Starting phenix.real_space_refine
on Thu Jul 31 11:28:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8thz_41275/07_2025/8thz_41275_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8thz_41275/07_2025/8thz_41275.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8thz_41275/07_2025/8thz_41275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8thz_41275/07_2025/8thz_41275.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8thz_41275/07_2025/8thz_41275_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8thz_41275/07_2025/8thz_41275_trim.cif"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.029
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      40      5.16       5
     C    4344      2.51       5
     N    1153      2.21       5
     O    1384      1.98       5
     H    6400      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13321
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "H"
      Number of atoms: 3280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 3280
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "L"
      Number of atoms: 3192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 3192
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203}
    Chain: "A"
      Number of atoms: 3491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 3491
          Classifications: {'peptide': 235}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 214}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "E"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 1632
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "F"
      Number of atoms: 1531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 1531
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 7, 'TRANS': 97}
    Chain: "N"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 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: "G"
      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
  Time building chain proxies: 7.14, per 1000 atoms: 0.54
  Number of scatterers: 13321
  At special positions: 0
  Unit cell: (73.92, 89.6, 129.92, 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      40     16.00
     O    1384      8.00
     N    1153      7.00
     C    4344      6.00
     H    6400      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 223 " - pdb=" SG  CYS L 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.04
    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=2.03
    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=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  87 " 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
      " NAG B   1 " - " NAG B   2 "
      " BMA D   3 " - " BMA D   4 "
      " BMA G   3 " - " BMA G   4 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG N   1 " - " NAG N   2 "
    BETA1-6
      " BMA G   3 " - " BMA G   5 "
    NAG-ASN
      " NAG B   1 " - " ASN A 448 "
      " NAG C   1 " - " ASN A 532 "
      " NAG D   1 " - " ASN A 540 "
      " NAG N   1 " - " ASN A 430 "
  Time building additional restraints: 3.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1612

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 21 sheets defined
      8.9% alpha, 38.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 134 through 139
    Processing helix  chain 'H' and resid 194 through 198
      removed outlier: 3.726A  pdb=" N   GLY H 197 " --> pdb=" O   SER H 194 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.964A  pdb=" N   VAL L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 126
      removed outlier: 3.569A  pdb=" N   LYS L 126 " --> pdb=" O   ASP L 122 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 183 through 187
    Processing helix  chain 'A' and resid 438 through 442
      removed outlier: 3.703A  pdb=" N   LEU A 441 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE A 442 " --> pdb=" O   ALA A 439 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 438 through 442'
    Processing helix  chain 'A' and resid 452 through 457
    Processing helix  chain 'A' and resid 461 through 465
      removed outlier: 3.805A  pdb=" N   GLU A 464 " --> pdb=" O   PRO A 461 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   PHE A 465 " --> pdb=" O   ILE A 462 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 461 through 465'
    Processing helix  chain 'A' and resid 543 through 547
    Processing helix  chain 'A' and resid 613 through 618
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.765A  pdb=" N   ASN E  31 " --> pdb=" O   THR E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'F' and resid 26 through 30
      removed outlier: 3.513A  pdb=" N   ASP F  29 " --> pdb=" O   LYS F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 78 through 82
      removed outlier: 4.036A  pdb=" N   GLU F  82 " --> pdb=" O   ALA F  79 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.717A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU H  34 " --> pdb=" O   GLU H  50 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLU H  50 " --> pdb=" O   LEU H  34 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   MET H  48 " --> pdb=" O   ALA H  61 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU A 608 " --> pdb=" O   ALA A 643 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL A 609 " --> pdb=" O   TRP A 602 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   TRP A 602 " --> pdb=" O   VAL A 609 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.717A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU H  34 " --> pdb=" O   GLU H  50 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLU H  50 " --> pdb=" O   LEU H  34 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   MET H  48 " --> pdb=" O   ALA H  61 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 127 through 130
