8358 (tp30) cc_final: 0.8053 (mp0)
REVERT: F   34 TRP cc_start: 0.8929 (m100) cc_final: 0.8395 (m-90)
REVERT: F   93 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8553 (p)
REVERT: M  149 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8163 (p)
REVERT: M  150 ASP cc_start: 0.8584 (t0) cc_final: 0.8377 (t0)
REVERT: N  209 ASN cc_start: 0.7921 (m-40) cc_final: 0.7144 (p0)
  outliers start: 19
  outliers final: 16
  residues processed: 140
  average time/residue: 0.4021
  time to fit residues: 74.0335
Evaluate side-chains
  145 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  548 ASN
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain E residue   80 TYR
Chi-restraints excluded: chain E residue  166 SER
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain N residue  196 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 80 optimal weight:    0.0770
   chunk 77 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   chunk 44 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
E  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.163205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.132641 restraints weight = 31107.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.138222 restraints weight = 16753.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.141851 restraints weight = 11279.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   6901  Z= 0.123
  Angle     :  0.716  12.984   9464  Z= 0.329
  Chirality :  0.052   0.656   1096
  Planarity :  0.005   0.059   1193
  Dihedral  : 15.517 105.696   1216
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.40 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.60 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.83 (0.28), residues: 857
  helix: -1.51 (0.92), residues: 33
  sheet:  0.82 (0.29), residues: 312
  loop : -1.46 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 109 
 HIS   0.002   0.001   HIS A 649 
 PHE   0.009   0.001   PHE A 509 
 TYR   0.018   0.001   TYR N 150 
 ARG   0.002   0.000   ARG F 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00860 (    6)
  link_NAG-ASN         : angle       4.63183 (   18)
  link_BETA1-4         : bond        0.00893 (    6)
  link_BETA1-4         : angle       3.63065 (   18)
  hydrogen bonds       : bond        0.03145 (  226)
  hydrogen bonds       : angle       5.34616 (  669)
  link_BETA1-6         : bond        0.00471 (    1)
  link_BETA1-6         : angle       1.79408 (    3)
  SS BOND              : bond        0.00456 (   14)
  SS BOND              : angle       2.04891 (   28)
  link_BETA1-3         : bond        0.00002 (    1)
  link_BETA1-3         : angle       3.42099 (    3)
  covalent geometry    : bond        0.00303 ( 6873)
  covalent geometry    : angle       0.65768 ( 9394)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  413 is missing expected H atoms. Skipping.
Residue SER  419 is missing expected H atoms. Skipping.
Residue ILE  472 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it.
Residue SER  135 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LYS  187 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue SER  167 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue SER  181 is missing expected H atoms. Skipping.
Residue LYS  182 is missing expected H atoms. Skipping.
Residue LYS  134 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it.
Evaluate side-chains
  147 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 1.102 
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: A  454 GLU cc_start: 0.8357 (tp30) cc_final: 0.8091 (mp0)
REVERT: F   34 TRP cc_start: 0.8887 (m100) cc_final: 0.8350 (m-90)
REVERT: M  149 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8105 (p)
REVERT: M  150 ASP cc_start: 0.8566 (t0) cc_final: 0.8362 (t0)
REVERT: N  209 ASN cc_start: 0.7915 (m-40) cc_final: 0.7124 (p0)
  outliers start: 16
  outliers final: 13
  residues processed: 142
  average time/residue: 0.3858
  time to fit residues: 72.5360
Evaluate side-chains
  143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  548 ASN
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain E residue  166 SER
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain N residue  196 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 649 HIS
M 159 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.161537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.130589 restraints weight = 31492.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.136122 restraints weight = 17198.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.139765 restraints weight = 11630.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   6901  Z= 0.154
  Angle     :  0.731  12.993   9464  Z= 0.338
  Chirality :  0.052   0.655   1096
  Planarity :  0.005   0.058   1193
  Dihedral  : 15.133 104.591   1216
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.22 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.76 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.85 (0.28), residues: 857
  helix: -1.47 (0.92), residues: 32
  sheet:  0.81 (0.30), residues: 312
  loop : -1.47 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 109 
 HIS   0.003   0.001   HIS M 197 
 PHE   0.010   0.001   PHE F  97 
 TYR   0.021   0.001   TYR N 150 
 ARG   0.002   0.000   ARG A 543 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00799 (    6)
  link_NAG-ASN         : angle       4.56129 (   18)
  link_BETA1-4         : bond        0.00875 (    6)
  link_BETA1-4         : angle       3.60854 (   18)
  hydrogen bonds       : bond        0.03314 (  226)
  hydrogen bonds       : angle       5.39941 (  669)
  link_BETA1-6         : bond        0.00359 (    1)
  link_BETA1-6         : angle       1.76058 (    3)
  SS BOND              : bond        0.00472 (   14)
  SS BOND              : angle       1.98419 (   28)
  link_BETA1-3         : bond        0.00110 (    1)
  link_BETA1-3         : angle       3.37867 (    3)
  covalent geometry    : bond        0.00381 ( 6873)
  covalent geometry    : angle       0.67641 ( 9394)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  413 is missing expected H atoms. Skipping.
