Starting phenix.real_space_refine
on Tue Mar  3 20:33:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uzb_26885/03_2026/7uzb_26885.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uzb_26885/03_2026/7uzb_26885.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uzb_26885/03_2026/7uzb_26885.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uzb_26885/03_2026/7uzb_26885.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uzb_26885/03_2026/7uzb_26885.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uzb_26885/03_2026/7uzb_26885.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    5342      2.51       5
     N    1393      2.21       5
     O    1625      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8392
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 643, 5026
          Classifications: {'peptide': 643}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 35, 'TRANS': 607}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 28
    Chain: "H"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1662
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 14, 'TRANS': 205}
    Chain: "L"
      Number of atoms: 1648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1648
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          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
  Time building chain proxies: 1.88, per 1000 atoms: 0.22
  Number of scatterers: 8392
  At special positions: 0
  Unit cell: (99.066, 112.101, 128.612, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1625      8.00
     N    1393      7.00
     C    5342      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 155 " - pdb=" SG  CYS H 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 154 " - pdb=" SG  CYS L 214 " distance=2.03

  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
    NAG-ASN
      " NAG A1301 " - " ASN A 331 "
      " NAG A1302 " - " ASN A 343 "
      " NAG A1303 " - " ASN A 616 "
      " NAG A1304 " - " ASN A  61 "
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 265.4 milliseconds
  

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2002

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 21 sheets defined
      9.6% alpha, 37.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 245 through 250
      removed outlier: 3.532A  pdb=" N   THR A 250 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.901A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 384 through 390
      removed outlier: 4.377A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 3.823A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 498 through 502
      removed outlier: 4.153A  pdb=" N   GLY A 502 " --> pdb=" O   PRO A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 630
      removed outlier: 3.948A  pdb=" N   ALA A 626 " --> pdb=" O   VAL A 622 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR A 630 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 68 through 74
      removed outlier: 4.328A  pdb=" N   ASP H  74 " --> pdb=" O   GLY H  69 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 146 through 148
      No H-bonds generated for 'chain 'H' and resid 146 through 148'
    Processing helix  chain 'H' and resid 202 through 207
      removed outlier: 3.858A  pdb=" N   THR H 206 " --> pdb=" O   SER H 202 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 95 through 99
      removed outlier: 3.718A  pdb=" N   PHE L  99 " --> pdb=" O   PRO L  96 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 141 through 148
    Processing helix  chain 'L' and resid 203 through 209
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55
      removed outlier: 3.777A  pdb=" N   GLY A  89 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55
      removed outlier: 7.432A  pdb=" N   THR A 274 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   ASP A 290 " --> pdb=" O   THR A 274 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   LEU A 276 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ALA A 288 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LYS A 278 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85
      removed outlier: 5.651A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   MET A 153 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.769A  pdb=" N   LEU A 241 " --> pdb=" O   GLY A 103 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315
      removed outlier: 4.443A  pdb=" N   VAL A 595 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   GLY A 594 " --> pdb=" O   GLN A 613 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   CYS A 649 " --> pdb=" O   TYR A 612 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328
      removed outlier: 3.646A  pdb=" N   ARG A 328 " --> pdb=" O   ASN A 542 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.843A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TRP A 436 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554
