Starting phenix.real_space_refine
on Sat Aug 23 15:18:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tgz_41247/08_2025/8tgz_41247_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tgz_41247/08_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_41247/08_2025/8tgz_41247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tgz_41247/08_2025/8tgz_41247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tgz_41247/08_2025/8tgz_41247_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tgz_41247/08_2025/8tgz_41247_trim.cif"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.042
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2}
          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: 2.02, per 1000 atoms: 0.16
  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: 1.00
  Conformation dependent library (CDL) restraints added in 317.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.34
  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: 2.77

  Time building geometry restraints manager: 1.33 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:             1.260
  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:             0.050
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.590
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.950
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (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
 ARG   0.004   0.000   ARG F 141 
 TYR   0.021   0.001   TYR N 150 
 PHE   0.012   0.001   PHE A 509 
 TRP   0.009   0.001   TRP A 469 
 HIS   0.003   0.001   HIS A 421 

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

*********************** 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  : 0.403 
Fit side-chains
   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: 0.1741
  time to fit residues: 31.3354
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  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0770
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.6938

-------------------------------------------------------------------------------
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 = 0.3973 r_free = 0.3973 target = 0.162540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.131621 restraints weight = 31135.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.137268 restraints weight = 16790.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.140984 restraints weight = 11280.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.143481 restraints weight = 8564.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.145144 restraints weight = 7019.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.0695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   6901  Z= 0.162
  Angle     :  0.821  19.242   9464  Z= 0.373
  Chirality :  0.058   0.724   1096
  Planarity :  0.006   0.064   1193
  Dihedral  : 21.933 114.937   1216
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.76 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.28), residues: 857
  helix: -1.58 (0.94), residues: 32
  sheet:  0.70 (0.29), residues: 324
  loop : -1.66 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  38 
 TYR   0.013   0.001   TYR M 139 
 PHE   0.009   0.001   PHE F  97 
 TRP   0.007   0.001   TRP E 109 
 HIS   0.003   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 6873)
  covalent geometry    : angle       0.73802 ( 9394)
  SS BOND              : bond        0.00456 (   14)
  SS BOND              : angle       1.90417 (   28)
  hydrogen bonds       : bond        0.03855 (  226)
  hydrogen bonds       : angle       5.87385 (  669)
  link_BETA1-3         : bond        0.00601 (    1)
  link_BETA1-3         : angle       2.60756 (    3)
  link_BETA1-4         : bond        0.01261 (    6)
  link_BETA1-4         : angle       4.07408 (   18)
  link_BETA1-6         : bond        0.00771 (    1)
  link_BETA1-6         : angle       3.06098 (    3)
  link_NAG-ASN         : bond        0.01341 (    6)
  link_NAG-ASN         : angle       6.72127 (   18)

*********************** 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
  147 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  209 ASN cc_start: 0.7900 (m-40) cc_final: 0.7137 (p0)
  outliers start: 12
  outliers final: 5
  residues processed: 140
  average time/residue: 0.1514
  time to fit residues: 27.7946
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  : 0.260 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.163122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.132132 restraints weight = 31363.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.137899 restraints weight = 16896.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.141602 restraints weight = 11251.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.144068 restraints weight = 8560.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.145758 restraints weight = 7026.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   6901  Z= 0.155
  Angle     :  0.793  15.891   9464  Z= 0.357
  Chirality :  0.054   0.704   1096
  Planarity :  0.005   0.061   1193
  Dihedral  : 18.711 110.880   1216
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.82 %
    Favored  : 92.07 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.28), residues: 857
  helix: -1.60 (0.93), residues: 32
  sheet:  0.67 (0.29), residues: 324
  loop : -1.65 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 460 
 TYR   0.014   0.001   TYR N 150 
 PHE   0.008   0.001   PHE F  97 
 TRP   0.007   0.001   TRP E 109 
 HIS   0.003   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6873)
  covalent geometry    : angle       0.71394 ( 9394)
  SS BOND              : bond        0.00443 (   14)
  SS BOND              : angle       1.83120 (   28)
  hydrogen bonds       : bond        0.03706 (  226)
  hydrogen bonds       : angle       5.72979 (  669)
  link_BETA1-3         : bond        0.00016 (    1)
  link_BETA1-3         : angle       2.89714 (    3)
  link_BETA1-4         : bond        0.01166 (    6)
  link_BETA1-4         : angle       3.82394 (   18)
  link_BETA1-6         : bond        0.00041 (    1)
  link_BETA1-6         : angle       2.31684 (    3)
  link_NAG-ASN         : bond        0.01442 (    6)
  link_NAG-ASN         : angle       6.54468 (   18)

