Starting phenix.real_space_refine
on Fri Aug 22 22:21:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k0e_36762/08_2025/8k0e_36762.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k0e_36762/08_2025/8k0e_36762.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k0e_36762/08_2025/8k0e_36762.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k0e_36762/08_2025/8k0e_36762.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k0e_36762/08_2025/8k0e_36762.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k0e_36762/08_2025/8k0e_36762.map"
  }
  resolution = 3.65
  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=   0.005 sd=   0.077
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
     Fe      1      7.16       5
     S      47      5.16       5
     C    5273      2.51       5
     N    1403      2.21       5
     O    1576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8300
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 646, 5193
          Classifications: {'peptide': 646}
          Link IDs: {'PTRANS': 33, 'TRANS': 612}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2994
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 18, 'TRANS': 343}
    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: 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: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' FE': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.55, per 1000 atoms: 0.19
  Number of scatterers: 8300
  At special positions: 0
  Unit cell: (81.4, 105.6, 125.4, 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)
     Fe      1     26.01
     S      47     16.00
     O    1576      8.00
     N    1403      7.00
     C    5273      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 242 " - pdb=" SG  CYS A 282 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 540 "
      " NAG D   1 " - " ASN A 316 "
      " NAG E   1 " - " ASN B 363 "
      " NAG F   1 " - " ASN B  87 "
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 259.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1922

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 3 sheets defined
      65.2% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 49
      removed outlier: 3.746A  pdb=" N   LEU A  38 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 83
      removed outlier: 3.814A  pdb=" N   ALA A  80 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 125
      removed outlier: 3.692A  pdb=" N   GLY A 125 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 142
      removed outlier: 3.923A  pdb=" N   GLU A 137 " --> pdb=" O   SER A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 156
    Processing helix  chain 'A' and resid 158 through 173
    Processing helix  chain 'A' and resid 176 through 189
      removed outlier: 3.521A  pdb=" N   GLN A 180 " --> pdb=" O   HIS A 176 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET A 189 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 197
    Processing helix  chain 'A' and resid 203 through 217
      removed outlier: 3.549A  pdb=" N   GLN A 207 " --> pdb=" O   GLN A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.038A  pdb=" N   HIS A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TYR A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 281
      removed outlier: 3.644A  pdb=" N   THR A 269 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 285
    Processing helix  chain 'A' and resid 298 through 315
    Processing helix  chain 'A' and resid 316 through 329
    Processing helix  chain 'A' and resid 334 through 348
    Processing helix  chain 'A' and resid 349 through 356
      removed outlier: 3.541A  pdb=" N   ILE A 356 " --> pdb=" O   HIS A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 384
    Processing helix  chain 'A' and resid 400 through 428
    Processing helix  chain 'A' and resid 441 through 447
    Processing helix  chain 'A' and resid 479 through 493
      removed outlier: 3.578A  pdb=" N   CYS A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA A 493 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 528
    Processing helix  chain 'A' and resid 531 through 553
      removed outlier: 3.862A  pdb=" N   ALA A 535 " --> pdb=" O   PRO A 531 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   PHE A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 576
      removed outlier: 3.863A  pdb=" N   GLN A 576 " --> pdb=" O   GLU A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 598
    Processing helix  chain 'A' and resid 686 through 699
    Processing helix  chain 'B' and resid 37 through 41
      removed outlier: 3.864A  pdb=" N   GLU B  40 " --> pdb=" O   PRO B  37 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU B  41 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 37 through 41'
    Processing helix  chain 'B' and resid 43 through 57
    Processing helix  chain 'B' and resid 60 through 90
      removed outlier: 3.776A  pdb=" N   CYS B  88 " --> pdb=" O   CYS B  84 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER B  89 " --> pdb=" O   HIS B  85 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ALA B  90 " --> pdb=" O   ARG B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 102
