Starting phenix.real_space_refine
on Mon Nov 17 20:57:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jt2_9885/11_2025/6jt2_9885.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jt2_9885/11_2025/6jt2_9885.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jt2_9885/11_2025/6jt2_9885.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jt2_9885/11_2025/6jt2_9885.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6jt2_9885/11_2025/6jt2_9885.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jt2_9885/11_2025/6jt2_9885.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 7
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     P       3      5.49       5
     Mg      2      5.21       5
     S      56      5.16       5
     C    5262      2.51       5
     N    1392      2.21       5
     O    1475      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8191
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3742
          Classifications: {'peptide': 506}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 23, 'TRANS': 482}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 261
          Unresolved non-hydrogen angles: 319
          Unresolved non-hydrogen dihedrals: 216
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 16, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'ASP:plan': 7, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 162
    Chain: "B"
      Number of atoms: 4372
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 569, 4368
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 148
          Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 4, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 138
      Conformer: "B"
        Number of residues, atoms: 569, 4368
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 148
          Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 4, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 138
          bond proxies already assigned to first conformer: 4452
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {' MG': 2, 'G2P': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LEU A 254 " occ=0.92
      ... (3 atoms not shown)
      pdb=" CB  LEU A 254 " occ=0.92
  Time building chain proxies: 3.04, per 1000 atoms: 0.37
  Number of scatterers: 8191
  At special positions: 0
  Unit cell: (147.345, 87.78, 98.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      1     26.01
     S      56     16.00
     P       3     15.00
     Mg      2     11.99
     O    1475      8.00
     N    1392      7.00
     C    5262      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 482.5 milliseconds
  

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2026

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 8 sheets defined
      50.4% alpha, 15.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 83
    Processing helix  chain 'A' and resid 85 through 101
    Processing helix  chain 'A' and resid 115 through 126
    Processing helix  chain 'A' and resid 128 through 149
      removed outlier: 3.585A  pdb=" N   ILE A 132 " --> pdb=" O   PRO A 128 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU A 147 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ASP A 148 " --> pdb=" O   CYS A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 4.375A  pdb=" N   VAL A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   VAL A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 150 through 155'
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 3.800A  pdb=" N   PHE A 166 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   SER A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   THR A 168 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LYS A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 226
      removed outlier: 4.660A  pdb=" N   LEU A 213 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ILE A 214 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 215 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
      Proline residue:  A 216  - end of helix
      removed outlier: 3.643A  pdb=" N   LYS A 220 " --> pdb=" O   PRO A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'A' and resid 302 through 309
    Processing helix  chain 'A' and resid 334 through 341
    Processing helix  chain 'A' and resid 408 through 458
      removed outlier: 4.206A  pdb=" N   VAL A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 468
      removed outlier: 4.336A  pdb=" N   GLN A 468 " --> pdb=" O   GLN A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 497
      removed outlier: 3.508A  pdb=" N   ILE A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 519
      removed outlier: 3.517A  pdb=" N   GLN A 516 " --> pdb=" O   ARG A 512 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU A 519 " --> pdb=" O   GLN A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 561
      removed outlier: 3.649A  pdb=" N   GLN A 548 " --> pdb=" O   THR A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 608
      removed outlier: 3.642A  pdb=" N   ASN A 605 " --> pdb=" O   VAL A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 628
