Starting phenix.real_space_refine
on Wed Sep 17 09:36:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xxw_38763/09_2025/8xxw_38763.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xxw_38763/09_2025/8xxw_38763.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xxw_38763/09_2025/8xxw_38763.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xxw_38763/09_2025/8xxw_38763.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xxw_38763/09_2025/8xxw_38763.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xxw_38763/09_2025/8xxw_38763.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.018
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
     Zn      1      6.06       5
     S      41      5.16       5
     C    4932      2.51       5
     N    1278      2.21       5
     O    1471      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7723
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4595
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 561, 4588
          Classifications: {'peptide': 561}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 537}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 561, 4588
          Classifications: {'peptide': 561}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 537}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 4703
    Chain: "E"
      Number of atoms: 1300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1300
          Classifications: {'peptide': 162}
          Link IDs: {'PTRANS': 8, 'TRANS': 153}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 940
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 845
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' ZN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          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: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.70, per 1000 atoms: 0.35
  Number of scatterers: 7723
  At special positions: 0
  Unit cell: (70.55, 86.7, 141.1, 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)
     Zn      1     29.99
     S      41     16.00
     O    1471      8.00
     N    1278      7.00
     C    4932      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 902 " - " ASN A 546 "
      " NAG A 903 " - " ASN A  90 "
      " NAG E 701 " - " ASN E 343 "
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 494.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 378 "


  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1774

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 9 sheets defined
      50.0% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 52
      removed outlier: 3.590A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 4.021A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 88'
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.891A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.989A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 127
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 193
      removed outlier: 3.747A  pdb=" N   VAL A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 219 through 252
      removed outlier: 4.157A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.690A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.735A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.975A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 413
      removed outlier: 3.740A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 4.245A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 4.478A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 503
    Processing helix  chain 'A' and resid 505 through 509
      removed outlier: 3.723A  pdb=" N   ASP A 509 " --> pdb=" O   VAL A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.837A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.932A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.607A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'E' and resid 337 through 343
      removed outlier: 3.712A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 367 through 371
    Processing helix  chain 'E' and resid 406 through 410
    Processing helix  chain 'E' and resid 416 through 422
    Processing helix  chain 'E' and resid 438 through 443
      removed outlier: 3.586A  pdb=" N   SER E 443 " --> pdb=" O   ASN E 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 502 through 505
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.944A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 104
      removed outlier: 3.570A  pdb=" N   GLY H 103 " --> pdb=" O   ASP H 100 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.593A  pdb=" N   MET L  83 " --> pdb=" O   TYR L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.039A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.129A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358
    Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.579A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.482A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLY L  84 " --> pdb=" O   LEU L 104 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1028 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.24