*********************** 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
  147 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   93 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8503 (p)
REVERT: M  149 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8046 (p)
REVERT: N  209 ASN cc_start: 0.7906 (m-40) cc_final: 0.7135 (p0)
  outliers start: 15
  outliers final: 9
  residues processed: 141
  average time/residue: 0.1563
  time to fit residues: 28.9541
Evaluate side-chains
  141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0980
   chunk 47 optimal weight:    0.9980
   chunk 55 optimal weight:    0.1980
   chunk 0 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.163590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.132764 restraints weight = 31224.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138458 restraints weight = 16810.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.142165 restraints weight = 11239.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.144420 restraints weight = 8528.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.146232 restraints weight = 7090.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1294

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= 0.131
  Angle     :  0.740  13.654   9464  Z= 0.338
  Chirality :  0.054   0.677   1096
  Planarity :  0.005   0.061   1193
  Dihedral  : 16.852 107.730   1216
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.05 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 20.90 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.28), residues: 857
  helix: -1.54 (0.94), residues: 32
  sheet:  0.76 (0.29), residues: 317
  loop : -1.54 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 543 
 TYR   0.019   0.001   TYR N 150 
 PHE   0.009   0.001   PHE A 509 
 TRP   0.005   0.001   TRP E 109 
 HIS   0.004   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6873)
  covalent geometry    : angle       0.67375 ( 9394)
  SS BOND              : bond        0.00439 (   14)
  SS BOND              : angle       1.80137 (   28)
  hydrogen bonds       : bond        0.03315 (  226)
  hydrogen bonds       : angle       5.52156 (  669)
  link_BETA1-3         : bond        0.00054 (    1)
  link_BETA1-3         : angle       3.24975 (    3)
  link_BETA1-4         : bond        0.00859 (    6)
  link_BETA1-4         : angle       3.73399 (   18)
  link_BETA1-6         : bond        0.00359 (    1)
  link_BETA1-6         : angle       1.91285 (    3)
  link_NAG-ASN         : bond        0.00948 (    6)
  link_NAG-ASN         : angle       5.44826 (   18)

*********************** 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
  147 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 GLU cc_start: 0.8274 (tp30) cc_final: 0.8037 (mp0)
REVERT: F   93 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8526 (p)
REVERT: M  149 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8078 (p)
REVERT: M  150 ASP cc_start: 0.8482 (t0) cc_final: 0.8274 (t0)
REVERT: N  209 ASN cc_start: 0.7903 (m-40) cc_final: 0.7127 (p0)
  outliers start: 14
  outliers final: 9
  residues processed: 142
  average time/residue: 0.1792
  time to fit residues: 33.4977
Evaluate side-chains
  140 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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  166 SER
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 35 optimal weight:    0.4980
   chunk 69 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
E  65 GLN
M 159 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.161783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.130962 restraints weight = 31230.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.136562 restraints weight = 16839.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.140174 restraints weight = 11332.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.142667 restraints weight = 8650.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.144160 restraints weight = 7092.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.1519