      removed outlier: 4.133A  pdb=" N   ASP A 628 " --> pdb=" O   ARG A 624 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 18
      removed outlier: 4.201A  pdb=" N   ASN B   6 " --> pdb=" O   TYR B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 30
      removed outlier: 3.931A  pdb=" N   TRP B  22 " --> pdb=" O   GLY B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 59
      removed outlier: 3.803A  pdb=" N   THR B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 82
    Processing helix  chain 'B' and resid 83 through 90
      removed outlier: 3.938A  pdb=" N   LEU B  87 " --> pdb=" O   TYR B  83 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LEU B  90 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 112
      removed outlier: 4.732A  pdb=" N   ASP B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   ALA B 103 " --> pdb=" O   GLN B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 157
      removed outlier: 4.206A  pdb=" N   ILE B 147 " --> pdb=" O   GLN B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'B' and resid 235 through 240
    Processing helix  chain 'B' and resid 249 through 253
      removed outlier: 3.692A  pdb=" N   VAL B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 249 through 253'
    Processing helix  chain 'B' and resid 264 through 271
      removed outlier: 3.892A  pdb=" N   SER B 270 " --> pdb=" O   HIS B 266 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   HIS B 271 " --> pdb=" O   GLY B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 285
      removed outlier: 4.350A  pdb=" N   LEU B 285 " --> pdb=" O   GLU B 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 282 through 285'
    Processing helix  chain 'B' and resid 329 through 335
      removed outlier: 3.575A  pdb=" N   LEU B 333 " --> pdb=" O   ASN B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 343
    Processing helix  chain 'B' and resid 348 through 398
      removed outlier: 4.370A  pdb=" N   LEU B 354 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 408
      removed outlier: 4.384A  pdb=" N   HIS B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 437
    Processing helix  chain 'B' and resid 443 through 461
    Processing helix  chain 'B' and resid 491 through 507
      removed outlier: 3.532A  pdb=" N   SER B 495 " --> pdb=" O   HIS B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 557
      removed outlier: 3.641A  pdb=" N   ASN B 548 " --> pdb=" O   GLY B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 573
    Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 204
    Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300
      removed outlier: 6.563A  pdb=" N   MET A 291 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 525
      removed outlier: 4.409A  pdb=" N   CYS A 533 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   LYS A 476 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   ALA A 584 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   SER A 478 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   VAL A 582 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   MET A 573 " --> pdb=" O   LYS A 615 " (cutoff:3.500A)
      removed outlier: 8.261A  pdb=" N   ASN A 617 " --> pdb=" O   MET A 573 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ILE A 575 " --> pdb=" O   ASN A 617 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   ILE A 616 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LEU A 657 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 124
    Processing sheet with id=AA5, first strand: chain 'B' and resid 229 through 231
      removed outlier: 3.692A  pdb=" N   GLN B 231 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   VAL B 277 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 415 through 416
      removed outlier: 3.532A  pdb=" N   GLY B 531 " --> pdb=" O   CYS B 541 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 469 through 474
      removed outlier: 7.068A  pdb=" N   MET B 480 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   THR B 474 " --> pdb=" O   LYS B 478 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LYS B 478 " --> pdb=" O   THR B 474 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR B 421 " --> pdb=" O   SER B 483 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   ASN B 563 " --> pdb=" O   ILE B 519 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   SER B 565 " --> pdb=" O   ILE B 521 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   ILE B 523 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   ILE B 562 " --> pdb=" O   LEU B 604 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   GLY B 588 " --> pdb=" O   VAL B 601 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   PHE B 603 " --> pdb=" O   HIS B 586 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   HIS B 586 " --> pdb=" O   PHE B 603 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   SER B 605 " --> pdb=" O   LEU B 584 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   LEU B 584 " --> pdb=" O   SER B 605 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 512

    461 hydrogen bonds defined for protein.