      removed outlier: 6.098A  pdb=" N   TYR H 183 " --> pdb=" O   ASP H 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 142 through 145
      removed outlier: 3.515A  pdb=" N   VAL H 188 " --> pdb=" O   HIS H 171 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 158 through 161
    Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13
      removed outlier: 4.027A  pdb=" N   ALA L  13 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LEU L  33 " --> pdb=" O   SER L  49 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   SER L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13
      removed outlier: 4.027A  pdb=" N   ALA L  13 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.559A  pdb=" N   SER L 114 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
      removed outlier: 5.150A  pdb=" N   SER L 131 " --> pdb=" O   LEU L 181 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   LEU L 181 " --> pdb=" O   SER L 131 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 179 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   LEU L 179 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   LEU L 135 " --> pdb=" O   SER L 177 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   SER L 177 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   ASN L 137 " --> pdb=" O   LEU L 175 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   LEU L 175 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 150
    Processing sheet with id=AB3, first strand: chain 'A' and resid 426 through 427
      removed outlier: 4.397A  pdb=" N   ALA A 426 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 426 through 427
      removed outlier: 4.397A  pdb=" N   ALA A 426 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET A 555 " --> pdb=" O   CYS A 503 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   THR A 553 " --> pdb=" O   PRO A 505 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   TYR A 507 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLY A 551 " --> pdb=" O   TYR A 507 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 497 through 498
    Processing sheet with id=AB6, first strand: chain 'A' and resid 519 through 520
      removed outlier: 3.509A  pdb=" N   ALA A 524 " --> pdb=" O   ASP A 520 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 17 through 18
    Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 51
      removed outlier: 3.682A  pdb=" N   MET E  48 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   TRP E  36 " --> pdb=" O   MET E  48 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   GLY E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   ILE E  34 " --> pdb=" O   GLY E  50 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 51
      removed outlier: 3.682A  pdb=" N   MET E  48 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   TRP E  36 " --> pdb=" O   MET E  48 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   GLY E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   ILE E  34 " --> pdb=" O   GLY E  50 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 9 through 11
      removed outlier: 3.512A  pdb=" N   TYR F  85 " --> pdb=" O   THR F 101 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   TRP F  34 " --> pdb=" O   VAL F  46 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 9 through 11
      removed outlier: 3.512A  pdb=" N   TYR F  85 " --> pdb=" O   THR F 101 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 18 through 23

    231 hydrogen bonds defined for protein.
    546 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.90

  Time building geometry restraints manager: 4.20 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 6400
        1.04 -     1.25: 979
        1.25 -     1.45: 2311
        1.45 -     1.66: 3759
        1.66 -     1.86: 50
  Bond restraints: 13499
  Sorted by residual:
  bond pdb=" C5  BMA D   4 "
       pdb=" O5  BMA D   4 "
    ideal  model  delta    sigma   weight residual
    1.417  1.464 -0.047 2.00e-02 2.50e+03 5.58e+00
  bond pdb=" CB  CYS A 552 "
       pdb=" HB3 CYS A 552 "
    ideal  model  delta    sigma   weight residual
    0.970  0.928  0.042 2.00e-02 2.50e+03 4.39e+00
  bond pdb=" C4  BMA D   3 "
       pdb=" C5  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.528  1.568 -0.040 2.00e-02 2.50e+03 3.93e+00
  bond pdb=" C3  BMA D   3 "
       pdb=" C4  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.541  1.578 -0.037 2.00e-02 2.50e+03 3.35e+00
  bond pdb=" N   ASP L   1 "
       pdb=" CA  ASP L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  ... (remaining 13494 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 23797
        1.83 -     3.66: 326
        3.66 -     5.49: 43
        5.49 -     7.33: 11
        7.33 -     9.16: 5
  Bond angle restraints: 24182
  Sorted by residual:
  angle pdb=" N   CYS A 552 "
        pdb=" CA  CYS A 552 "
        pdb=" C   CYS A 552 "
      ideal   model   delta    sigma   weight residual
     108.14  113.10   -4.96 1.52e+00 4.33e-01 1.06e+01
  angle pdb=" C3  NAG N   1 "
        pdb=" C4  NAG N   1 "
        pdb=" C5  NAG N   1 "
      ideal   model   delta    sigma   weight residual
     109.38  118.54   -9.16 3.00e+00 1.11e-01 9.32e+00
  angle pdb=" C1  BMA G   4 "
        pdb=" O5  BMA G   4 "
        pdb=" C5  BMA G   4 "
      ideal   model   delta    sigma   weight residual
     118.82  110.40    8.42 3.00e+00 1.11e-01 7.89e+00
  angle pdb=" C   ASP A 431 "
        pdb=" CA  ASP A 431 "
        pdb=" CB  ASP A 431 "