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2473
        1.34 -     1.46: 1947
        1.46 -     1.58: 3437
        1.58 -     1.69: 1
        1.69 -     1.81: 67
  Bond restraints: 7925
  Sorted by residual:
  bond pdb=" C   LEU A 262 "
       pdb=" N   PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.331  1.360 -0.029 1.31e-02 5.83e+03 4.99e+00
  bond pdb=" N   ASP E 428 "
       pdb=" CA  ASP E 428 "
    ideal  model  delta    sigma   weight residual
    1.463  1.490 -0.027 1.31e-02 5.83e+03 4.27e+00
  bond pdb=" N   LEU A 262 "
       pdb=" CA  LEU A 262 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.024 1.41e-02 5.03e+03 2.93e+00
  bond pdb=" C1  NAG E 701 "
       pdb=" O5  NAG E 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.12e+00
  bond pdb=" C1  NAG A 902 "
       pdb=" O5  NAG A 902 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.81e+00
  ... (remaining 7920 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 10421
        1.36 -     2.72: 241
        2.72 -     4.07: 63
        4.07 -     5.43: 18
        5.43 -     6.79: 4
  Bond angle restraints: 10747
  Sorted by residual:
  angle pdb=" O   CYS A 261 "
        pdb=" C   CYS A 261 "
        pdb=" N   LEU A 262 "
      ideal   model   delta    sigma   weight residual
     123.10  127.10   -4.00 1.15e+00 7.56e-01 1.21e+01
  angle pdb=" N   GLY H 103 "
        pdb=" CA  GLY H 103 "
        pdb=" C   GLY H 103 "
      ideal   model   delta    sigma   weight residual
     115.46  110.53    4.93 1.63e+00 3.76e-01 9.14e+00
  angle pdb=" CA  MET A 270 "
        pdb=" CB  MET A 270 "
        pdb=" CG  MET A 270 "
      ideal   model   delta    sigma   weight residual
     114.10  120.00   -5.90 2.00e+00 2.50e-01 8.71e+00
  angle pdb=" CA  PRO A 500 "
        pdb=" N   PRO A 500 "
        pdb=" CD  PRO A 500 "
      ideal   model   delta    sigma   weight residual
     112.00  107.93    4.07 1.40e+00 5.10e-01 8.46e+00
  angle pdb=" CA  CYS A 261 "
        pdb=" C   CYS A 261 "
        pdb=" N   LEU A 262 "
      ideal   model   delta    sigma   weight residual
     115.55  111.87    3.68 1.33e+00 5.65e-01 7.67e+00
  ... (remaining 10742 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 4085
       17.19 -    34.37: 453
       34.37 -    51.56: 137
       51.56 -    68.75: 26
       68.75 -    85.94: 9
  Dihedral angle restraints: 4710
    sinusoidal: 1935
      harmonic: 2775
  Sorted by residual:
  dihedral pdb=" CA  ASP A 597 "
           pdb=" CB  ASP A 597 "
           pdb=" CG  ASP A 597 "
           pdb=" OD1 ASP A 597 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.84   57.84     1      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CA  TYR H  60 "
           pdb=" C   TYR H  60 "
           pdb=" N   ASP H  61 "
           pdb=" CA  ASP H  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -59.17  -26.83     1      1.00e+01 1.00e-02 1.03e+01
  ... (remaining 4707 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 791
       0.038 -    0.076: 247
       0.076 -    0.114: 82
       0.114 -    0.152: 11
       0.152 -    0.190: 1
  Chirality restraints: 1132
  Sorted by residual:
  chirality pdb=" CA  LEU A 262 "
            pdb=" N   LEU A 262 "
            pdb=" C   LEU A 262 "
            pdb=" CB  LEU A 262 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.00e-01
  chirality pdb=" CA  ARG A 192 "
            pdb=" N   ARG A 192 "
            pdb=" C   ARG A 192 "
            pdb=" CB  ARG A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  PRO A 500 "
            pdb=" N   PRO A 500 "
            pdb=" C   PRO A 500 "
            pdb=" CB  PRO A 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.14 2.00e-01 2.50e+01 5.22e-01
  ... (remaining 1129 not shown)

  Planarity restraints: 1388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 499 "    0.057 5.00e-02 4.00e+02   8.45e-02 1.14e+01
        pdb=" N   PRO A 500 "   -0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H  61 "    0.049 5.00e-02 4.00e+02   7.39e-02 8.73e+00
        pdb=" N   PRO H  62 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO H  62 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO H  62 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H  52 "    0.039 5.00e-02 4.00e+02   6.03e-02 5.82e+00
        pdb=" N   PRO H  53 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO H  53 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO H  53 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1385 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 817
        2.75 -     3.29: 7301
        3.29 -     3.82: 12512
        3.82 -     4.36: 14663
        4.36 -     4.90: 25812
  Nonbonded interactions: 61105
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 269 "
            pdb=" N   GLY A 272 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OG  SER E 438 "
            pdb=" OD2 ASP E 442 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OH  TYR A 279 "
            pdb=" OD1 ASN A 290 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" N   GLU A 430 "
            pdb=" OE1 GLU A 430 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   SER H   7 "
            pdb=" OG1 THR H 116 "
     model   vdw
     2.303 3.040
  ... (remaining 61100 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.24 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.550
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7936  Z= 0.143
  Angle     :  0.569   6.790  10768  Z= 0.306
  Chirality :  0.041   0.190   1132
  Planarity :  0.005   0.084   1385
  Dihedral  : 16.104  85.937   2918
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 19.42 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.00 (0.28), residues: 935
  helix:  1.22 (0.27), residues: 390
  sheet:  0.91 (0.39), residues: 179
  loop :  0.07 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 306 
 TYR   0.012   0.001   TYR A  50 
 PHE   0.029   0.001   PHE A 504 
 TRP   0.012   0.001   TRP A 566 
 HIS   0.003   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7925)
  covalent geometry    : angle       0.56747 (10747)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       0.60067 (   12)
  hydrogen bonds       : bond        0.15791 (  376)
  hydrogen bonds       : angle       6.07891 ( 1028)
  metal coordination   : bond        0.00096 (    2)
  link_NAG-ASN         : bond        0.00049 (    3)
  link_NAG-ASN         : angle       1.38433 (    9)