    1326 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: 1.44

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.39: 3335
        1.39 -     1.56: 4924
        1.56 -     1.73: 6
        1.73 -     1.90: 86
        1.90 -     2.07: 4
  Bond restraints: 8355
  Sorted by residual:
  bond pdb=" O3B G2P A1001 "
       pdb=" PG  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.716  1.610  0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" O1A G2P A1001 "
       pdb=" PA  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.507  1.610 -0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" O1B G2P A1001 "
       pdb=" PB  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.510  1.609 -0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" C4  G2P A1001 "
       pdb=" C5  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.384  1.469 -0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C5  G2P A1001 "
       pdb=" C6  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.420  1.483 -0.063 2.00e-02 2.50e+03 9.79e+00
  ... (remaining 8350 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 11160
        2.27 -     4.54: 170
        4.54 -     6.81: 22
        6.81 -     9.09: 11
        9.09 -    11.36: 4
  Bond angle restraints: 11367
  Sorted by residual:
  angle pdb=" PA  G2P A1001 "
        pdb=" C3A G2P A1001 "
        pdb=" PB  G2P A1001 "
      ideal   model   delta    sigma   weight residual
     120.83  109.47   11.36 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" C3A G2P A1001 "
        pdb=" PB  G2P A1001 "
        pdb=" O3B G2P A1001 "
      ideal   model   delta    sigma   weight residual
      99.71  109.82  -10.11 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" C5  G2P A1001 "
        pdb=" C4  G2P A1001 "
        pdb=" N3  G2P A1001 "
      ideal   model   delta    sigma   weight residual
     128.08  118.69    9.39 3.00e+00 1.11e-01 9.79e+00
  angle pdb=" C   TYR B 339 "
        pdb=" N   LEU B 340 "
        pdb=" CA  LEU B 340 "
      ideal   model   delta    sigma   weight residual
     121.54  127.36   -5.82 1.91e+00 2.74e-01 9.28e+00
  angle pdb=" C3A G2P A1001 "
        pdb=" PA  G2P A1001 "
        pdb=" O5' G2P A1001 "
      ideal   model   delta    sigma   weight residual
      99.14  108.27   -9.13 3.00e+00 1.11e-01 9.26e+00
  ... (remaining 11362 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.26: 4668
       16.26 -    32.52: 249
       32.52 -    48.78: 56
       48.78 -    65.03: 15
       65.03 -    81.29: 4
  Dihedral angle restraints: 4992
    sinusoidal: 1869
      harmonic: 3123
  Sorted by residual:
  dihedral pdb=" CA  ASP B 262 "
           pdb=" C   ASP B 262 "
           pdb=" N   ILE B 263 "
           pdb=" CA  ILE B 263 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.33  -24.67     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  TYR B 339 "
           pdb=" C   TYR B 339 "
           pdb=" N   LEU B 340 "
           pdb=" CA  LEU B 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.25  -21.75     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  PHE A 301 "
           pdb=" C   PHE A 301 "
           pdb=" N   GLY A 302 "
           pdb=" CA  GLY A 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.67   20.33     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 4989 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1106
       0.055 -    0.111: 213
       0.111 -    0.166: 22
       0.166 -    0.221: 0
       0.221 -    0.276: 1
  Chirality restraints: 1342
  Sorted by residual:
  chirality pdb=" CB  VAL A 462 "
            pdb=" CA  VAL A 462 "
            pdb=" CG1 VAL A 462 "
            pdb=" CG2 VAL A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  VAL A 462 "
            pdb=" N   VAL A 462 "
            pdb=" C   VAL A 462 "
            pdb=" CB  VAL A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.18e-01
  chirality pdb=" C2' G2P A1001 "
            pdb=" C1' G2P A1001 "
            pdb=" C3' G2P A1001 "
            pdb=" O2' G2P A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.62    0.15 2.00e-01 2.50e+01 5.31e-01
  ... (remaining 1339 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 462 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.06e+00