    Processing helix  chain 'B' and resid 103 through 123
    Processing helix  chain 'B' and resid 124 through 125
      No H-bonds generated for 'chain 'B' and resid 124 through 125'
    Processing helix  chain 'B' and resid 126 through 131
      removed outlier: 4.205A  pdb=" N   GLN B 131 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 144
    Processing helix  chain 'B' and resid 146 through 157
      removed outlier: 4.200A  pdb=" N   PHE B 150 " --> pdb=" O   GLU B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 175
      removed outlier: 3.820A  pdb=" N   LYS B 174 " --> pdb=" O   THR B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 191
    Processing helix  chain 'B' and resid 204 through 219
      removed outlier: 3.729A  pdb=" N   SER B 208 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 246
      Proline residue:  B 234  - end of helix
    Processing helix  chain 'B' and resid 258 through 276
      removed outlier: 4.427A  pdb=" N   HIS B 266 " --> pdb=" O   SER B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 308
    Processing helix  chain 'B' and resid 310 through 325
      Proline residue:  B 316  - end of helix
    Processing helix  chain 'B' and resid 328 through 341
      removed outlier: 3.722A  pdb=" N   HIS B 341 " --> pdb=" O   TYR B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 352
      removed outlier: 3.827A  pdb=" N   PHE B 352 " --> pdb=" O   ASP B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 376
    Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 461
      removed outlier: 6.194A  pdb=" N   LEU A 459 " --> pdb=" O   ASP A 475 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASP A 475 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ARG A 647 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 673 " --> pdb=" O   HIS A 565 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   HIS A 565 " --> pdb=" O   ALA A 673 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   TYR A 563 " --> pdb=" O   TRP A 675 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   THR A 677 " --> pdb=" O   PHE A 561 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   PHE A 561 " --> pdb=" O   THR A 677 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   VAL A 516 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 584 through 587
      removed outlier: 6.223A  pdb=" N   VAL A 661 " --> pdb=" O   PRO A 585 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   HIS A 587 " --> pdb=" O   HIS A 659 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   PHE A 627 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLU A 640 " --> pdb=" O   PHE A 627 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   PHE A 629 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 284 through 285
      removed outlier: 4.194A  pdb=" N   ILE B 285 " --> pdb=" O   TYR B 288 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1407 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: 0.93

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1735
        1.33 -     1.45: 2087
        1.45 -     1.58: 4613
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 8505
  Sorted by residual:
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.479 -0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.62e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.27e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.26e+00
  ... (remaining 8500 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 11437
        3.30 -     6.60: 64
        6.60 -     9.90: 9
        9.90 -    13.20: 3
       13.20 -    16.50: 2
  Bond angle restraints: 11515
  Sorted by residual:
  angle pdb=" CA  LEU A 183 "
        pdb=" CB  LEU A 183 "
        pdb=" CG  LEU A 183 "
      ideal   model   delta    sigma   weight residual
     116.30  132.80  -16.50 3.50e+00 8.16e-02 2.22e+01
  angle pdb=" CB  MET A 177 "
        pdb=" CG  MET A 177 "
        pdb=" SD  MET A 177 "
      ideal   model   delta    sigma   weight residual
     112.70  126.80  -14.10 3.00e+00 1.11e-01 2.21e+01
  angle pdb=" CA  LEU A 445 "
        pdb=" CB  LEU A 445 "
        pdb=" CG  LEU A 445 "
      ideal   model   delta    sigma   weight residual
     116.30  129.47  -13.17 3.50e+00 8.16e-02 1.41e+01
  angle pdb=" CA  LEU A 215 "
        pdb=" CB  LEU A 215 "
        pdb=" CG  LEU A 215 "
      ideal   model   delta    sigma   weight residual
     116.30  128.23  -11.93 3.50e+00 8.16e-02 1.16e+01
  angle pdb=" N   GLY B 125 "
        pdb=" CA  GLY B 125 "
        pdb=" C   GLY B 125 "
      ideal   model   delta    sigma   weight residual
     110.21  113.23   -3.02 9.10e-01 1.21e+00 1.10e+01
  ... (remaining 11510 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.71: 4638
       24.71 -    49.42: 474
       49.42 -    74.12: 69
       74.12 -    98.83: 26
       98.83 -   123.54: 18
  Dihedral angle restraints: 5225
    sinusoidal: 2237
      harmonic: 2988