      removed outlier: 4.515A  pdb=" N   GLU A 583 " --> pdb=" O   ASP A 578 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.809A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  26 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 13
      removed outlier: 6.288A  pdb=" N   GLU H  11 " --> pdb=" O   THR H 125 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   MET H  39 " --> pdb=" O   ARG H  55 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   ARG H  55 " --> pdb=" O   MET H  39 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   TRP H  41 " --> pdb=" O   ILE H  53 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 13
      removed outlier: 6.288A  pdb=" N   GLU H  11 " --> pdb=" O   THR H 125 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   TYR H 117 " --> pdb=" O   ARG H 106 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 136 through 139
      removed outlier: 3.904A  pdb=" N   ASP H 159 " --> pdb=" O   TYR H 191 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   TYR H 191 " --> pdb=" O   ASP H 159 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 136 through 139
      removed outlier: 3.904A  pdb=" N   ASP H 159 " --> pdb=" O   TYR H 191 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   TYR H 191 " --> pdb=" O   ASP H 159 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 166 through 169
      removed outlier: 4.495A  pdb=" N   TYR H 209 " --> pdb=" O   VAL H 226 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.819A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 125 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   LYS L 127 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   ALA L  13 " --> pdb=" O   LYS L 127 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLY L 100 " --> pdb=" O   LEU L 124 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU L  39 " --> pdb=" O   ARG L  56 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   GLN L  43 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   LEU L  52 " --> pdb=" O   GLN L  43 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 134 through 138
      removed outlier: 3.761A  pdb=" N   VAL L 153 " --> pdb=" O   PHE L 138 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   TYR L 193 " --> pdb=" O   ASN L 158 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 174 through 175
      removed outlier: 4.630A  pdb=" N   TRP L 168 " --> pdb=" O   GLN L 175 " (cutoff:3.500A)

    292 hydrogen bonds defined for protein.
    753 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.55

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2676
        1.34 -     1.46: 2181
        1.46 -     1.58: 3717
        1.58 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 8610
  Sorted by residual:
  bond pdb=" C1  NAG A1302 "
       pdb=" O5  NAG A1302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 6.05e+00
  bond pdb=" C5  NAG A1302 "
       pdb=" O5  NAG A1302 "
    ideal  model  delta    sigma   weight residual
    1.413  1.441 -0.028 2.00e-02 2.50e+03 1.91e+00
  bond pdb=" N   ASP A 198 "
       pdb=" CA  ASP A 198 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.72e+00
  bond pdb=" C1  NAG A1304 "
       pdb=" O5  NAG A1304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.68e+00
  bond pdb=" C1  NAG A1303 "
       pdb=" O5  NAG A1303 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.63e+00
  ... (remaining 8605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 11293
        1.37 -     2.74: 359
        2.74 -     4.11: 62
        4.11 -     5.48: 14
        5.48 -     6.85: 4
  Bond angle restraints: 11732
  Sorted by residual:
  angle pdb=" N   SER A 637 "
        pdb=" CA  SER A 637 "
        pdb=" C   SER A 637 "
      ideal   model   delta    sigma   weight residual
     112.86  107.39    5.47 1.22e+00 6.72e-01 2.01e+01
  angle pdb=" C   PRO A 631 "
        pdb=" N   THR A 632 "
        pdb=" CA  THR A 632 "
      ideal   model   delta    sigma   weight residual
     121.54  128.39   -6.85 1.91e+00 2.74e-01 1.29e+01
  angle pdb=" C   THR A 638 "
        pdb=" CA  THR A 638 "
        pdb=" CB  THR A 638 "
      ideal   model   delta    sigma   weight residual
     110.42  116.18   -5.76 1.99e+00 2.53e-01 8.38e+00
  angle pdb=" N   GLU H 163 "
        pdb=" CA  GLU H 163 "
        pdb=" C   GLU H 163 "
      ideal   model   delta    sigma   weight residual
     109.81  115.12   -5.31 2.21e+00 2.05e-01 5.77e+00
  angle pdb=" C   LEU A 546 "
        pdb=" N   THR A 547 "
        pdb=" CA  THR A 547 "
      ideal   model   delta    sigma   weight residual
     122.40  125.87   -3.47 1.45e+00 4.76e-01 5.72e+00
  ... (remaining 11727 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.07: 4889
       23.07 -    46.13: 216
       46.13 -    69.20: 19
       69.20 -    92.26: 5
       92.26 -   115.33: 17
  Dihedral angle restraints: 5146
    sinusoidal: 2015