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 GLN cc_start: 0.8402 (mp10) cc_final: 0.8155 (mp10)
REVERT: E  443 SER cc_start: 0.8660 (m) cc_final: 0.8331 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1080
  time to fit residues: 22.0186
Evaluate side-chains
  153 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  63 ASN
E 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.132490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.108704 restraints weight = 15599.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.58
r_work: 0.3223 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.0925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7936  Z= 0.146
  Angle     :  0.537   8.730  10768  Z= 0.282
  Chirality :  0.042   0.130   1132
  Planarity :  0.005   0.063   1385
  Dihedral  :  4.336  35.373   1099
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 18.58 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.06 (0.27), residues: 935
  helix:  1.21 (0.26), residues: 390
  sheet:  0.85 (0.39), residues: 183
  loop :  0.23 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 219 
 TYR   0.017   0.001   TYR A 243 
 PHE   0.017   0.001   PHE H  99 
 TRP   0.010   0.001   TRP A 566 
 HIS   0.003   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7925)
  covalent geometry    : angle       0.53468 (10747)
  SS BOND              : bond        0.00495 (    6)
  SS BOND              : angle       0.83960 (   12)
  hydrogen bonds       : bond        0.05415 (  376)
  hydrogen bonds       : angle       4.63216 ( 1028)
  metal coordination   : bond        0.00225 (    2)
  link_NAG-ASN         : bond        0.00138 (    3)
  link_NAG-ASN         : angle       1.75082 (    9)

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 165
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5216 (mmp) cc_final: 0.4567 (mmm)
REVERT: A  183 TYR cc_start: 0.7193 (t80) cc_final: 0.6925 (t80)
REVERT: E  443 SER cc_start: 0.8585 (m) cc_final: 0.8202 (p)
  outliers start: 8
  outliers final: 4
  residues processed: 168
  average time/residue: 0.1049
  time to fit residues: 22.9594
Evaluate side-chains
  173 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 169
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain E residue  471 GLU
Chi-restraints excluded: chain L residue   10 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 84 optimal weight:    0.3980
   chunk 37 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0770
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
E 394 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.131807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.106979 restraints weight = 20790.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 3.10
r_work: 0.3181 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7936  Z= 0.146
  Angle     :  0.525   7.974  10768  Z= 0.274
  Chirality :  0.041   0.134   1132
  Planarity :  0.004   0.053   1385
  Dihedral  :  4.194  33.747   1099
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.97 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.13 (0.28), residues: 935
  helix:  1.24 (0.26), residues: 392
  sheet:  0.86 (0.39), residues: 183
  loop :  0.30 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.016   0.001   TYR A 243 
 PHE   0.014   0.001   PHE H  99 
 TRP   0.011   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7925)
  covalent geometry    : angle       0.52245 (10747)
  SS BOND              : bond        0.00493 (    6)
  SS BOND              : angle       0.88113 (   12)
  hydrogen bonds       : bond        0.05389 (  376)
  hydrogen bonds       : angle       4.50755 ( 1028)
  metal coordination   : bond        0.00228 (    2)
  link_NAG-ASN         : bond        0.00071 (    3)
  link_NAG-ASN         : angle       1.81232 (    9)