      ideal   model   delta    sigma   weight residual
     111.82  115.68   -3.86 1.38e+00 5.25e-01 7.84e+00
  angle pdb=" C   CYS A 508 "
        pdb=" CA  CYS A 508 "
        pdb=" HA  CYS A 508 "
      ideal   model   delta    sigma   weight residual
     109.00  100.78    8.22 3.00e+00 1.11e-01 7.51e+00
  ... (remaining 24177 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.76: 6074
       25.76 -    51.51: 490
       51.51 -    77.27: 111
       77.27 -   103.02: 68
      103.02 -   128.78: 27
  Dihedral angle restraints: 6770
    sinusoidal: 3738
      harmonic: 3032
  Sorted by residual:
  dihedral pdb=" CB  CYS H 223 "
           pdb=" SG  CYS H 223 "
           pdb=" SG  CYS L 214 "
           pdb=" CB  CYS L 214 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -137.84   51.84     1      1.00e+01 1.00e-02 3.67e+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
     -86.00  -36.17  -49.83     1      1.00e+01 1.00e-02 3.41e+01
  dihedral pdb=" CB  CYS A 569 "
           pdb=" SG  CYS A 569 "
           pdb=" SG  CYS A 597 "
           pdb=" CB  CYS A 597 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -43.40  -42.60     1      1.00e+01 1.00e-02 2.53e+01
  ... (remaining 6767 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 990
       0.083 -    0.166: 110
       0.166 -    0.248: 4
       0.248 -    0.331: 2
       0.331 -    0.414: 3
  Chirality restraints: 1109
  Sorted by residual:
  chirality pdb=" C1  BMA G   5 "
            pdb=" O6  BMA G   3 "
            pdb=" C2  BMA G   5 "
            pdb=" O5  BMA G   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-02 2.50e+03 1.49e+02
  chirality pdb=" C1  BMA G   3 "
            pdb=" O4  NAG G   2 "
            pdb=" C2  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-02 2.50e+03 5.46e+01
  chirality pdb=" C1  NAG G   2 "
            pdb=" O4  NAG G   1 "
            pdb=" C2  NAG G   2 "
            pdb=" O5  NAG G   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.29   -0.11 2.00e-02 2.50e+03 3.11e+01
  ... (remaining 1106 not shown)

  Planarity restraints: 2058
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 219 "   -0.035 5.00e-02 4.00e+02   5.31e-02 4.52e+00
        pdb=" N   PRO H 220 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO H 220 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO H 220 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG G   1 "    0.020 2.00e-02 2.50e+03   1.80e-02 4.04e+00
        pdb=" C7  NAG G   1 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8  NAG G   1 "    0.019 2.00e-02 2.50e+03
        pdb=" N2  NAG G   1 "   -0.022 2.00e-02 2.50e+03
        pdb=" O7  NAG G   1 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 524 "   -0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO A 525 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 525 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 525 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 2055 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 389
        2.13 -     2.75: 23140
        2.75 -     3.36: 35323
        3.36 -     3.98: 46593
        3.98 -     4.60: 71799
  Nonbonded interactions: 177244
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 464 "
            pdb=" H   GLU A 464 "
     model   vdw
     1.510 2.450
  nonbonded pdb="HE22 GLN H   6 "
            pdb=" O   TYR H  94 "
     model   vdw
     1.523 2.450
  nonbonded pdb=" OE1 GLU E  89 "
            pdb=" H   GLU E  89 "
     model   vdw
     1.530 2.450
  nonbonded pdb=" OE1 GLN E  62 "
            pdb=" H   GLN E  62 "
     model   vdw
     1.532 2.450
  nonbonded pdb="HD21 ASN H 162 "
            pdb=" O   THR H 200 "
     model   vdw
     1.583 2.450
  ... (remaining 177239 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.150
  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:             0.230
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     31.830
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
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   0.055   7128  Z= 0.194
  Angle     :  0.763   9.438   9751  Z= 0.364
  Chirality :  0.054   0.414   1109
  Planarity :  0.005   0.056   1225
  Dihedral  : 25.912 128.781   2733
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.13 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 20.35 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.29), residues: 879
  helix: -1.34 (0.81), residues: 37
  sheet:  0.41 (0.30), residues: 326
  loop : -1.87 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  36 
 HIS   0.005   0.001   HIS A 488 
 PHE   0.016   0.001   PHE A 522 
 TYR   0.009   0.001   TYR H 201 
 ARG   0.008   0.001   ARG F  53 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00602 (    4)
  link_NAG-ASN         : angle       2.62537 (   12)
  link_BETA1-4         : bond        0.01667 (    6)
  link_BETA1-4         : angle       3.08692 (   18)
  hydrogen bonds       : bond        0.17762 (  197)
  hydrogen bonds       : angle       8.61870 (  546)
  link_BETA1-6         : bond        0.01849 (    1)
  link_BETA1-6         : angle       0.72145 (    3)
  SS BOND              : bond        0.00583 (   15)
  SS BOND              : angle       1.71017 (   30)
  link_BETA1-3         : bond        0.00745 (    3)
  link_BETA1-3         : angle       1.80461 (    9)
  covalent geometry    : bond        0.00412 ( 7099)
  covalent geometry    : angle       0.74014 ( 9679)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   75 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue SER  139 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  112 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7201 (pt0)