  Sorted by residual:
  dihedral pdb=" CB  CYS A  75 "
           pdb=" SG  CYS A  75 "
           pdb=" SG  CYS A 123 "
           pdb=" CB  CYS A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.25  -88.75     1      1.00e+01 1.00e-02 9.39e+01
  dihedral pdb=" CB  CYS A 242 "
           pdb=" SG  CYS A 242 "
           pdb=" SG  CYS A 282 "
           pdb=" CB  CYS A 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.78  -43.78     1      1.00e+01 1.00e-02 2.67e+01
  dihedral pdb=" C2  NAG C   1 "
           pdb=" C1  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C5  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   60.58 -123.54     1      3.00e+01 1.11e-03 1.66e+01
  ... (remaining 5222 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 904
       0.041 -    0.081: 243
       0.081 -    0.122: 70
       0.122 -    0.162: 6
       0.162 -    0.203: 3
  Chirality restraints: 1226
  Sorted by residual:
  chirality pdb=" CG  LEU A 138 "
            pdb=" CB  LEU A 138 "
            pdb=" CD1 LEU A 138 "
            pdb=" CD2 LEU A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  MET B 331 "
            pdb=" N   MET B 331 "
            pdb=" C   MET B 331 "
            pdb=" CB  MET B 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.45e-01
  chirality pdb=" CB  THR A  34 "
            pdb=" CA  THR A  34 "
            pdb=" OG1 THR A  34 "
            pdb=" CG2 THR A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 6.95e-01
  ... (remaining 1223 not shown)

  Planarity restraints: 1512
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  94 "   -0.061 5.00e-02 4.00e+02   8.98e-02 1.29e+01
        pdb=" N   PRO A  95 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 604 "   -0.042 5.00e-02 4.00e+02   6.33e-02 6.41e+00
        pdb=" N   PRO A 605 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 605 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 605 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 657 "   -0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO A 658 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 658 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 658 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1509 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 125
        2.66 -     3.22: 7857
        3.22 -     3.78: 12732
        3.78 -     4.34: 15006
        4.34 -     4.90: 24964
  Nonbonded interactions: 60684
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 312 "
            pdb=" OH  TYR A 343 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" O   TYR A 185 "
            pdb=" OG1 THR A 188 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OG  SER A 133 "
            pdb=" OE1 GLU A 135 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O4  NAG D   2 "
            pdb=" O7  NAG D   2 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OD2 ASP A 199 "
            pdb=" OG1 THR A 202 "
     model   vdw
     2.256 3.040
  ... (remaining 60679 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 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.410
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.080
  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:0.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
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   0.074   8515  Z= 0.172
  Angle     :  0.745  16.502  11543  Z= 0.362
  Chirality :  0.041   0.203   1226
  Planarity :  0.005   0.090   1508
  Dihedral  : 21.029 123.539   3297
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 28.88 %
    Favored  : 71.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.22 (0.27), residues: 1000
  helix:  2.07 (0.21), residues: 605
  sheet: -0.25 (0.86), residues: 38
  loop : -1.35 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 471 
 TYR   0.019   0.001   TYR B 338 
 PHE   0.018   0.001   PHE A 110 
 TRP   0.010   0.001   TRP B 345 
 HIS   0.003   0.001   HIS B 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8505)
  covalent geometry    : angle       0.73798 (11515)
  SS BOND              : bond        0.00253 (    2)
  SS BOND              : angle       0.38200 (    4)
  hydrogen bonds       : bond        0.14031 (  482)
  hydrogen bonds       : angle       5.13183 ( 1407)
  link_BETA1-4         : bond        0.00571 (    4)
  link_BETA1-4         : angle       2.36309 (   12)
  link_NAG-ASN         : bond        0.00301 (    4)
  link_NAG-ASN         : angle       2.29855 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  471 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7828 (mtt90)
REVERT: A  696 MET cc_start: 0.8437 (ttm) cc_final: 0.8191 (ttm)
REVERT: B  308 LEU cc_start: 0.8808 (tp) cc_final: 0.8494 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 108
  average time/residue: 0.0564
  time to fit residues: 9.2875
Evaluate side-chains
  102 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0170
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    8.9990
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN
B 276 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.145384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.101772 restraints weight = 15775.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.106039 restraints weight = 9265.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.108719 restraints weight = 6790.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.110372 restraints weight = 5646.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.111410 restraints weight = 5050.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.0812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8515  Z= 0.131
  Angle     :  0.642  10.452  11543  Z= 0.311
  Chirality :  0.041   0.214   1226
  Planarity :  0.005   0.061   1508
  Dihedral  : 14.853 109.510   1301
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 25.89 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.53 (0.27), residues: 1000
  helix:  2.26 (0.21), residues: 614
  sheet:  0.16 (0.82), residues: 38
  loop : -1.26 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 354 
 TYR   0.019   0.001   TYR B 338 
 PHE   0.014   0.001   PHE A 622 
 TRP   0.009   0.001   TRP B 345 
 HIS   0.006   0.001   HIS A 481 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8505)
  covalent geometry    : angle       0.63084 (11515)
  SS BOND              : bond        0.00228 (    2)
  SS BOND              : angle       0.82576 (    4)
  hydrogen bonds       : bond        0.05109 (  482)
  hydrogen bonds       : angle       4.02105 ( 1407)
  link_BETA1-4         : bond        0.00326 (    4)
  link_BETA1-4         : angle       2.91344 (   12)
  link_NAG-ASN         : bond        0.00407 (    4)
  link_NAG-ASN         : angle       2.36273 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 TYR cc_start: 0.9300 (t80) cc_final: 0.8938 (t80)
REVERT: A  234 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8116 (mp0)
REVERT: A  444 ARG cc_start: 0.8978 (ttm170) cc_final: 0.8410 (mtt-85)
REVERT: B  338 TYR cc_start: 0.8662 (m-10) cc_final: 0.8440 (m-10)
  outliers start: 18
  outliers final: 8
  residues processed: 121
  average time/residue: 0.0578
  time to fit residues: 10.6890
Evaluate side-chains
  110 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  674 LEU
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 14 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 83 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 481 HIS
** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.144243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.100565 restraints weight = 15735.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.104698 restraints weight = 9282.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.107375 restraints weight = 6831.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.109043 restraints weight = 5683.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.110091 restraints weight = 5089.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8515  Z= 0.139
  Angle     :  0.618   9.438  11543  Z= 0.298
  Chirality :  0.040   0.241   1226
  Planarity :  0.004   0.059   1508
  Dihedral  : 13.294 108.332   1301
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 24.97 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.67 (0.27), residues: 1000
  helix:  2.31 (0.21), residues: 620
  sheet:  0.52 (0.74), residues: 48
  loop : -1.24 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 471 
 TYR   0.015   0.001   TYR A 312 
 PHE   0.012   0.001   PHE A 331 
 TRP   0.016   0.001   TRP B 345 
 HIS   0.004   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8505)
  covalent geometry    : angle       0.60671 (11515)
  SS BOND              : bond        0.00107 (    2)
  SS BOND              : angle       1.06388 (    4)
  hydrogen bonds       : bond        0.04919 (  482)
  hydrogen bonds       : angle       3.91283 ( 1407)
  link_BETA1-4         : bond        0.00556 (    4)
  link_BETA1-4         : angle       2.81570 (   12)
  link_NAG-ASN         : bond        0.00346 (    4)
  link_NAG-ASN         : angle       2.53702 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7935 (pt0)
REVERT: A  185 TYR cc_start: 0.9326 (t80) cc_final: 0.8948 (t80)
REVERT: A  234 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8103 (mp0)
REVERT: A  444 ARG cc_start: 0.8992 (ttm170) cc_final: 0.8612 (mtt-85)
REVERT: B  345 TRP cc_start: 0.8598 (m-90) cc_final: 0.8359 (m-90)
  outliers start: 31
  outliers final: 16
  residues processed: 124
  average time/residue: 0.0517
  time to fit residues: 10.0047
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  674 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  347 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 31 optimal weight:    7.9990
   chunk 86 optimal weight:    0.7980
   chunk 87 optimal weight:    0.3980
   chunk 81 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.146571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.103413 restraints weight = 17042.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.107740 restraints weight = 9989.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.110587 restraints weight = 7299.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.112383 restraints weight = 6022.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.113509 restraints weight = 5354.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8515  Z= 0.114