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5283 (mmp) cc_final: 0.4766 (mmm)
REVERT: A  157 ASP cc_start: 0.6499 (p0) cc_final: 0.6037 (p0)
REVERT: A  355 ASP cc_start: 0.8304 (t0) cc_final: 0.7841 (t0)
REVERT: E  442 ASP cc_start: 0.8383 (m-30) cc_final: 0.8107 (m-30)
REVERT: E  443 SER cc_start: 0.8599 (m) cc_final: 0.8176 (p)
  outliers start: 13
  outliers final: 9
  residues processed: 175
  average time/residue: 0.1035
  time to fit residues: 23.7916
Evaluate side-chains
  164 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 155
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 9 optimal weight:    4.9990
   chunk 74 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0670
   chunk 52 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0970
   chunk 63 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.3716

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.132747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.109769 restraints weight = 13833.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.42
r_work: 0.3251 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7936  Z= 0.125
  Angle     :  0.508   7.826  10768  Z= 0.264
  Chirality :  0.041   0.129   1132
  Planarity :  0.004   0.051   1385
  Dihedral  :  4.053  31.618   1099
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 18.58 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.30 (0.28), residues: 935
  helix:  1.30 (0.27), residues: 394
  sheet:  1.06 (0.40), residues: 177
  loop :  0.44 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.017   0.001   TYR A 279 
 PHE   0.012   0.001   PHE H  99 
 TRP   0.011   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7925)
  covalent geometry    : angle       0.50557 (10747)
  SS BOND              : bond        0.00389 (    6)
  SS BOND              : angle       0.86725 (   12)
  hydrogen bonds       : bond        0.04894 (  376)
  hydrogen bonds       : angle       4.41345 ( 1028)
  metal coordination   : bond        0.00162 (    2)
  link_NAG-ASN         : bond        0.00084 (    3)
  link_NAG-ASN         : angle       1.67595 (    9)

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5321 (mmp) cc_final: 0.4905 (mmm)
REVERT: E  442 ASP cc_start: 0.8558 (m-30) cc_final: 0.8288 (m-30)
REVERT: E  443 SER cc_start: 0.8612 (m) cc_final: 0.8188 (p)
  outliers start: 13
  outliers final: 11
  residues processed: 170
  average time/residue: 0.1087
  time to fit residues: 23.9989
Evaluate side-chains
  173 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 162
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain L residue   10 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   chunk 66 optimal weight:    0.7980
   chunk 73 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   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  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.129430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.105174 restraints weight = 20644.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 3.00
r_work: 0.3159 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   7936  Z= 0.171
  Angle     :  0.547   7.155  10768  Z= 0.285
  Chirality :  0.042   0.137   1132
  Planarity :  0.004   0.052   1385
  Dihedral  :  4.217  31.700   1099
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.82 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.15 (0.28), residues: 935
  helix:  1.27 (0.27), residues: 390
  sheet:  0.81 (0.39), residues: 183
  loop :  0.35 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.021   0.002   TYR A 279 
 PHE   0.014   0.001   PHE H  99 
 TRP   0.016   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 7925)
  covalent geometry    : angle       0.54260 (10747)
  SS BOND              : bond        0.00477 (    6)
  SS BOND              : angle       1.12090 (   12)
  hydrogen bonds       : bond        0.05717 (  376)
  hydrogen bonds       : angle       4.50217 ( 1028)
  metal coordination   : bond        0.00277 (    2)
  link_NAG-ASN         : bond        0.00135 (    3)
  link_NAG-ASN         : angle       2.07294 (    9)