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     :  0.740  12.885   9464  Z= 0.341
  Chirality :  0.053   0.677   1096
  Planarity :  0.005   0.060   1193
  Dihedral  : 16.329 106.437   1216
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.87 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 20.62 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.94 (0.28), residues: 857
  helix: -1.59 (0.91), residues: 32
  sheet:  0.73 (0.29), residues: 323
  loop : -1.57 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  56 
 TYR   0.015   0.001   TYR N 150 
 PHE   0.009   0.001   PHE F  97 
 TRP   0.008   0.001   TRP E 109 
 HIS   0.003   0.001   HIS M 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6873)
  covalent geometry    : angle       0.67947 ( 9394)
  SS BOND              : bond        0.00440 (   14)
  SS BOND              : angle       1.84269 (   28)
  hydrogen bonds       : bond        0.03457 (  226)
  hydrogen bonds       : angle       5.52525 (  669)
  link_BETA1-3         : bond        0.00084 (    1)
  link_BETA1-3         : angle       3.24386 (    3)
  link_BETA1-4         : bond        0.00862 (    6)
  link_BETA1-4         : angle       3.69398 (   18)
  link_BETA1-6         : bond        0.00284 (    1)
  link_BETA1-6         : angle       1.81538 (    3)
  link_NAG-ASN         : bond        0.00904 (    6)
  link_NAG-ASN         : angle       5.09935 (   18)

*********************** 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
  149 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 GLU cc_start: 0.8258 (tp30) cc_final: 0.8013 (mp0)
REVERT: F   93 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8554 (p)
REVERT: M  149 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8166 (p)
REVERT: N  209 ASN cc_start: 0.7925 (m-40) cc_final: 0.7139 (p0)
  outliers start: 18
  outliers final: 13
  residues processed: 141
  average time/residue: 0.1739
  time to fit residues: 32.0512
Evaluate side-chains
  141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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  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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0970
   chunk 54 optimal weight:    0.5980
   chunk 83 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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
M 159 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.162451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.131711 restraints weight = 30926.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.137303 restraints weight = 16710.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.140985 restraints weight = 11242.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.143461 restraints weight = 8538.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.144991 restraints weight = 7004.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1699

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= 0.131
  Angle     :  0.722  12.955   9464  Z= 0.331
  Chirality :  0.053   0.657   1096
  Planarity :  0.005   0.060   1193
  Dihedral  : 15.836 106.304   1216
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.52 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.28), residues: 857
  helix: -1.57 (0.91), residues: 33
  sheet:  0.78 (0.29), residues: 317
  loop : -1.55 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  38 
 TYR   0.020   0.001   TYR N 150 
 PHE   0.009   0.001   PHE F  97 
 TRP   0.006   0.001   TRP A 554 
 HIS   0.002   0.001   HIS A 638 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6873)
  covalent geometry    : angle       0.66398 ( 9394)
  SS BOND              : bond        0.00425 (   14)
  SS BOND              : angle       1.80885 (   28)
  hydrogen bonds       : bond        0.03237 (  226)
  hydrogen bonds       : angle       5.41980 (  669)
  link_BETA1-3         : bond        0.00070 (    1)
  link_BETA1-3         : angle       3.38102 (    3)
  link_BETA1-4         : bond        0.00865 (    6)
  link_BETA1-4         : angle       3.66108 (   18)
  link_BETA1-6         : bond        0.00423 (    1)
  link_BETA1-6         : angle       1.79147 (    3)
  link_NAG-ASN         : bond        0.00866 (    6)
  link_NAG-ASN         : angle       4.76872 (   18)