      harmonic: 3131
  Sorted by residual:
  dihedral pdb=" CA  TYR A 636 "
           pdb=" C   TYR A 636 "
           pdb=" N   SER A 637 "
           pdb=" CA  SER A 637 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.26  -25.74     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  TYR H  57 "
           pdb=" C   TYR H  57 "
           pdb=" N   PRO H  58 "
           pdb=" CA  PRO H  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.37  -22.63     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CB  CYS L 154 "
           pdb=" SG  CYS L 154 "
           pdb=" SG  CYS L 214 "
           pdb=" CB  CYS L 214 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.46  -35.46     1      1.00e+01 1.00e-02 1.78e+01
  ... (remaining 5143 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1078
       0.050 -    0.100: 169
       0.100 -    0.149: 65
       0.149 -    0.199: 0
       0.199 -    0.249: 1
  Chirality restraints: 1313
  Sorted by residual:
  chirality pdb=" C1  NAG A1302 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG A1302 "
            pdb=" O5  NAG A1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  PRO H  58 "
            pdb=" N   PRO H  58 "
            pdb=" C   PRO H  58 "
            pdb=" CB  PRO H  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CA  ASP A 198 "
            pdb=" N   ASP A 198 "
            pdb=" C   ASP A 198 "
            pdb=" CB  ASP A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.70e-01
  ... (remaining 1310 not shown)

  Planarity restraints: 1514
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 620 "    0.030 5.00e-02 4.00e+02   4.48e-02 3.20e+00
        pdb=" N   PRO A 621 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 621 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 621 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 328 "   -0.145 9.50e-02 1.11e+02   6.49e-02 2.60e+00
        pdb=" NE  ARG A 328 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 328 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 328 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 328 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR L 114 "   -0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO L 115 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO L 115 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO L 115 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1511 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 107
        2.61 -     3.18: 7505
        3.18 -     3.75: 13434
        3.75 -     4.33: 18618
        4.33 -     4.90: 29299
  Nonbonded interactions: 68963
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 393 "
            pdb=" OH  TYR H 110 "
     model   vdw
     2.037 3.040
  nonbonded pdb=" OG1 THR A 109 "
            pdb=" OD1 ASP A 111 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" NH2 ARG A 328 "
            pdb=" O   SER A 530 "
     model   vdw
     2.147 3.120
  nonbonded pdb=" OG1 THR A 645 "
            pdb=" O   GLY A 648 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" OD1 ASN A 122 "
            pdb=" OG1 THR A 124 "
     model   vdw
     2.187 3.040
  ... (remaining 68958 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.200
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
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      :  0.003   0.049   8627  Z= 0.152
  Angle     :  0.600   6.850  11770  Z= 0.332
  Chirality :  0.042   0.249   1313
  Planarity :  0.004   0.065   1510
  Dihedral  : 14.481 115.325   3105
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.25), residues: 1067
  helix: -0.62 (0.63), residues: 63
  sheet:  1.07 (0.27), residues: 365
  loop : -0.04 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  24 
 TYR   0.022   0.001   TYR H  57 
 PHE   0.018   0.002   PHE A 541 
 TRP   0.015   0.001   TRP A 104 
 HIS   0.003   0.001   HIS L 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8610)
  covalent geometry    : angle       0.59867 (11732)
  SS BOND              : bond        0.00171 (   13)
  SS BOND              : angle       0.76895 (   26)
  hydrogen bonds       : bond        0.27901 (  270)
  hydrogen bonds       : angle      10.57782 (  753)
  link_NAG-ASN         : bond        0.00197 (    4)
  link_NAG-ASN         : angle       1.02794 (   12)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: H   39 MET cc_start: 0.7894 (ttp) cc_final: 0.7315 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0792
  time to fit residues: 4.9022
Evaluate side-chains
  30 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0050
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    1.4002