  Angle     :  0.607   9.598  11543  Z= 0.286
  Chirality :  0.040   0.263   1226
  Planarity :  0.004   0.056   1508
  Dihedral  : 12.466 107.584   1301
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 25.89 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.77 (0.27), residues: 1000
  helix:  2.33 (0.21), residues: 624
  sheet:  0.75 (0.75), residues: 48
  loop : -1.12 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 471 
 TYR   0.016   0.001   TYR A 312 
 PHE   0.010   0.001   PHE A 331 
 TRP   0.011   0.001   TRP B 345 
 HIS   0.004   0.000   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8505)
  covalent geometry    : angle       0.59434 (11515)
  SS BOND              : bond        0.00160 (    2)
  SS BOND              : angle       0.77467 (    4)
  hydrogen bonds       : bond        0.04363 (  482)
  hydrogen bonds       : angle       3.72629 ( 1407)
  link_BETA1-4         : bond        0.00574 (    4)
  link_BETA1-4         : angle       3.00782 (   12)
  link_NAG-ASN         : bond        0.00297 (    4)
  link_NAG-ASN         : angle       2.41125 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 TYR cc_start: 0.9358 (t80) cc_final: 0.8977 (t80)
REVERT: A  234 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8031 (mp0)
REVERT: A  444 ARG cc_start: 0.9054 (ttm170) cc_final: 0.8457 (mtt-85)
REVERT: B  345 TRP cc_start: 0.8590 (m-90) cc_final: 0.8388 (m-90)
  outliers start: 25
  outliers final: 14
  residues processed: 125
  average time/residue: 0.0500
  time to fit residues: 9.6585
Evaluate side-chains
  121 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  623 ASP
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 70 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN
** A 619 ASN ** 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 = 0.3935 r_free = 0.3935 target = 0.146338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.103367 restraints weight = 16754.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.107524 restraints weight = 9993.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.110262 restraints weight = 7366.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.111975 restraints weight = 6113.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.112903 restraints weight = 5450.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8515  Z= 0.116
  Angle     :  0.609  12.320  11543  Z= 0.286
  Chirality :  0.040   0.279   1226
  Planarity :  0.004   0.056   1508
  Dihedral  : 11.767 107.173   1301
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 27.16 %
    Favored  : 70.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.84 (0.27), residues: 1000
  helix:  2.35 (0.21), residues: 626
  sheet:  0.93 (0.76), residues: 48
  loop : -1.05 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 471 
 TYR   0.013   0.001   TYR B 188 
 PHE   0.010   0.001   PHE A 676 
 TRP   0.007   0.001   TRP B 345 
 HIS   0.003   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8505)
  covalent geometry    : angle       0.59668 (11515)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       0.78593 (    4)
  hydrogen bonds       : bond        0.04179 (  482)
  hydrogen bonds       : angle       3.64407 ( 1407)
  link_BETA1-4         : bond        0.00620 (    4)
  link_BETA1-4         : angle       3.11869 (   12)
  link_NAG-ASN         : bond        0.00268 (    4)
  link_NAG-ASN         : angle       2.33759 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7879 (pt0)
REVERT: A  180 GLN cc_start: 0.9129 (tp40) cc_final: 0.8681 (tp-100)
REVERT: A  185 TYR cc_start: 0.9363 (t80) cc_final: 0.9018 (t80)
REVERT: A  234 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7948 (mp0)
REVERT: A  444 ARG cc_start: 0.8999 (ttm170) cc_final: 0.8597 (mtt-85)
REVERT: B  181 MET cc_start: 0.9450 (mmm) cc_final: 0.9029 (mmp)
REVERT: B  345 TRP cc_start: 0.8581 (m-90) cc_final: 0.8379 (m-90)
  outliers start: 24
  outliers final: 17
  residues processed: 118
  average time/residue: 0.0581
  time to fit residues: 10.1617
Evaluate side-chains
  117 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  347 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 32 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0040
   chunk 72 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A 481 HIS
** A 619 ASN ** 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 = 0.3955 r_free = 0.3955 target = 0.147493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.105562 restraints weight = 15835.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.109656 restraints weight = 10427.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.110645 restraints weight = 7293.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.110709 restraints weight = 7140.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.111003 restraints weight = 6799.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8515  Z= 0.112
  Angle     :  0.614  11.151  11543  Z= 0.285