REVERT: E   87 ARG cc_start: 0.5385 (tpm170) cc_final: 0.5156 (tpt90)
  outliers start: 4
  outliers final: 3
  residues processed: 101
  average time/residue: 0.4630
  time to fit residues: 61.7489
Evaluate side-chains
  95 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   35 SER
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain H residue  208 LYS
Chi-restraints excluded: chain A residue  540 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.156182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.130087 restraints weight = 29606.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.77
r_work: 0.3652 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.0753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7128  Z= 0.159
  Angle     :  0.766   8.107   9751  Z= 0.362
  Chirality :  0.051   0.296   1109
  Planarity :  0.005   0.049   1225
  Dihedral  : 23.124 118.676   1276
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 10.47 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.00 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.28), residues: 879
  helix: -0.93 (0.82), residues: 44
  sheet:  0.41 (0.30), residues: 318
  loop : -1.79 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 420 
 HIS   0.005   0.001   HIS A 458 
 PHE   0.017   0.002   PHE A 509 
 TYR   0.011   0.001   TYR H  95 
 ARG   0.007   0.001   ARG A 521 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00430 (    4)
  link_NAG-ASN         : angle       2.34946 (   12)
  link_BETA1-4         : bond        0.00585 (    6)
  link_BETA1-4         : angle       2.43659 (   18)
  hydrogen bonds       : bond        0.04491 (  197)
  hydrogen bonds       : angle       6.76772 (  546)
  link_BETA1-6         : bond        0.00629 (    1)
  link_BETA1-6         : angle       2.71995 (    3)
  SS BOND              : bond        0.00598 (   15)
  SS BOND              : angle       1.49081 (   30)
  link_BETA1-3         : bond        0.00530 (    3)
  link_BETA1-3         : angle       2.85697 (    9)
  covalent geometry    : bond        0.00367 ( 7099)
  covalent geometry    : angle       0.74557 ( 9679)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   75 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue SER  139 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    3 GLN cc_start: 0.8151 (mt0) cc_final: 0.7791 (mp10)
REVERT: H  178 GLN cc_start: 0.8172 (tt0) cc_final: 0.7908 (tt0)
REVERT: E   67 ARG cc_start: 0.6497 (mtm-85) cc_final: 0.6257 (mtm180)
  outliers start: 14
  outliers final: 8
  residues processed: 106
  average time/residue: 0.5467
  time to fit residues: 76.7773
Evaluate side-chains
  97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 1.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  208 LYS
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain A residue  586 PHE
Chi-restraints excluded: chain A residue  639 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0030
   chunk 22 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.5990

-------------------------------------------------------------------------------
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 = 0.4083 r_free = 0.4083 target = 0.155188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.128330 restraints weight = 30017.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.88
r_work: 0.3618 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7128  Z= 0.138
  Angle     :  0.725   8.894   9751  Z= 0.338
  Chirality :  0.049   0.253   1109
  Planarity :  0.005   0.052   1225
  Dihedral  : 19.053 114.721   1272
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.78 %
    Favored  : 89.99 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.13 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.28), residues: 879
  helix: -0.76 (0.85), residues: 44
  sheet:  0.49 (0.29), residues: 324
  loop : -1.89 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.005   0.001   HIS A 488 
 PHE   0.016   0.001   PHE A 509 
 TYR   0.010   0.001   TYR H  95 
 ARG   0.002   0.000   ARG H  99 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00432 (    4)
  link_NAG-ASN         : angle       3.31333 (   12)
  link_BETA1-4         : bond        0.00580 (    6)
  link_BETA1-4         : angle       2.20811 (   18)
  hydrogen bonds       : bond        0.03857 (  197)
  hydrogen bonds       : angle       6.04325 (  546)
  link_BETA1-6         : bond        0.00499 (    1)
  link_BETA1-6         : angle       3.32641 (    3)
  SS BOND              : bond        0.00644 (   15)
  SS BOND              : angle       1.61414 (   30)
  link_BETA1-3         : bond        0.00441 (    3)
  link_BETA1-3         : angle       3.50026 (    9)
  covalent geometry    : bond        0.00323 ( 7099)
  covalent geometry    : angle       0.69583 ( 9679)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   75 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue SER  139 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.945 
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: H    3 GLN cc_start: 0.7970 (mt0) cc_final: 0.7732 (mp10)
REVERT: H  178 GLN cc_start: 0.8106 (tt0) cc_final: 0.7823 (tt0)
REVERT: L  170 ASP cc_start: 0.7052 (t0) cc_final: 0.6670 (t0)
REVERT: A  627 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.5476 (t80)
REVERT: E   23 GLU cc_start: 0.4975 (OUTLIER) cc_final: 0.4339 (pm20)
  outliers start: 20
  outliers final: 13
  residues processed: 113
  average time/residue: 0.4376
  time to fit residues: 65.6577
Evaluate side-chains
  106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  208 LYS