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 215 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 = 0.3343 r_free = 0.3343 target = 0.046932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.036571 restraints weight = 61340.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.037938 restraints weight = 35245.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.038917 restraints weight = 24176.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.039603 restraints weight = 18424.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.040105 restraints weight = 15045.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.1080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8627  Z= 0.148
  Angle     :  0.588   9.529  11770  Z= 0.305
  Chirality :  0.045   0.288   1313
  Planarity :  0.005   0.090   1510
  Dihedral  : 10.723 102.952   1248
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.39 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.26), residues: 1067
  helix: -0.71 (0.60), residues: 73
  sheet:  1.09 (0.27), residues: 384
  loop : -0.08 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  24 
 TYR   0.017   0.001   TYR H  57 
 PHE   0.014   0.002   PHE A 238 
 TRP   0.010   0.002   TRP A 104 
 HIS   0.003   0.001   HIS L 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8610)
  covalent geometry    : angle       0.58641 (11732)
  SS BOND              : bond        0.00260 (   13)
  SS BOND              : angle       0.80881 (   26)
  hydrogen bonds       : bond        0.04836 (  270)
  hydrogen bonds       : angle       7.59841 (  753)
  link_NAG-ASN         : bond        0.00236 (    4)
  link_NAG-ASN         : angle       1.12774 (   12)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 PHE cc_start: 0.8619 (m-10) cc_final: 0.8397 (m-10)
REVERT: L   24 ARG cc_start: 0.8808 (mtm110) cc_final: 0.8545 (mtm110)
  outliers start: 1
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0739
  time to fit residues: 4.5443
Evaluate side-chains
  28 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0270
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 75 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.7644

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 215 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 = 0.3323 r_free = 0.3323 target = 0.046364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.036147 restraints weight = 61835.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.037524 restraints weight = 35429.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.038483 restraints weight = 24202.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.039149 restraints weight = 18438.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.039591 restraints weight = 15082.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8627  Z= 0.163
  Angle     :  0.574   8.478  11770  Z= 0.298
  Chirality :  0.043   0.203   1313
  Planarity :  0.004   0.065   1510
  Dihedral  :  7.515  82.081   1248
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.82 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.26), residues: 1067
  helix: -0.80 (0.61), residues: 73
  sheet:  0.95 (0.27), residues: 372
  loop : -0.14 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 328 
 TYR   0.015   0.001   TYR H  57 
 PHE   0.015   0.002   PHE A 238 
 TRP   0.007   0.002   TRP H  52 
 HIS   0.005   0.001   HIS L 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8610)
  covalent geometry    : angle       0.57064 (11732)
  SS BOND              : bond        0.00293 (   13)
  SS BOND              : angle       0.86035 (   26)
  hydrogen bonds       : bond        0.04194 (  270)
  hydrogen bonds       : angle       6.95749 (  753)
  link_NAG-ASN         : bond        0.00314 (    4)
  link_NAG-ASN         : angle       1.77805 (   12)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 PHE cc_start: 0.8702 (m-10) cc_final: 0.8486 (m-10)
REVERT: L    4 MET cc_start: 0.8603 (mmp) cc_final: 0.8368 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0758
  time to fit residues: 4.6689
Evaluate side-chains
  28 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0270
   chunk 42 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.4046

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.046910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.036573 restraints weight = 63202.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.037973 restraints weight = 35986.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.038966 restraints weight = 24507.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.039624 restraints weight = 18571.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.040130 restraints weight = 15245.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8627  Z= 0.137
  Angle     :  0.550   6.683  11770  Z= 0.285
  Chirality :  0.043   0.199   1313
  Planarity :  0.004   0.051   1510
  Dihedral  :  7.309  80.916   1248
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.26), residues: 1067
  helix: -0.75 (0.62), residues: 72
  sheet:  0.84 (0.27), residues: 372
  loop : -0.17 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  24 