  Chirality :  0.040   0.287   1226
  Planarity :  0.004   0.055   1508
  Dihedral  : 11.286 107.266   1301
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 27.27 %
    Favored  : 69.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.93 (0.27), residues: 1000
  helix:  2.39 (0.21), residues: 625
  sheet:  1.07 (0.77), residues: 48
  loop : -0.97 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 471 
 TYR   0.018   0.001   TYR B 337 
 PHE   0.009   0.001   PHE A 676 
 TRP   0.006   0.001   TRP B 345 
 HIS   0.003   0.000   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8505)
  covalent geometry    : angle       0.60140 (11515)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       0.67331 (    4)
  hydrogen bonds       : bond        0.03984 (  482)
  hydrogen bonds       : angle       3.59288 ( 1407)
  link_BETA1-4         : bond        0.00599 (    4)
  link_BETA1-4         : angle       3.17348 (   12)
  link_NAG-ASN         : bond        0.00261 (    4)
  link_NAG-ASN         : angle       2.23826 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8284 (mm)
REVERT: A   86 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8040 (pt0)
REVERT: A  185 TYR cc_start: 0.9387 (t80) cc_final: 0.9098 (t80)
REVERT: A  234 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7905 (mp0)
REVERT: A  444 ARG cc_start: 0.9010 (ttm170) cc_final: 0.8566 (mtt-85)
REVERT: B  113 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7578 (tt)
REVERT: B  181 MET cc_start: 0.9411 (mmm) cc_final: 0.9014 (mmp)
REVERT: B  345 TRP cc_start: 0.8753 (m-90) cc_final: 0.8474 (m-90)
  outliers start: 27
  outliers final: 13
  residues processed: 119
  average time/residue: 0.0526
  time to fit residues: 9.4891
Evaluate side-chains
  116 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  481 HIS
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    0.0070
   chunk 15 optimal weight:    0.1980
   chunk 36 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 83 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 79 optimal weight:    0.2980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.3798

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

Flipped N/Q/H residues before XYZ refinement:
A 481 HIS
** A 619 ASN ** 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 = 0.3963 r_free = 0.3963 target = 0.148248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.105737 restraints weight = 15957.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.109426 restraints weight = 10239.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.111943 restraints weight = 7847.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.113529 restraints weight = 6644.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.114365 restraints weight = 5998.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8515  Z= 0.108
  Angle     :  0.626  12.779  11543  Z= 0.286
  Chirality :  0.040   0.289   1226
  Planarity :  0.004   0.054   1508
  Dihedral  : 10.945 107.080   1301
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 27.85 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.99 (0.27), residues: 1000
  helix:  2.42 (0.21), residues: 626
  sheet:  1.19 (0.77), residues: 48
  loop : -0.93 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 471 
 TYR   0.016   0.001   TYR B 337 
 PHE   0.011   0.001   PHE B 256 
 TRP   0.006   0.000   TRP B 345 
 HIS   0.012   0.001   HIS A 481 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 8505)
  covalent geometry    : angle       0.61353 (11515)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       0.63535 (    4)
  hydrogen bonds       : bond        0.03763 (  482)
  hydrogen bonds       : angle       3.52350 ( 1407)
  link_BETA1-4         : bond        0.00615 (    4)
  link_BETA1-4         : angle       3.23248 (   12)
  link_NAG-ASN         : bond        0.00317 (    4)
  link_NAG-ASN         : angle       2.15974 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7938 (pt0)
REVERT: A  185 TYR cc_start: 0.9381 (t80) cc_final: 0.9097 (t80)
REVERT: A  234 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7871 (mp0)
REVERT: A  444 ARG cc_start: 0.9000 (ttm170) cc_final: 0.8580 (mtt-85)
REVERT: A  485 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8101 (mt-10)
REVERT: B  181 MET cc_start: 0.9442 (mmm) cc_final: 0.9022 (mmp)
  outliers start: 24
  outliers final: 12
  residues processed: 118
  average time/residue: 0.0572
  time to fit residues: 10.2894
Evaluate side-chains
  111 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 45 optimal weight:    0.2980
   chunk 12 optimal weight:    4.9990
   chunk 16 optimal weight:    0.4980
   chunk 11 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 481 HIS
A 536 HIS
** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.147271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.103928 restraints weight = 15725.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.108120 restraints weight = 9349.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.110879 restraints weight = 6903.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.112560 restraints weight = 5723.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.113733 restraints weight = 5103.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8515  Z= 0.109
  Angle     :  0.611   9.993  11543  Z= 0.283
  Chirality :  0.040   0.301   1226
  Planarity :  0.004   0.055   1508
  Dihedral  : 10.521 107.253   1301
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 27.73 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.02 (0.27), residues: 1000
  helix:  2.47 (0.21), residues: 624
  sheet:  1.27 (0.77), residues: 48
  loop : -0.98 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 471 
 TYR   0.015   0.001   TYR B 337 
 PHE   0.009   0.001   PHE A 676 
 TRP   0.021   0.001   TRP B 345 
 HIS   0.005   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8505)
  covalent geometry    : angle       0.59885 (11515)
  SS BOND              : bond        0.00159 (    2)
  SS BOND              : angle       0.52993 (    4)
  hydrogen bonds       : bond        0.03698 (  482)
  hydrogen bonds       : angle       3.49985 ( 1407)
  link_BETA1-4         : bond        0.00587 (    4)
  link_BETA1-4         : angle       3.29128 (   12)
  link_NAG-ASN         : bond        0.00267 (    4)
  link_NAG-ASN         : angle       2.12613 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7962 (pt0)
REVERT: A  185 TYR cc_start: 0.9407 (t80) cc_final: 0.9092 (t80)
REVERT: A  234 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7867 (mp0)
REVERT: A  343 TYR cc_start: 0.8730 (t80) cc_final: 0.8452 (t80)
REVERT: A  444 ARG cc_start: 0.9000 (ttm170) cc_final: 0.8556 (mtt-85)
REVERT: A  485 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8154 (mt-10)
REVERT: B  113 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7597 (tt)
REVERT: B  181 MET cc_start: 0.9438 (mmm) cc_final: 0.9067 (mmp)
  outliers start: 22
  outliers final: 15
  residues processed: 111
  average time/residue: 0.0568
  time to fit residues: 9.7544
Evaluate side-chains
  112 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 83 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0040
   chunk 1 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   chunk 22 optimal weight:    0.4980
   chunk 96 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0040
   overall best weight:    0.5006

-------------------------------------------------------------------------------
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 = 0.3957 r_free = 0.3957 target = 0.147776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.104418 restraints weight = 15876.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.108626 restraints weight = 9401.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.111441 restraints weight = 6921.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.113171 restraints weight = 5735.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.114295 restraints weight = 5112.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8515  Z= 0.107
  Angle     :  0.628  13.887  11543  Z= 0.286
  Chirality :  0.040   0.304   1226
  Planarity :  0.004   0.054   1508
  Dihedral  : 10.199 106.325   1301
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 27.85 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.27), residues: 1000
  helix:  2.50 (0.21), residues: 624
  sheet:  1.36 (0.77), residues: 48
  loop : -0.95 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 471 
 TYR   0.014   0.001   TYR B 337 
 PHE   0.012   0.001   PHE B 256 
 TRP   0.022   0.001   TRP B 345 
 HIS   0.004   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8505)
  covalent geometry    : angle       0.61554 (11515)
  SS BOND              : bond        0.00094 (    2)
  SS BOND              : angle       0.80144 (    4)
  hydrogen bonds       : bond        0.03556 (  482)
  hydrogen bonds       : angle       3.45253 ( 1407)
  link_BETA1-4         : bond        0.00592 (    4)
  link_BETA1-4         : angle       3.32505 (   12)
  link_NAG-ASN         : bond        0.00286 (    4)
  link_NAG-ASN         : angle       2.06623 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7970 (pt0)
REVERT: A  180 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8691 (tp-100)
REVERT: A  185 TYR cc_start: 0.9405 (t80) cc_final: 0.9099 (t80)
REVERT: A  234 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7833 (mp0)
REVERT: A  246 CYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8379 (t)
REVERT: A  343 TYR cc_start: 0.8627 (t80) cc_final: 0.8419 (t80)
REVERT: A  444 ARG cc_start: 0.8927 (ttm170) cc_final: 0.8624 (mtt-85)
REVERT: A  485 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8140 (mt-10)
REVERT: B  113 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7564 (tt)
REVERT: B  181 MET cc_start: 0.9428 (mmm) cc_final: 0.9051 (mmp)
REVERT: B  351 HIS cc_start: 0.8661 (m90) cc_final: 0.8258 (m90)
  outliers start: 19
  outliers final: 13
  residues processed: 108