*********************** 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
  151 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.274 
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: 0.8249 (tp30) cc_final: 0.7987 (mp0)
REVERT: F   34 TRP cc_start: 0.8915 (m100) cc_final: 0.8314 (m-90)
REVERT: F   93 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8560 (p)
REVERT: M  149 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8109 (p)
REVERT: M  150 ASP cc_start: 0.8541 (t0) cc_final: 0.8337 (t0)
REVERT: N  209 ASN cc_start: 0.7913 (m-40) cc_final: 0.7135 (p0)
  outliers start: 17
  outliers final: 12
  residues processed: 144
  average time/residue: 0.1682
  time to fit residues: 31.7076
Evaluate side-chains
  147 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
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 F residue  179 THR
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 73 optimal weight:    0.2980
   chunk 44 optimal weight:    0.0020
   chunk 66 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 13 optimal weight:    0.2980
   chunk 50 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.3788

-------------------------------------------------------------------------------
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 = 0.4000 r_free = 0.4000 target = 0.165346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.135511 restraints weight = 30619.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.141146 restraints weight = 15282.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.144781 restraints weight = 9796.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.147287 restraints weight = 7279.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.148968 restraints weight = 5853.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1773

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= 0.122
  Angle     :  0.715  13.004   9464  Z= 0.328
  Chirality :  0.052   0.658   1096
  Planarity :  0.005   0.059   1193
  Dihedral  : 15.456 105.547   1216
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.52 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.18 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.28), residues: 857
  helix: -1.51 (0.92), residues: 33
  sheet:  0.85 (0.29), residues: 312
  loop : -1.46 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  38 
 TYR   0.019   0.001   TYR N 150 
 PHE   0.009   0.001   PHE A 509 
 TRP   0.007   0.001   TRP A 487 
 HIS   0.002   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6873)
  covalent geometry    : angle       0.65894 ( 9394)
  SS BOND              : bond        0.00413 (   14)
  SS BOND              : angle       1.78278 (   28)
  hydrogen bonds       : bond        0.03102 (  226)
  hydrogen bonds       : angle       5.31687 (  669)
  link_BETA1-3         : bond        0.00049 (    1)
  link_BETA1-3         : angle       3.41611 (    3)
  link_BETA1-4         : bond        0.00889 (    6)
  link_BETA1-4         : angle       3.62324 (   18)
  link_BETA1-6         : bond        0.00431 (    1)
  link_BETA1-6         : angle       1.75852 (    3)
  link_NAG-ASN         : bond        0.00861 (    6)
  link_NAG-ASN         : angle       4.63370 (   18)

*********************** 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
  149 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.214 
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: F   34 TRP cc_start: 0.8877 (m100) cc_final: 0.8269 (m-90)
REVERT: F   93 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8548 (p)
REVERT: M  149 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.7997 (p)
REVERT: M  150 ASP cc_start: 0.8597 (t0) cc_final: 0.8378 (t0)
REVERT: N  209 ASN cc_start: 0.7911 (m-40) cc_final: 0.7151 (p0)
  outliers start: 17
  outliers final: 13
  residues processed: 144
  average time/residue: 0.1657
  time to fit residues: 31.1705
Evaluate side-chains
  143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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   87 CYS
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 65 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 83 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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
M 159 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.162064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.131258 restraints weight = 30971.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.136743 restraints weight = 16960.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.140399 restraints weight = 11485.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.142775 restraints weight = 8765.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.144465 restraints weight = 7251.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   6901  Z= 0.144
  Angle     :  0.724  12.976   9464  Z= 0.334
  Chirality :  0.052   0.653   1096
  Planarity :  0.005   0.056   1193
  Dihedral  : 15.123 104.750   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 :  2.38 %
    Allowed  : 21.18 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (0.28), residues: 857
  helix: -1.55 (0.89), residues: 33
  sheet:  0.86 (0.29), residues: 312
  loop : -1.46 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 141 
 TYR   0.023   0.001   TYR N 150 
 PHE   0.009   0.001   PHE F  97 
 TRP   0.005   0.001   TRP A 487 
 HIS   0.002   0.001   HIS A 589 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6873)
  covalent geometry    : angle       0.66816 ( 9394)
  SS BOND              : bond        0.00510 (   14)
  SS BOND              : angle       2.09452 (   28)
  hydrogen bonds       : bond        0.03258 (  226)
  hydrogen bonds       : angle       5.34687 (  669)
  link_BETA1-3         : bond        0.00067 (    1)
  link_BETA1-3         : angle       3.39501 (    3)
  link_BETA1-4         : bond        0.00874 (    6)
  link_BETA1-4         : angle       3.59426 (   18)
  link_BETA1-6         : bond        0.00358 (    1)
  link_BETA1-6         : angle       1.74726 (    3)
  link_NAG-ASN         : bond        0.00804 (    6)
  link_NAG-ASN         : angle       4.55199 (   18)