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 171
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   88 ILE cc_start: 0.7808 (mm) cc_final: 0.7578 (mt)
REVERT: A  123 MET cc_start: 0.5401 (mmp) cc_final: 0.5020 (mmm)
REVERT: A  310 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7623 (mm-30)
REVERT: A  312 GLU cc_start: 0.8302 (tt0) cc_final: 0.7776 (tt0)
REVERT: E  442 ASP cc_start: 0.8566 (m-30) cc_final: 0.8249 (m-30)
REVERT: E  443 SER cc_start: 0.8567 (m) cc_final: 0.8145 (p)
REVERT: L   19 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7942 (m)
  outliers start: 18
  outliers final: 15
  residues processed: 180
  average time/residue: 0.1063
  time to fit residues: 25.0049
Evaluate side-chains
  178 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  471 GLU
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0020
   chunk 86 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 55 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.131140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.108589 restraints weight = 13186.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.30
r_work: 0.3239 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   7936  Z= 0.133
  Angle     :  0.519   6.473  10768  Z= 0.270
  Chirality :  0.041   0.131   1132
  Planarity :  0.004   0.051   1385
  Dihedral  :  4.049  29.779   1099
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.18 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.31 (0.28), residues: 935
  helix:  1.35 (0.27), residues: 392
  sheet:  0.99 (0.39), residues: 177
  loop :  0.43 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.021   0.001   TYR A 279 
 PHE   0.013   0.001   PHE H  99 
 TRP   0.012   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7925)
  covalent geometry    : angle       0.51646 (10747)
  SS BOND              : bond        0.00431 (    6)
  SS BOND              : angle       0.91328 (   12)
  hydrogen bonds       : bond        0.04971 (  376)
  hydrogen bonds       : angle       4.41006 ( 1028)
  metal coordination   : bond        0.00189 (    2)
  link_NAG-ASN         : bond        0.00103 (    3)
  link_NAG-ASN         : angle       1.77982 (    9)

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5544 (mmp) cc_final: 0.5260 (mmm)
REVERT: A  310 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7785 (mm-30)
REVERT: A  312 GLU cc_start: 0.8408 (tt0) cc_final: 0.7847 (tt0)
REVERT: E  443 SER cc_start: 0.8597 (m) cc_final: 0.8156 (p)
REVERT: L    4 MET cc_start: 0.8119 (mmm) cc_final: 0.7613 (mmm)
REVERT: L   19 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7953 (m)
  outliers start: 19
  outliers final: 14
  residues processed: 175
  average time/residue: 0.1095
  time to fit residues: 24.9418
Evaluate side-chains
  176 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0070
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.130093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.105941 restraints weight = 20288.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.96
r_work: 0.3175 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   7936  Z= 0.152
  Angle     :  0.540   6.243  10768  Z= 0.282
  Chirality :  0.042   0.134   1132
  Planarity :  0.004   0.051   1385
  Dihedral  :  4.093  29.099   1099
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.46 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.25 (0.28), residues: 935
  helix:  1.30 (0.27), residues: 392
  sheet:  1.00 (0.39), residues: 176
  loop :  0.40 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 115 
 TYR   0.018   0.001   TYR A 279 
 PHE   0.013   0.001   PHE H  99 
 TRP   0.014   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7925)
  covalent geometry    : angle       0.53668 (10747)
  SS BOND              : bond        0.00454 (    6)
  SS BOND              : angle       1.05319 (   12)
  hydrogen bonds       : bond        0.05347 (  376)
  hydrogen bonds       : angle       4.44757 ( 1028)
  metal coordination   : bond        0.00240 (    2)
  link_NAG-ASN         : bond        0.00115 (    3)
  link_NAG-ASN         : angle       1.93159 (    9)