 TYR   0.015   0.001   TYR L  55 
 PHE   0.017   0.002   PHE A 306 
 TRP   0.009   0.001   TRP H  52 
 HIS   0.005   0.001   HIS L 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8610)
  covalent geometry    : angle       0.54691 (11732)
  SS BOND              : bond        0.00221 (   13)
  SS BOND              : angle       0.71562 (   26)
  hydrogen bonds       : bond        0.03654 (  270)
  hydrogen bonds       : angle       6.64066 (  753)
  link_NAG-ASN         : bond        0.00125 (    4)
  link_NAG-ASN         : angle       1.73134 (   12)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0653
  time to fit residues: 4.1301
Evaluate side-chains
  32 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 60 optimal weight:    0.4980
   chunk 96 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 46 optimal weight:    0.8980
   chunk 79 optimal weight:    0.1980
   chunk 17 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 215 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 = 0.3353 r_free = 0.3353 target = 0.047326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.037019 restraints weight = 62658.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.038448 restraints weight = 35555.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.039444 restraints weight = 24106.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.040139 restraints weight = 18217.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.040647 restraints weight = 14840.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8627  Z= 0.121
  Angle     :  0.551   6.487  11770  Z= 0.283
  Chirality :  0.044   0.193   1313
  Planarity :  0.005   0.122   1510
  Dihedral  :  7.130  78.049   1248
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.26), residues: 1067
  helix: -0.73 (0.62), residues: 72
  sheet:  0.81 (0.27), residues: 377
  loop : -0.15 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  24 
 TYR   0.014   0.001   TYR L  55 
 PHE   0.026   0.002   PHE A 318 
 TRP   0.009   0.001   TRP H  52 
 HIS   0.003   0.001   HIS L 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8610)
  covalent geometry    : angle       0.54732 (11732)
  SS BOND              : bond        0.00222 (   13)
  SS BOND              : angle       1.04177 (   26)
  hydrogen bonds       : bond        0.03458 (  270)
  hydrogen bonds       : angle       6.41293 (  753)
  link_NAG-ASN         : bond        0.00177 (    4)
  link_NAG-ASN         : angle       1.76014 (   12)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 PHE cc_start: 0.8793 (m-10) cc_final: 0.8566 (m-10)
REVERT: A  458 LYS cc_start: 0.9339 (mtpt) cc_final: 0.8984 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0838
  time to fit residues: 5.3826
Evaluate side-chains
  32 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0040
   chunk 43 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A 146 HIS
** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.048035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.037577 restraints weight = 62346.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.039056 restraints weight = 34880.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.040058 restraints weight = 23482.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.040812 restraints weight = 17719.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.041319 restraints weight = 14313.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8627  Z= 0.099
  Angle     :  0.528   6.777  11770  Z= 0.271
  Chirality :  0.043   0.183   1313
  Planarity :  0.004   0.093   1510
  Dihedral  :  6.902  75.638   1248
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.26), residues: 1067
  helix: -0.72 (0.62), residues: 72
  sheet:  0.85 (0.27), residues: 377
  loop : -0.15 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 237 
 TYR   0.013   0.001   TYR L  55 
 PHE   0.014   0.001   PHE A 318 
 TRP   0.008   0.001   TRP A 633 
 HIS   0.002   0.001   HIS L 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 8610)
  covalent geometry    : angle       0.52394 (11732)
  SS BOND              : bond        0.00159 (   13)
  SS BOND              : angle       0.92153 (   26)
  hydrogen bonds       : bond        0.03212 (  270)
  hydrogen bonds       : angle       6.17232 (  753)
  link_NAG-ASN         : bond        0.00133 (    4)
  link_NAG-ASN         : angle       1.80340 (   12)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 PHE cc_start: 0.8401 (t80) cc_final: 0.8178 (t80)
REVERT: A  458 LYS cc_start: 0.9333 (mtpt) cc_final: 0.8984 (mmtt)
REVERT: H   53 ILE cc_start: 0.8107 (mm) cc_final: 0.7888 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0812
  time to fit residues: 5.6153
Evaluate side-chains
  34 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 80 optimal weight:   10.0000
   chunk 47 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0010