  average time/residue: 0.0598
  time to fit residues: 9.8550
Evaluate side-chains
  111 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  322 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 95 optimal weight:    0.0010
   chunk 97 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 93 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.6786

-------------------------------------------------------------------------------
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 = 0.3957 r_free = 0.3957 target = 0.148070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.105086 restraints weight = 16962.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.109377 restraints weight = 10092.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.112224 restraints weight = 7435.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.113997 restraints weight = 6158.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.115113 restraints weight = 5494.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8515  Z= 0.112
  Angle     :  0.634  13.999  11543  Z= 0.290
  Chirality :  0.040   0.313   1226
  Planarity :  0.004   0.055   1508
  Dihedral  :  9.984 106.663   1301
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 28.42 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.08 (0.28), residues: 1000
  helix:  2.49 (0.21), residues: 626
  sheet:  1.41 (0.77), residues: 48
  loop : -0.92 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 471 
 TYR   0.015   0.001   TYR B 337 
 PHE   0.009   0.001   PHE A 676 
 TRP   0.032   0.001   TRP B 345 
 HIS   0.004   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8505)
  covalent geometry    : angle       0.62218 (11515)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.67051 (    4)
  hydrogen bonds       : bond        0.03602 (  482)
  hydrogen bonds       : angle       3.47557 ( 1407)
  link_BETA1-4         : bond        0.00585 (    4)
  link_BETA1-4         : angle       3.32770 (   12)
  link_NAG-ASN         : bond        0.00243 (    4)
  link_NAG-ASN         : angle       2.07331 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7933 (pt0)
REVERT: A  185 TYR cc_start: 0.9402 (t80) cc_final: 0.9090 (t80)
REVERT: A  234 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7864 (mp0)
REVERT: A  444 ARG cc_start: 0.8927 (ttm170) cc_final: 0.8628 (mtt-85)
REVERT: A  485 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8147 (mt-10)
REVERT: B  113 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7647 (tt)
REVERT: B  181 MET cc_start: 0.9433 (mmm) cc_final: 0.9051 (mmp)
REVERT: B  345 TRP cc_start: 0.7499 (m-90) cc_final: 0.7286 (m-90)
REVERT: B  351 HIS cc_start: 0.8706 (m90) cc_final: 0.8313 (m90)
  outliers start: 18
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0529
  time to fit residues: 8.7392
Evaluate side-chains
  112 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  246 CYS
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  380 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 72 optimal weight:    0.3980
   chunk 49 optimal weight:    0.0070
   chunk 39 optimal weight:    1.9990
   chunk 75 optimal weight:    0.4980
   overall best weight:    0.4598

-------------------------------------------------------------------------------
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 = 0.3969 r_free = 0.3969 target = 0.148532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.105244 restraints weight = 15759.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.109464 restraints weight = 9300.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.112309 restraints weight = 6829.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.114098 restraints weight = 5657.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.115060 restraints weight = 5042.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.072   8515  Z= 0.108
  Angle     :  0.642  14.340  11543  Z= 0.294
  Chirality :  0.040   0.311   1226
  Planarity :  0.004   0.055   1508
  Dihedral  :  9.761 107.038   1301
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 28.54 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.03 (0.28), residues: 1000
  helix:  2.41 (0.21), residues: 631
  sheet:  1.50 (0.78), residues: 48
  loop : -0.93 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 471 
 TYR   0.023   0.001   TYR A 312 
 PHE   0.016   0.001   PHE B 256 
 TRP   0.019   0.001   TRP B 345 
 HIS   0.003   0.000   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8505)
  covalent geometry    : angle       0.62987 (11515)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       0.58028 (    4)
  hydrogen bonds       : bond        0.03449 (  482)
  hydrogen bonds       : angle       3.49055 ( 1407)
  link_BETA1-4         : bond        0.00612 (    4)
  link_BETA1-4         : angle       3.35187 (   12)
  link_NAG-ASN         : bond        0.00284 (    4)
  link_NAG-ASN         : angle       2.02998 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1287.31 seconds
wall clock time: 22 minutes 50.70 seconds (1370.70 seconds total)