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  460 ARG
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain A residue  552 CYS
Chi-restraints excluded: chain A residue  586 PHE
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain E residue   16 SER
Chi-restraints excluded: chain E residue   23 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 27 optimal weight:    0.1980
   chunk 74 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0670
   chunk 81 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0770
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.3276

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

Flipped N/Q/H residues before XYZ refinement:
A 589 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.154776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.127958 restraints weight = 29769.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.87
r_work: 0.3627 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7128  Z= 0.118
  Angle     :  0.703   8.601   9751  Z= 0.328
  Chirality :  0.049   0.277   1109
  Planarity :  0.005   0.053   1225
  Dihedral  : 16.930 112.824   1272
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.19 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 18.72 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.28), residues: 879
  helix: -0.82 (0.84), residues: 44
  sheet:  0.52 (0.29), residues: 324
  loop : -1.82 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.006   0.001   HIS A 488 
 PHE   0.014   0.001   PHE A 509 
 TYR   0.008   0.001   TYR H  95 
 ARG   0.007   0.000   ARG E  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00400 (    4)
  link_NAG-ASN         : angle       2.96931 (   12)
  link_BETA1-4         : bond        0.00594 (    6)
  link_BETA1-4         : angle       2.22661 (   18)
  hydrogen bonds       : bond        0.03171 (  197)
  hydrogen bonds       : angle       5.50543 (  546)
  link_BETA1-6         : bond        0.00344 (    1)
  link_BETA1-6         : angle       3.30269 (    3)
  SS BOND              : bond        0.00542 (   15)
  SS BOND              : angle       1.36020 (   30)
  link_BETA1-3         : bond        0.00371 (    3)
  link_BETA1-3         : angle       3.75107 (    9)
  covalent geometry    : bond        0.00277 ( 7099)
  covalent geometry    : angle       0.67543 ( 9679)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   75 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue SER  139 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 1.239 
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: H    3 GLN cc_start: 0.7996 (mt0) cc_final: 0.7748 (mp10)
REVERT: H  178 GLN cc_start: 0.8052 (tt0) cc_final: 0.7764 (tt0)
REVERT: A  555 MET cc_start: 0.8014 (mmm) cc_final: 0.7537 (mmm)
REVERT: E   23 GLU cc_start: 0.4894 (OUTLIER) cc_final: 0.4209 (pm20)
  outliers start: 20
  outliers final: 13
  residues processed: 117
  average time/residue: 0.4623
  time to fit residues: 74.2622
Evaluate side-chains
  106 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  208 LYS
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain A residue  460 ARG
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  520 ASP
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain A residue  552 CYS
Chi-restraints excluded: chain A residue  586 PHE
Chi-restraints excluded: chain E residue   23 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4044 r_free = 0.4044 target = 0.152310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.125447 restraints weight = 30164.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 2.87
r_work: 0.3587 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7128  Z= 0.163
  Angle     :  0.722   8.632   9751  Z= 0.340
  Chirality :  0.049   0.299   1109
  Planarity :  0.005   0.051   1225
  Dihedral  : 15.571 108.531   1272
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.13 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.00 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.28), residues: 879
  helix: -0.65 (0.89), residues: 44
  sheet:  0.54 (0.30), residues: 320
  loop : -1.95 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP H  47 
 HIS   0.004   0.001   HIS A 488 
 PHE   0.014   0.001   PHE E  55 
 TYR   0.012   0.001   TYR H  95 
 ARG   0.002   0.000   ARG H  99 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00412 (    4)
  link_NAG-ASN         : angle       3.03073 (   12)
  link_BETA1-4         : bond        0.00658 (    6)
  link_BETA1-4         : angle       2.34201 (   18)
  hydrogen bonds       : bond        0.03351 (  197)
  hydrogen bonds       : angle       5.50362 (  546)
  link_BETA1-6         : bond        0.00309 (    1)
  link_BETA1-6         : angle       3.16089 (    3)
  SS BOND              : bond        0.00547 (   15)
  SS BOND              : angle       1.65114 (   30)
  link_BETA1-3         : bond        0.00329 (    3)
  link_BETA1-3         : angle       3.26691 (    9)
  covalent geometry    : bond        0.00387 ( 7099)
  covalent geometry    : angle       0.69479 ( 9679)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   75 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue SER  139 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Evaluate side-chains
  116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.982 
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: H    3 GLN cc_start: 0.8011 (mt0) cc_final: 0.7719 (mp10)
REVERT: H  178 GLN cc_start: 0.8073 (tt0) cc_final: 0.7842 (tt0)
REVERT: A  455 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.7040 (mtt180)
REVERT: A  555 MET cc_start: 0.8071 (mmm) cc_final: 0.7570 (mmm)