   chunk 63 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   overall best weight:    2.1992

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

Flipped N/Q/H residues before XYZ refinement:
** H 215 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 = 0.3310 r_free = 0.3310 target = 0.046274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.036115 restraints weight = 65138.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.037472 restraints weight = 37115.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.038440 restraints weight = 25331.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.039082 restraints weight = 19206.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.039585 restraints weight = 15773.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8627  Z= 0.189
  Angle     :  0.590   6.998  11770  Z= 0.303
  Chirality :  0.043   0.199   1313
  Planarity :  0.004   0.085   1510
  Dihedral  :  7.107  74.184   1248
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.25), residues: 1067
  helix: -0.71 (0.61), residues: 75
  sheet:  0.72 (0.27), residues: 372
  loop : -0.24 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  24 
 TYR   0.013   0.001   TYR A 365 
 PHE   0.016   0.002   PHE A 318 
 TRP   0.008   0.002   TRP A 436 
 HIS   0.004   0.001   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8610)
  covalent geometry    : angle       0.58520 (11732)
  SS BOND              : bond        0.00299 (   13)
  SS BOND              : angle       1.11236 (   26)
  hydrogen bonds       : bond        0.03647 (  270)
  hydrogen bonds       : angle       6.29343 (  753)
  link_NAG-ASN         : bond        0.00134 (    4)
  link_NAG-ASN         : angle       1.83772 (   12)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.323 
Fit side-chains
REVERT: H   51 GLU cc_start: 0.9026 (tp30) cc_final: 0.8718 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0759
  time to fit residues: 4.5889
Evaluate side-chains
  30 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 15 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 2 optimal weight:    9.9990
   chunk 86 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  86 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.047546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.037346 restraints weight = 62922.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.038751 restraints weight = 35862.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.039707 restraints weight = 24411.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.040432 restraints weight = 18627.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.040903 restraints weight = 15143.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8627  Z= 0.104
  Angle     :  0.534   6.939  11770  Z= 0.273
  Chirality :  0.043   0.176   1313
  Planarity :  0.004   0.092   1510
  Dihedral  :  6.764  70.192   1248
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.26), residues: 1067
  helix: -0.56 (0.65), residues: 70
  sheet:  0.77 (0.27), residues: 376
  loop : -0.14 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 237 
 TYR   0.013   0.001   TYR L  55 
 PHE   0.016   0.001   PHE A 318 
 TRP   0.011   0.001   TRP H  52 
 HIS   0.002   0.001   HIS L 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8610)
  covalent geometry    : angle       0.52969 (11732)
  SS BOND              : bond        0.00183 (   13)
  SS BOND              : angle       0.80890 (   26)
  hydrogen bonds       : bond        0.03240 (  270)
  hydrogen bonds       : angle       6.13224 (  753)
  link_NAG-ASN         : bond        0.00114 (    4)
  link_NAG-ASN         : angle       1.88618 (   12)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.9373 (mtpt) cc_final: 0.9004 (mmtt)
REVERT: H   51 GLU cc_start: 0.9052 (tp30) cc_final: 0.8730 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0913
  time to fit residues: 5.6711
Evaluate side-chains
  31 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   chunk 56 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 44 optimal weight:    0.8980
   chunk 98 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0000
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  86 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.048130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.037882 restraints weight = 63771.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.039321 restraints weight = 36347.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.040341 restraints weight = 24672.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.041008 restraints weight = 18682.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.041539 restraints weight = 15336.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8627  Z= 0.101
  Angle     :  0.537   7.593  11770  Z= 0.274
  Chirality :  0.043   0.162   1313
  Planarity :  0.003   0.039   1510