Residue SER  419 is missing expected H atoms. Skipping.
Residue ILE  472 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it.
Residue SER  135 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LYS  187 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue SER  167 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue SER  181 is missing expected H atoms. Skipping.
Residue LYS  182 is missing expected H atoms. Skipping.
Residue LYS  134 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it.
Evaluate side-chains
  150 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   34 TRP cc_start: 0.8918 (m100) cc_final: 0.8403 (m-90)
REVERT: M  149 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8189 (p)
REVERT: M  150 ASP cc_start: 0.8564 (t0) cc_final: 0.8349 (t0)
  outliers start: 22
  outliers final: 20
  residues processed: 141
  average time/residue: 0.3816
  time to fit residues: 70.9939
Evaluate side-chains
  146 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  548 ASN
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain E residue   80 TYR
Chi-restraints excluded: chain E residue  140 THR
Chi-restraints excluded: chain E residue  166 SER
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   87 CYS
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain N residue  196 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 60 optimal weight:    0.0980
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** E  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 159 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.162454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.131515 restraints weight = 31238.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.137090 restraints weight = 16941.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.140760 restraints weight = 11402.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6901  Z= 0.130
  Angle     :  0.719  13.032   9464  Z= 0.331
  Chirality :  0.052   0.633   1096
  Planarity :  0.005   0.057   1193
  Dihedral  : 14.904 104.483   1216
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.17 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 21.60 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.78 (0.29), residues: 857
  helix: -1.41 (0.93), residues: 33
  sheet:  0.85 (0.29), residues: 312
  loop : -1.42 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 487 
 HIS   0.003   0.001   HIS A 649 
 PHE   0.009   0.001   PHE F  97 
 TYR   0.023   0.001   TYR N 150 
 ARG   0.002   0.000   ARG F 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00791 (    6)
  link_NAG-ASN         : angle       4.41643 (   18)
  link_BETA1-4         : bond        0.00914 (    6)
  link_BETA1-4         : angle       3.58336 (   18)
  hydrogen bonds       : bond        0.03146 (  226)
  hydrogen bonds       : angle       5.31820 (  669)
  link_BETA1-6         : bond        0.00402 (    1)
  link_BETA1-6         : angle       1.76956 (    3)
  SS BOND              : bond        0.00465 (   14)
  SS BOND              : angle       1.99449 (   28)
  link_BETA1-3         : bond        0.00036 (    1)
  link_BETA1-3         : angle       3.46394 (    3)
  covalent geometry    : bond        0.00324 ( 6873)
  covalent geometry    : angle       0.66462 ( 9394)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  413 is missing expected H atoms. Skipping.
Residue SER  419 is missing expected H atoms. Skipping.
Residue ILE  472 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it.
Residue SER  135 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LYS  187 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue SER  167 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue SER  181 is missing expected H atoms. Skipping.
Residue LYS  182 is missing expected H atoms. Skipping.
Residue LYS  134 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it.