        pdb=" C   VAL A 462 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   VAL A 462 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ALA A 463 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 258 "    0.038 5.00e-02 4.00e+02   5.76e-02 5.31e+00
        pdb=" N   PRO B 259 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 259 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 259 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 209 "    0.037 5.00e-02 4.00e+02   5.67e-02 5.14e+00
        pdb=" N   PRO B 210 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 210 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 210 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 47
        2.56 -     3.15: 6531
        3.15 -     3.73: 12626
        3.73 -     4.32: 16476
        4.32 -     4.90: 27806
  Nonbonded interactions: 63486
  Sorted by model distance:
  nonbonded pdb=" O2B G2P A1001 "
            pdb="MG    MG A1002 "
     model   vdw
     1.980 2.170
  nonbonded pdb=" OD1 ASP A 486 "
            pdb="MG    MG A1002 "
     model   vdw
     2.095 2.170
  nonbonded pdb=" OD2 ASP A 486 "
            pdb="MG    MG A1002 "
     model   vdw
     2.101 2.170
  nonbonded pdb=" O5' G2P A1001 "
            pdb="MG    MG A1003 "
     model   vdw
     2.172 2.170
  nonbonded pdb=" O   LEU A 520 "
            pdb=" NE2 GLN A 548 "
     model   vdw
     2.259 3.120
  ... (remaining 63481 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=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:             0.020
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.860
  Find NCS groups from input model:        0.050
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   8355  Z= 0.217
  Angle     :  0.738  11.357  11367  Z= 0.377
  Chirality :  0.042   0.276   1342
  Planarity :  0.005   0.058   1431
  Dihedral  : 11.363  81.292   2966
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.00 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  :  5.19 %
    Favored  : 91.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.23), residues: 1049
  helix: -1.24 (0.20), residues: 478
  sheet: -1.17 (0.35), residues: 192
  loop : -2.34 (0.28), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 552 
 TYR   0.013   0.001   TYR B 479 
 PHE   0.016   0.002   PHE A 292 
 TRP   0.010   0.001   TRP B 602 
 HIS   0.005   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 8355)
  covalent geometry    : angle       0.73770 (11367)
  hydrogen bonds       : bond        0.13493 (  461)
  hydrogen bonds       : angle       6.73972 ( 1326)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 188
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 CYS cc_start: 0.8998 (t) cc_final: 0.8778 (m)
REVERT: A  455 CYS cc_start: 0.8971 (m) cc_final: 0.8406 (t)
REVERT: A  479 ASN cc_start: 0.7920 (m110) cc_final: 0.7647 (p0)
REVERT: A  514 ASP cc_start: 0.9019 (m-30) cc_final: 0.8740 (m-30)
REVERT: A  516 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8498 (mm-40)
REVERT: A  543 ASP cc_start: 0.8435 (m-30) cc_final: 0.7491 (p0)
REVERT: A  554 VAL cc_start: 0.9375 (t) cc_final: 0.9168 (t)
REVERT: A  556 MET cc_start: 0.9443 (tpp) cc_final: 0.8926 (mmm)
REVERT: A  583 PHE cc_start: 0.8186 (m-80) cc_final: 0.7859 (m-10)
REVERT: B   73 MET cc_start: 0.8564 (tpp) cc_final: 0.8300 (tpp)
REVERT: B  106 ASP cc_start: 0.9202 (t0) cc_final: 0.8917 (t0)
REVERT: B  119 SER cc_start: 0.9177 (m) cc_final: 0.8363 (p)
REVERT: B  160 THR cc_start: 0.8562 (m) cc_final: 0.8351 (p)
REVERT: B  211 TYR cc_start: 0.8649 (t80) cc_final: 0.8372 (t80)
REVERT: B  228 VAL cc_start: 0.8802 (t) cc_final: 0.8571 (p)
REVERT: B  320 LEU cc_start: 0.8545 (tt) cc_final: 0.8089 (tp)
REVERT: B  323 CYS cc_start: 0.8540 (p) cc_final: 0.8244 (p)
REVERT: B  394 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8711 (tt)
REVERT: B  491 HIS cc_start: 0.8482 (p90) cc_final: 0.7513 (t-170)
REVERT: B  537 MET cc_start: 0.8659 (ttm) cc_final: 0.8425 (ttt)
  outliers start: 30
  outliers final: 11
  residues processed: 212
  average time/residue: 0.0899
  time to fit residues: 26.5734
Evaluate side-chains
  123 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  260 HIS
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.0030
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0670
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.4328