  Dihedral  :  6.535  65.638   1248
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.26), residues: 1067
  helix: -0.48 (0.66), residues: 70
  sheet:  0.83 (0.27), residues: 372
  loop : -0.18 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG L  24 
 TYR   0.021   0.001   TYR H 160 
 PHE   0.016   0.001   PHE A 318 
 TRP   0.011   0.001   TRP H  41 
 HIS   0.002   0.001   HIS L 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8610)
  covalent geometry    : angle       0.53236 (11732)
  SS BOND              : bond        0.00135 (   13)
  SS BOND              : angle       0.82847 (   26)
  hydrogen bonds       : bond        0.03084 (  270)
  hydrogen bonds       : angle       6.01143 (  753)
  link_NAG-ASN         : bond        0.00116 (    4)
  link_NAG-ASN         : angle       2.00712 (   12)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.9369 (mtpt) cc_final: 0.9013 (mmtt)
REVERT: H   51 GLU cc_start: 0.9020 (tp30) cc_final: 0.8707 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0783
  time to fit residues: 5.4847
Evaluate side-chains
  35 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 12 optimal weight:    9.9990
   chunk 59 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** H 215 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 = 0.3351 r_free = 0.3351 target = 0.047598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.037358 restraints weight = 63740.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.038767 restraints weight = 36332.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.039779 restraints weight = 24865.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.040484 restraints weight = 18833.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.040987 restraints weight = 15357.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8627  Z= 0.122
  Angle     :  0.542   6.853  11770  Z= 0.277
  Chirality :  0.043   0.161   1313
  Planarity :  0.004   0.049   1510
  Dihedral  :  6.476  62.031   1248
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.26), residues: 1067
  helix: -0.50 (0.65), residues: 70
  sheet:  0.78 (0.27), residues: 373
  loop : -0.17 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG L  24 
 TYR   0.011   0.001   TYR L  55 
 PHE   0.016   0.001   PHE A 318 
 TRP   0.017   0.001   TRP A 633 
 HIS   0.006   0.001   HIS L 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8610)
  covalent geometry    : angle       0.53783 (11732)
  SS BOND              : bond        0.00167 (   13)
  SS BOND              : angle       0.86635 (   26)
  hydrogen bonds       : bond        0.03179 (  270)
  hydrogen bonds       : angle       5.98504 (  753)
  link_NAG-ASN         : bond        0.00109 (    4)
  link_NAG-ASN         : angle       2.05850 (   12)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.9384 (mtpt) cc_final: 0.9023 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0890
  time to fit residues: 5.2725
Evaluate side-chains
  31 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 56 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 75 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 28 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 44 optimal weight:    0.0870
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  86 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.048619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.038354 restraints weight = 63266.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.039808 restraints weight = 35853.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.040838 restraints weight = 24393.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.041518 restraints weight = 18448.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.042066 restraints weight = 15122.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8627  Z= 0.094
  Angle     :  0.531   7.497  11770  Z= 0.269
  Chirality :  0.043   0.149   1313
  Planarity :  0.003   0.039   1510
  Dihedral  :  6.124  59.228   1248
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.26), residues: 1067
  helix: -0.46 (0.65), residues: 70
  sheet:  0.87 (0.27), residues: 372
  loop : -0.20 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 328 
 TYR   0.021   0.001   TYR H 160 
 PHE   0.015   0.001   PHE A 318 
 TRP   0.012   0.001   TRP H  52 
 HIS   0.004   0.001   HIS L 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 8610)
  covalent geometry    : angle       0.52624 (11732)
  SS BOND              : bond        0.00160 (   13)
  SS BOND              : angle       0.79655 (   26)
  hydrogen bonds       : bond        0.03008 (  270)
  hydrogen bonds       : angle       5.86461 (  753)
  link_NAG-ASN         : bond        0.00110 (    4)
  link_NAG-ASN         : angle       2.15483 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1468.65 seconds
wall clock time: 26 minutes 12.27 seconds (1572.27 seconds total)