*********************** 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
  143 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.346 
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: 0.7914 (m-80) cc_final: 0.7380 (m-80)
REVERT: F   34 TRP cc_start: 0.8905 (m100) cc_final: 0.8338 (m-90)
REVERT: M  149 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8106 (p)
REVERT: M  150 ASP cc_start: 0.8507 (t0) cc_final: 0.8299 (t0)
REVERT: N  209 ASN cc_start: 0.7920 (m-40) cc_final: 0.7134 (p0)
  outliers start: 17
  outliers final: 15
  residues processed: 137
  average time/residue: 0.1607
  time to fit residues: 29.1692
Evaluate side-chains
  141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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  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   87 CYS
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain M residue  149 VAL
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0770
   chunk 5 optimal weight:    0.0070
   chunk 81 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.4956

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.162576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.131907 restraints weight = 31243.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.137269 restraints weight = 16814.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.140929 restraints weight = 11390.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.143367 restraints weight = 8692.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.145000 restraints weight = 7164.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1996

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= 0.129
  Angle     :  0.718  13.027   9464  Z= 0.331
  Chirality :  0.052   0.640   1096
  Planarity :  0.005   0.058   1193
  Dihedral  : 14.918 104.592   1216
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.52 %
    Favored  : 91.37 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.28), residues: 857
  helix: -1.44 (0.91), residues: 33
  sheet:  0.89 (0.29), residues: 312
  loop : -1.42 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 141 
 TYR   0.021   0.001   TYR N 150 
 PHE   0.009   0.001   PHE F  97 
 TRP   0.005   0.001   TRP A 487 
 HIS   0.003   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6873)
  covalent geometry    : angle       0.66350 ( 9394)
  SS BOND              : bond        0.00453 (   14)
  SS BOND              : angle       1.93971 (   28)
  hydrogen bonds       : bond        0.03122 (  226)
  hydrogen bonds       : angle       5.29379 (  669)
  link_BETA1-3         : bond        0.00034 (    1)
  link_BETA1-3         : angle       3.45499 (    3)
  link_BETA1-4         : bond        0.00905 (    6)
  link_BETA1-4         : angle       3.56989 (   18)
  link_BETA1-6         : bond        0.00416 (    1)
  link_BETA1-6         : angle       1.77416 (    3)
  link_NAG-ASN         : bond        0.00792 (    6)
  link_NAG-ASN         : angle       4.45160 (   18)

*********************** 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
  144 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   60 TYR cc_start: 0.7923 (m-80) cc_final: 0.7278 (m-80)
REVERT: F   34 TRP cc_start: 0.8891 (m100) cc_final: 0.8333 (m-90)
REVERT: M  149 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8075 (p)
REVERT: M  150 ASP cc_start: 0.8507 (t0) cc_final: 0.8295 (t0)
REVERT: N  209 ASN cc_start: 0.7914 (m-40) cc_final: 0.7138 (p0)
  outliers start: 18
  outliers final: 17
  residues processed: 137
  average time/residue: 0.1526
  time to fit residues: 27.7136
Evaluate side-chains
  136 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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 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 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 50 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 74 optimal weight:    0.2980
   chunk 52 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.162535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.131653 restraints weight = 31031.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.137193 restraints weight = 16874.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.140839 restraints weight = 11387.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.143276 restraints weight = 8688.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.144942 restraints weight = 7160.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2060