REVERT: E   23 GLU cc_start: 0.5012 (OUTLIER) cc_final: 0.4317 (pm20)
  outliers start: 21
  outliers final: 15
  residues processed: 111
  average time/residue: 0.4257
  time to fit residues: 62.1855
Evaluate side-chains
  108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain A residue  455 ARG
Chi-restraints excluded: chain A residue  460 ARG
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain A residue  552 CYS
Chi-restraints excluded: chain A residue  586 PHE
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain E residue   23 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 72 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
F  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.152873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.125659 restraints weight = 30547.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 2.93
r_work: 0.3576 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7128  Z= 0.151
  Angle     :  0.707   8.859   9751  Z= 0.334
  Chirality :  0.049   0.337   1109
  Planarity :  0.005   0.056   1225
  Dihedral  : 13.944 100.998   1268
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.33 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.95 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.28), residues: 879
  helix: -0.73 (0.87), residues: 44
  sheet:  0.54 (0.30), residues: 318
  loop : -1.93 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 420 
 HIS   0.006   0.001   HIS A 488 
 PHE   0.012   0.001   PHE A 509 
 TYR   0.010   0.001   TYR H  95 
 ARG   0.009   0.000   ARG A 521 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00379 (    4)
  link_NAG-ASN         : angle       3.03405 (   12)
  link_BETA1-4         : bond        0.00723 (    6)
  link_BETA1-4         : angle       2.30017 (   18)
  hydrogen bonds       : bond        0.03174 (  197)
  hydrogen bonds       : angle       5.33284 (  546)
  link_BETA1-6         : bond        0.00326 (    1)
  link_BETA1-6         : angle       2.94121 (    3)
  SS BOND              : bond        0.00576 (   15)
  SS BOND              : angle       1.57854 (   30)
  link_BETA1-3         : bond        0.00367 (    3)
  link_BETA1-3         : angle       2.85239 (    9)
  covalent geometry    : bond        0.00363 ( 7099)
  covalent geometry    : angle       0.68150 ( 9679)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   75 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue SER  139 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Evaluate side-chains
  112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    3 GLN cc_start: 0.8011 (mt0) cc_final: 0.7675 (mp10)
REVERT: H  178 GLN cc_start: 0.8089 (tt0) cc_final: 0.7831 (tt0)
REVERT: E   23 GLU cc_start: 0.4919 (OUTLIER) cc_final: 0.4183 (pm20)
  outliers start: 18
  outliers final: 16
  residues processed: 108
  average time/residue: 0.4028
  time to fit residues: 58.0283
Evaluate side-chains
  110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  198 THR
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain A residue  460 ARG
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain A residue  552 CYS
Chi-restraints excluded: chain A residue  586 PHE
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain E residue   23 GLU
Chi-restraints excluded: chain F residue   88 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 33 optimal weight:    0.4980
   chunk 37 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0170
   chunk 46 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0000
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.4624

-------------------------------------------------------------------------------
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 = 0.4059 r_free = 0.4059 target = 0.153757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.126705 restraints weight = 30191.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.90
r_work: 0.3591 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7128  Z= 0.128
  Angle     :  0.689   8.916   9751  Z= 0.324
  Chirality :  0.048   0.341   1109
  Planarity :  0.005   0.053   1225
  Dihedral  : 13.261  96.980   1268
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.99 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.22 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.28), residues: 879
  helix: -0.72 (0.88), residues: 44
  sheet:  0.63 (0.30), residues: 313
  loop : -1.92 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F  90 
 HIS   0.005   0.001   HIS A 488 
 PHE   0.012   0.001   PHE A 509 
 TYR   0.009   0.001   TYR H  95 
 ARG   0.006   0.000   ARG A 521 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00364 (    4)
  link_NAG-ASN         : angle       3.07291 (   12)
  link_BETA1-4         : bond        0.00716 (    6)
  link_BETA1-4         : angle       2.35005 (   18)
  hydrogen bonds       : bond        0.03044 (  197)
  hydrogen bonds       : angle       5.25028 (  546)
  link_BETA1-6         : bond        0.00423 (    1)
  link_BETA1-6         : angle       2.78993 (    3)
  SS BOND              : bond        0.00683 (   15)
  SS BOND              : angle       1.61613 (   30)
  link_BETA1-3         : bond        0.00328 (    3)
  link_BETA1-3         : angle       2.58967 (    9)
  covalent geometry    : bond        0.00305 ( 7099)
  covalent geometry    : angle       0.66288 ( 9679)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   75 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue SER  139 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Evaluate side-chains
  112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 1.011 