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5479 (mmp) cc_final: 0.5181 (mmm)
REVERT: A  310 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7626 (mm-30)
REVERT: A  312 GLU cc_start: 0.8298 (tt0) cc_final: 0.7759 (tt0)
REVERT: A  441 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6706 (mtmm)
REVERT: E  443 SER cc_start: 0.8556 (m) cc_final: 0.8123 (p)
REVERT: L   19 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7951 (m)
  outliers start: 22
  outliers final: 16
  residues processed: 178
  average time/residue: 0.1071
  time to fit residues: 24.7835
Evaluate side-chains
  184 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  471 GLU
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 60 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 76 optimal weight:    0.3980
   chunk 48 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.129495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.106720 restraints weight = 15608.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.53
r_work: 0.3201 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   7936  Z= 0.160
  Angle     :  0.547   6.461  10768  Z= 0.287
  Chirality :  0.042   0.137   1132
  Planarity :  0.005   0.051   1385
  Dihedral  :  4.149  28.761   1099
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 18.70 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.20 (0.28), residues: 935
  helix:  1.29 (0.27), residues: 392
  sheet:  0.83 (0.38), residues: 182
  loop :  0.41 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.025   0.002   TYR A 279 
 PHE   0.014   0.001   PHE H  99 
 TRP   0.016   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 7925)
  covalent geometry    : angle       0.54359 (10747)
  SS BOND              : bond        0.00461 (    6)
  SS BOND              : angle       1.14058 (   12)
  hydrogen bonds       : bond        0.05442 (  376)
  hydrogen bonds       : angle       4.45707 ( 1028)
  metal coordination   : bond        0.00262 (    2)
  link_NAG-ASN         : bond        0.00126 (    3)
  link_NAG-ASN         : angle       2.01263 (    9)

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5568 (mmp) cc_final: 0.5294 (mmm)
REVERT: A  290 ASN cc_start: 0.4523 (OUTLIER) cc_final: 0.4252 (m-40)
REVERT: A  310 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7557 (mm-30)
REVERT: A  312 GLU cc_start: 0.8285 (tt0) cc_final: 0.7740 (tt0)
REVERT: A  441 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6814 (mtmm)
REVERT: E  442 ASP cc_start: 0.8467 (m-30) cc_final: 0.8203 (m-30)
REVERT: E  443 SER cc_start: 0.8576 (m) cc_final: 0.8127 (p)
REVERT: L    4 MET cc_start: 0.7960 (mmm) cc_final: 0.7412 (mmm)
REVERT: L   19 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7928 (m)
  outliers start: 20
  outliers final: 16
  residues processed: 174
  average time/residue: 0.1064
  time to fit residues: 24.1563
Evaluate side-chains
  182 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  471 GLU
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    0.0030
   chunk 64 optimal weight:    2.9990
   chunk 40 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    0.3980
   chunk 4 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.129795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.107473 restraints weight = 13710.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.33
r_work: 0.3220 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090   7936  Z= 0.144
  Angle     :  0.552   7.889  10768  Z= 0.288
  Chirality :  0.041   0.136   1132
  Planarity :  0.004   0.051   1385
  Dihedral  :  4.134  28.617   1099
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.34 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.23 (0.28), residues: 935
  helix:  1.30 (0.27), residues: 392
  sheet:  1.00 (0.38), residues: 176
  loop :  0.36 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.025   0.001   TYR A 279 
 PHE   0.012   0.001   PHE H  99 
 TRP   0.014   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7925)
  covalent geometry    : angle       0.54807 (10747)
  SS BOND              : bond        0.00412 (    6)
  SS BOND              : angle       1.11548 (   12)
  hydrogen bonds       : bond        0.05289 (  376)
  hydrogen bonds       : angle       4.45365 ( 1028)
  metal coordination   : bond        0.00207 (    2)
  link_NAG-ASN         : bond        0.00112 (    3)
  link_NAG-ASN         : angle       1.96127 (    9)