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= 0.131
  Angle     :  0.722  13.005   9464  Z= 0.334
  Chirality :  0.052   0.633   1096
  Planarity :  0.005   0.058   1193
  Dihedral  : 14.685 104.089   1216
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.63 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.18 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.28), residues: 857
  helix: -1.43 (0.92), residues: 33
  sheet:  0.93 (0.29), residues: 312
  loop : -1.41 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 141 
 TYR   0.022   0.001   TYR N 150 
 PHE   0.008   0.001   PHE F  97 
 TRP   0.005   0.001   TRP A 469 
 HIS   0.002   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6873)
  covalent geometry    : angle       0.66939 ( 9394)
  SS BOND              : bond        0.00453 (   14)
  SS BOND              : angle       1.95511 (   28)
  hydrogen bonds       : bond        0.03107 (  226)
  hydrogen bonds       : angle       5.24948 (  669)
  link_BETA1-3         : bond        0.00023 (    1)
  link_BETA1-3         : angle       3.45903 (    3)
  link_BETA1-4         : bond        0.00923 (    6)
  link_BETA1-4         : angle       3.55821 (   18)
  link_BETA1-6         : bond        0.00387 (    1)
  link_BETA1-6         : angle       1.76294 (    3)
  link_NAG-ASN         : bond        0.00792 (    6)
  link_NAG-ASN         : angle       4.38642 (   18)

********************** 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
  140 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   34 TRP cc_start: 0.8880 (m100) cc_final: 0.8335 (m-90)
REVERT: M  149 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8196 (p)
REVERT: M  150 ASP cc_start: 0.8517 (t0) cc_final: 0.8308 (t0)
REVERT: N  209 ASN cc_start: 0.7915 (m-40) cc_final: 0.7138 (p0)
  outliers start: 20
  outliers final: 19
  residues processed: 133
  average time/residue: 0.1632
  time to fit residues: 28.7529
Evaluate side-chains
  136 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
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  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 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 4 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 75 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0870
   overall best weight:    0.4758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.162745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.131805 restraints weight = 31100.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.137380 restraints weight = 16839.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.141053 restraints weight = 11303.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.143508 restraints weight = 8616.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.145216 restraints weight = 7083.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2131

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= 0.131
  Angle     :  0.718  13.030   9464  Z= 0.332
  Chirality :  0.052   0.628   1096
  Planarity :  0.005   0.058   1193
  Dihedral  : 14.418 103.528   1216
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.52 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.46 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.29), residues: 857
  helix: -0.84 (1.03), residues: 27
  sheet:  0.93 (0.29), residues: 312
  loop : -1.37 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 141 
 TYR   0.023   0.001   TYR N 150 
 PHE   0.008   0.001   PHE F  97 
 TRP   0.005   0.001   TRP A 469 
 HIS   0.002   0.001   HIS A 649 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6873)
  covalent geometry    : angle       0.66525 ( 9394)
  SS BOND              : bond        0.00471 (   14)
  SS BOND              : angle       1.94831 (   28)
  hydrogen bonds       : bond        0.03091 (  226)
  hydrogen bonds       : angle       5.24129 (  669)
  link_BETA1-3         : bond        0.00042 (    1)
  link_BETA1-3         : angle       3.46829 (    3)
  link_BETA1-4         : bond        0.00933 (    6)
  link_BETA1-4         : angle       3.60016 (   18)
  link_BETA1-6         : bond        0.00387 (    1)
  link_BETA1-6         : angle       1.76856 (    3)
  link_NAG-ASN         : bond        0.00781 (    6)
  link_NAG-ASN         : angle       4.31607 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2165.67 seconds
wall clock time: 37 minutes 36.59 seconds (2256.59 seconds total)