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: H    3 GLN cc_start: 0.7997 (mt0) cc_final: 0.7691 (mp10)
REVERT: H  178 GLN cc_start: 0.8067 (tt0) cc_final: 0.7822 (tt0)
REVERT: L  170 ASP cc_start: 0.7101 (t0) cc_final: 0.6736 (t0)
REVERT: A  455 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6994 (mtt180)
REVERT: A  469 TRP cc_start: 0.6420 (m-10) cc_final: 0.5912 (m100)
REVERT: A  555 MET cc_start: 0.8075 (mmm) cc_final: 0.7545 (mmm)
REVERT: E   23 GLU cc_start: 0.4972 (OUTLIER) cc_final: 0.4252 (pm20)
REVERT: F   88 GLN cc_start: 0.6722 (OUTLIER) cc_final: 0.6188 (tt0)
  outliers start: 18
  outliers final: 12
  residues processed: 108
  average time/residue: 0.4069
  time to fit residues: 58.7915
Evaluate side-chains
  107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain A residue  455 ARG
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain A residue  552 CYS
Chi-restraints excluded: chain A residue  586 PHE
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain E residue   23 GLU
Chi-restraints excluded: chain F residue   88 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0970
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
F  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.151608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.125047 restraints weight = 29913.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.90
r_work: 0.3548 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7128  Z= 0.138
  Angle     :  0.692   8.993   9751  Z= 0.326
  Chirality :  0.048   0.348   1109
  Planarity :  0.005   0.052   1225
  Dihedral  : 12.599  93.264   1268
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.33 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.08 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.28), residues: 879
  helix: -0.71 (0.88), residues: 44
  sheet:  0.66 (0.30), residues: 313
  loop : -1.91 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 420 
 HIS   0.005   0.001   HIS A 488 
 PHE   0.012   0.001   PHE A 509 
 TYR   0.009   0.001   TYR H  95 
 ARG   0.006   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00362 (    4)
  link_NAG-ASN         : angle       3.09722 (   12)
  link_BETA1-4         : bond        0.00713 (    6)
  link_BETA1-4         : angle       2.49084 (   18)
  hydrogen bonds       : bond        0.02970 (  197)
  hydrogen bonds       : angle       5.17647 (  546)
  link_BETA1-6         : bond        0.00554 (    1)
  link_BETA1-6         : angle       2.24081 (    3)
  SS BOND              : bond        0.00529 (   15)
  SS BOND              : angle       1.65804 (   30)
  link_BETA1-3         : bond        0.00324 (    3)
  link_BETA1-3         : angle       2.35148 (    9)
  covalent geometry    : bond        0.00335 ( 7099)
  covalent geometry    : angle       0.66577 ( 9679)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   75 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue SER  139 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Evaluate side-chains
  114 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 1.095 
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: H    3 GLN cc_start: 0.8065 (mt0) cc_final: 0.7676 (mp10)
REVERT: L  170 ASP cc_start: 0.7106 (t0) cc_final: 0.6681 (t0)
REVERT: A  469 TRP cc_start: 0.6389 (m-10) cc_final: 0.5866 (m100)
REVERT: A  555 MET cc_start: 0.8052 (mmm) cc_final: 0.7510 (mmm)
REVERT: E   23 GLU cc_start: 0.4988 (OUTLIER) cc_final: 0.4276 (pm20)
  outliers start: 22
  outliers final: 19
  residues processed: 108
  average time/residue: 0.4054
  time to fit residues: 59.4201
Evaluate side-chains
  110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  460 ARG
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain A residue  552 CYS
Chi-restraints excluded: chain A residue  586 PHE
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain E residue   23 GLU
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain F residue   88 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3983 r_free = 0.3983 target = 0.150981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.124622 restraints weight = 29536.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.87
r_work: 0.3542 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7128  Z= 0.150
  Angle     :  0.703   9.066   9751  Z= 0.333
  Chirality :  0.048   0.352   1109
  Planarity :  0.005   0.052   1225
  Dihedral  : 12.154  90.224   1268
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.56 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 20.22 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.28), residues: 879
  helix: -0.75 (0.87), residues: 44
  sheet:  0.60 (0.30), residues: 318
  loop : -1.90 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 420 
 HIS   0.005   0.001   HIS A 488 
 PHE   0.012   0.001   PHE A 509 
 TYR   0.010   0.001   TYR H  95 
 ARG   0.005   0.000   ARG A 521 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00374 (    4)
  link_NAG-ASN         : angle       3.11980 (   12)
  link_BETA1-4         : bond        0.00715 (    6)
  link_BETA1-4         : angle       2.60401 (   18)
  hydrogen bonds       : bond        0.03069 (  197)
  hydrogen bonds       : angle       5.22975 (  546)
  link_BETA1-6         : bond        0.00602 (    1)
  link_BETA1-6         : angle       1.66254 (    3)
  SS BOND              : bond        0.00529 (   15)
  SS BOND              : angle       1.74215 (   30)
  link_BETA1-3         : bond        0.00267 (    3)
  link_BETA1-3         : angle       2.20145 (    9)
  covalent geometry    : bond        0.00361 ( 7099)