Evaluate side-chains
  143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   60 TYR cc_start: 0.7860 (m-80) cc_final: 0.7224 (m-80)
REVERT: F   34 TRP cc_start: 0.8888 (m100) cc_final: 0.8345 (m-90)
REVERT: M  149 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8098 (p)
REVERT: M  150 ASP cc_start: 0.8557 (t0) cc_final: 0.8344 (t0)
  outliers start: 18
  outliers final: 17
  residues processed: 136
  average time/residue: 0.3869
  time to fit residues: 69.3642
Evaluate side-chains
  135 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  548 ASN
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain E residue   80 TYR
Chi-restraints excluded: chain E residue  166 SER
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   87 CYS
Chi-restraints excluded: chain F residue   91 ASP
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain N residue  196 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 39 optimal weight:    1.0980
   chunk 78 optimal weight:    0.7980
   chunk 59 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** E  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 159 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.162476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.131684 restraints weight = 31243.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137131 restraints weight = 16794.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.140796 restraints weight = 11364.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6901  Z= 0.131
  Angle     :  0.717  13.055   9464  Z= 0.331
  Chirality :  0.051   0.631   1096
  Planarity :  0.005   0.058   1193
  Dihedral  : 14.530 103.609   1216
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.75 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 21.88 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.75 (0.29), residues: 857
  helix: -1.38 (0.93), residues: 33
  sheet:  0.89 (0.29), residues: 312
  loop : -1.41 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 469 
 HIS   0.003   0.001   HIS A 649 
 PHE   0.009   0.001   PHE F  97 
 TYR   0.022   0.001   TYR N 150 
 ARG   0.003   0.000   ARG F 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00787 (    6)
  link_NAG-ASN         : angle       4.34307 (   18)
  link_BETA1-4         : bond        0.00927 (    6)
  link_BETA1-4         : angle       3.58163 (   18)
  hydrogen bonds       : bond        0.03125 (  226)
  hydrogen bonds       : angle       5.26666 (  669)
  link_BETA1-6         : bond        0.00378 (    1)
  link_BETA1-6         : angle       1.76285 (    3)
  SS BOND              : bond        0.00454 (   14)
  SS BOND              : angle       2.03102 (   28)
  link_BETA1-3         : bond        0.00027 (    1)
  link_BETA1-3         : angle       3.46003 (    3)
  covalent geometry    : bond        0.00326 ( 6873)
  covalent geometry    : angle       0.66371 ( 9394)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  413 is missing expected H atoms. Skipping.
Residue SER  419 is missing expected H atoms. Skipping.
Residue ILE  472 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "HIS A 653 " (corrupted residue). Skipping it.
Residue SER  135 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue LYS  219 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "ASP E 222 " (corrupted residue). Skipping it.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LYS  187 is missing expected H atoms. Skipping.
Residue LYS  144 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue SER  167 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue SER  181 is missing expected H atoms. Skipping.
Residue LYS  182 is missing expected H atoms. Skipping.
Residue LYS  134 is missing expected H atoms. Skipping.
TARDY: cannot create tardy model for: "LYS N 223 " (corrupted residue). Skipping it.
Evaluate side-chains
  134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   34 TRP cc_start: 0.8821 (m100) cc_final: 0.8286 (m-90)
REVERT: F  141 ARG cc_start: 0.8335 (tpt90) cc_final: 0.8014 (tpt90)
REVERT: M  149 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8079 (p)
REVERT: M  150 ASP cc_start: 0.8439 (t0) cc_final: 0.8225 (t0)
  outliers start: 18
  outliers final: 17
  residues processed: 128
  average time/residue: 0.4015
  time to fit residues: 68.3220
Evaluate side-chains
  130 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  548 ASN
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain A residue  564 CYS
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain E residue   80 TYR
Chi-restraints excluded: chain E residue  166 SER
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain F residue   87 CYS
Chi-restraints excluded: chain F residue   91 ASP
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain N residue  196 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 65 optimal weight:    0.0370
   chunk 67 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** E  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 159 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.162398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.131449 restraints weight = 31199.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.136918 restraints weight = 17068.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.140587 restraints weight = 11560.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6901  Z= 0.135
  Angle     :  0.717  13.031   9464  Z= 0.331
  Chirality :  0.051   0.624   1096
  Planarity :  0.005   0.058   1193
  Dihedral  : 14.281 103.123   1216
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.28 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.44 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    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: -0.70 (0.29), residues: 857
  helix: -0.84 (1.03), residues: 27
  sheet:  0.87 (0.29), residues: 312
  loop : -1.37 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 487 
 HIS   0.002   0.001   HIS A 638 
 PHE   0.009   0.001   PHE F  97 
 TYR   0.021   0.001   TYR N 150 
 ARG   0.003   0.000   ARG F 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00771 (    6)
  link_NAG-ASN         : angle       4.28357 (   18)
  link_BETA1-4         : bond        0.00925 (    6)
  link_BETA1-4         : angle       3.66492 (   18)
  hydrogen bonds       : bond        0.03126 (  226)
  hydrogen bonds       : angle       5.25407 (  669)
  link_BETA1-6         : bond        0.00370 (    1)
  link_BETA1-6         : angle       1.77629 (    3)
  SS BOND              : bond        0.00453 (   14)
  SS BOND              : angle       2.00077 (   28)
  link_BETA1-3         : bond        0.00012 (    1)
  link_BETA1-3         : angle       3.48413 (    3)
  covalent geometry    : bond        0.00334 ( 6873)
  covalent geometry    : angle       0.66377 ( 9394)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4553.86 seconds
wall clock time: 79 minutes 17.04 seconds (4757.04 seconds total)