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.5622 (mmp) cc_final: 0.5356 (mmm)
REVERT: A  290 ASN cc_start: 0.4515 (OUTLIER) cc_final: 0.4100 (m-40)
REVERT: A  310 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7797 (mm-30)
REVERT: A  312 GLU cc_start: 0.8457 (tt0) cc_final: 0.7945 (tt0)
REVERT: A  441 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6875 (mtmm)
REVERT: E  442 ASP cc_start: 0.8545 (m-30) cc_final: 0.8277 (m-30)
REVERT: E  443 SER cc_start: 0.8634 (m) cc_final: 0.8179 (p)
REVERT: L    4 MET cc_start: 0.8076 (mmm) cc_final: 0.7411 (mmm)
REVERT: L   19 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7988 (m)
  outliers start: 22
  outliers final: 16
  residues processed: 176
  average time/residue: 0.1086
  time to fit residues: 24.8621
Evaluate side-chains
  182 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  471 GLU
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.128878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.106187 restraints weight = 15169.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.47
r_work: 0.3197 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   7936  Z= 0.198
  Angle     :  0.573   7.582  10768  Z= 0.299
  Chirality :  0.043   0.139   1132
  Planarity :  0.005   0.051   1385
  Dihedral  :  4.184  28.726   1099
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 18.82 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  1.11 (0.28), residues: 935
  helix:  1.22 (0.27), residues: 392
  sheet:  0.82 (0.38), residues: 182
  loop :  0.32 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.023   0.002   TYR A 279 
 PHE   0.016   0.001   PHE H  99 
 TRP   0.018   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 7925)
  covalent geometry    : angle       0.56872 (10747)
  SS BOND              : bond        0.00494 (    6)
  SS BOND              : angle       1.30939 (   12)
  hydrogen bonds       : bond        0.05646 (  376)
  hydrogen bonds       : angle       4.48669 ( 1028)
  metal coordination   : bond        0.00341 (    2)
  link_NAG-ASN         : bond        0.00169 (    3)
  link_NAG-ASN         : angle       2.07901 (    9)

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

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

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1870 Ramachandran restraints generated.
    935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.5601 (mmp) cc_final: 0.5332 (mmm)
REVERT: A  310 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7693 (mm-30)
REVERT: A  312 GLU cc_start: 0.8278 (tt0) cc_final: 0.7871 (tt0)
REVERT: A  441 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6904 (mmtt)
REVERT: E  442 ASP cc_start: 0.8472 (m-30) cc_final: 0.8204 (m-30)
REVERT: E  443 SER cc_start: 0.8586 (m) cc_final: 0.8146 (p)
REVERT: L    4 MET cc_start: 0.7952 (mmm) cc_final: 0.7401 (mmm)
REVERT: L   19 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7958 (m)
  outliers start: 20
  outliers final: 17
  residues processed: 174
  average time/residue: 0.1100
  time to fit residues: 25.0224
Evaluate side-chains
  182 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  471 GLU
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0970
   chunk 31 optimal weight:    0.8980
   chunk 52 optimal weight:    0.3980
   chunk 14 optimal weight:    0.7980
   chunk 71 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.129919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.107117 restraints weight = 15591.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.53
r_work: 0.3208 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3210
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084   7936  Z= 0.142
  Angle     :  0.555   8.026  10768  Z= 0.288
  Chirality :  0.042   0.147   1132
  Planarity :  0.004   0.051   1385
  Dihedral  :  4.112  28.253   1099
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 19.18 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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 (0.28), residues: 935
  helix:  1.31 (0.27), residues: 392
  sheet:  1.00 (0.38), residues: 176
  loop :  0.32 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.017   0.001   TYR A 243 
 PHE   0.013   0.001   PHE H  99 
 TRP   0.014   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7925)
  covalent geometry    : angle       0.55206 (10747)
  SS BOND              : bond        0.00420 (    6)
  SS BOND              : angle       1.05451 (   12)
  hydrogen bonds       : bond        0.05228 (  376)
  hydrogen bonds       : angle       4.45548 ( 1028)
  metal coordination   : bond        0.00209 (    2)
  link_NAG-ASN         : bond        0.00111 (    3)
  link_NAG-ASN         : angle       1.92648 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2412.61 seconds
wall clock time: 42 minutes 3.08 seconds (2523.08 seconds total)