  covalent geometry    : angle       0.67712 ( 9679)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   75 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue SER  139 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    3 GLN cc_start: 0.8108 (mt0) cc_final: 0.7633 (mp10)
REVERT: A  469 TRP cc_start: 0.6524 (m-10) cc_final: 0.5924 (m100)
REVERT: E   23 GLU cc_start: 0.4904 (OUTLIER) cc_final: 0.4185 (pm20)
  outliers start: 21
  outliers final: 17
  residues processed: 105
  average time/residue: 0.3914
  time to fit residues: 55.6936
Evaluate side-chains
  108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain A residue  552 CYS
Chi-restraints excluded: chain A residue  586 PHE
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain E residue   16 SER
Chi-restraints excluded: chain E residue   23 GLU
Chi-restraints excluded: chain E residue   35 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 82 optimal weight:    0.2980
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3992 r_free = 0.3992 target = 0.151786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.125298 restraints weight = 29651.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.92
r_work: 0.3547 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7128  Z= 0.136
  Angle     :  0.692   9.136   9751  Z= 0.326
  Chirality :  0.048   0.361   1109
  Planarity :  0.005   0.052   1225
  Dihedral  : 11.445  86.693   1268
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.53 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.62 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.28), residues: 879
  helix: -0.77 (0.86), residues: 44
  sheet:  0.67 (0.30), residues: 319
  loop : -1.93 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 420 
 HIS   0.005   0.001   HIS A 488 
 PHE   0.011   0.001   PHE A 509 
 TYR   0.008   0.001   TYR H  95 
 ARG   0.004   0.000   ARG A 521 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00372 (    4)
  link_NAG-ASN         : angle       3.21944 (   12)
  link_BETA1-4         : bond        0.00702 (    6)
  link_BETA1-4         : angle       2.60609 (   18)
  hydrogen bonds       : bond        0.02877 (  197)
  hydrogen bonds       : angle       5.07109 (  546)
  link_BETA1-6         : bond        0.00708 (    1)
  link_BETA1-6         : angle       1.40609 (    3)
  SS BOND              : bond        0.00553 (   15)
  SS BOND              : angle       1.62996 (   30)
  link_BETA1-3         : bond        0.00278 (    3)
  link_BETA1-3         : angle       2.05508 (    9)
  covalent geometry    : bond        0.00327 ( 7099)
  covalent geometry    : angle       0.66610 ( 9679)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   75 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue SER  137 is missing expected H atoms. Skipping.
Residue SER  139 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.982 
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: H    3 GLN cc_start: 0.7992 (mt0) cc_final: 0.7633 (mp10)
REVERT: A  469 TRP cc_start: 0.6347 (m-10) cc_final: 0.5871 (m100)
REVERT: A  555 MET cc_start: 0.8048 (mmm) cc_final: 0.7507 (mmm)
REVERT: E   23 GLU cc_start: 0.4812 (OUTLIER) cc_final: 0.4101 (pm20)
  outliers start: 18
  outliers final: 17
  residues processed: 104
  average time/residue: 0.3791
  time to fit residues: 53.6150
Evaluate side-chains
  109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  186 SER
Chi-restraints excluded: chain H residue  188 VAL
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  460 ARG
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain A residue  552 CYS
Chi-restraints excluded: chain A residue  586 PHE
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain E residue   23 GLU
Chi-restraints excluded: chain E residue   35 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 22 optimal weight:    0.1980
   chunk 34 optimal weight:    0.0670
   chunk 56 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0970
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.153471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.127038 restraints weight = 29638.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 2.93
r_work: 0.3566 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7128  Z= 0.115
  Angle     :  0.671   9.160   9751  Z= 0.315
  Chirality :  0.047   0.362   1109
  Planarity :  0.005   0.052   1225
  Dihedral  : 10.784  83.116   1268
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.08 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 20.90 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.28), residues: 879
  helix: -0.76 (0.86), residues: 44
  sheet:  0.80 (0.30), residues: 316
  loop : -1.82 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 420 
 HIS   0.005   0.001   HIS A 488 
 PHE   0.014   0.001   PHE L 209 
 TYR   0.007   0.001   TYR H  95 
 ARG   0.004   0.000   ARG A 521 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00379 (    4)
  link_NAG-ASN         : angle       3.31616 (   12)
  link_BETA1-4         : bond        0.00678 (    6)
  link_BETA1-4         : angle       2.51713 (   18)
  hydrogen bonds       : bond        0.02653 (  197)
  hydrogen bonds       : angle       4.88376 (  546)
  link_BETA1-6         : bond        0.00773 (    1)
  link_BETA1-6         : angle       1.45612 (    3)
  SS BOND              : bond        0.00456 (   15)
  SS BOND              : angle       1.39160 (   30)
  link_BETA1-3         : bond        0.00298 (    3)
  link_BETA1-3         : angle       1.96111 (    9)
  covalent geometry    : bond        0.00274 ( 7099)
  covalent geometry    : angle       0.64650 ( 9679)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6785.10 seconds
wall clock time: 120 minutes 4.74 seconds (7204.74 seconds total)