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN
B 266 HIS
B 408 HIS
B 548 ASN
B 563 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.108780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.085200 restraints weight = 23373.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.087964 restraints weight = 13526.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.089928 restraints weight = 9335.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.091244 restraints weight = 7206.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.092127 restraints weight = 6016.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3376
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3374
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8355  Z= 0.135
  Angle     :  0.686   9.692  11367  Z= 0.342
  Chirality :  0.043   0.195   1342
  Planarity :  0.005   0.046   1431
  Dihedral  :  7.805  70.681   1203
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 13.22 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.25), residues: 1049
  helix:  0.44 (0.22), residues: 487
  sheet: -0.89 (0.35), residues: 207
  loop : -2.00 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 381 
 TYR   0.024   0.002   TYR B 237 
 PHE   0.027   0.002   PHE A 335 
 TRP   0.034   0.006   TRP A 467 
 HIS   0.010   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8355)
  covalent geometry    : angle       0.68629 (11367)
  hydrogen bonds       : bond        0.04526 (  461)
  hydrogen bonds       : angle       4.83854 ( 1326)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.6395 (t80)
REVERT: A  455 CYS cc_start: 0.7668 (m) cc_final: 0.7113 (t)
REVERT: A  543 ASP cc_start: 0.7453 (m-30) cc_final: 0.6973 (p0)
REVERT: A  583 PHE cc_start: 0.8096 (m-80) cc_final: 0.7846 (m-10)
REVERT: B    9 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7961 (tt)
REVERT: B   69 MET cc_start: 0.7727 (ttm) cc_final: 0.7450 (mtm)
REVERT: B  106 ASP cc_start: 0.8605 (t0) cc_final: 0.8209 (t0)
REVERT: B  119 SER cc_start: 0.8910 (m) cc_final: 0.7875 (p)
REVERT: B  537 MET cc_start: 0.8134 (ttm) cc_final: 0.7823 (ttt)
  outliers start: 29
  outliers final: 18
  residues processed: 151
  average time/residue: 0.0702
  time to fit residues: 15.6197
Evaluate side-chains
  125 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 104 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 GLN
B 346 HIS
B 408 HIS
B 491 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.103503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.081464 restraints weight = 34409.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.082264 restraints weight = 23548.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.083107 restraints weight = 18402.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.085184 restraints weight = 12113.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.085396 restraints weight = 8995.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   8355  Z= 0.210
  Angle     :  0.703   8.654  11367  Z= 0.356
  Chirality :  0.045   0.274   1342
  Planarity :  0.005   0.049   1431
  Dihedral  :  7.504  66.214   1197
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 14.05 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.26), residues: 1049
  helix:  0.80 (0.23), residues: 494
  sheet: -0.84 (0.36), residues: 210
  loop : -1.81 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 381 
 TYR   0.017   0.002   TYR B 569 
 PHE   0.025   0.002   PHE A 458 
 TRP   0.021   0.003   TRP B  22 
 HIS   0.014   0.002   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 8355)
  covalent geometry    : angle       0.70251 (11367)
  hydrogen bonds       : bond        0.04659 (  461)
  hydrogen bonds       : angle       4.75888 ( 1326)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 102
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7060 (pp)
REVERT: A  203 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6536 (t80)
REVERT: A  399 TYR cc_start: 0.7159 (m-80) cc_final: 0.6826 (m-10)
REVERT: A  455 CYS cc_start: 0.7505 (m) cc_final: 0.7220 (t)
REVERT: B    9 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8253 (tt)
REVERT: B   61 LEU cc_start: 0.8338 (pt) cc_final: 0.8005 (tt)
REVERT: B  106 ASP cc_start: 0.8711 (t0) cc_final: 0.8262 (t0)
REVERT: B  119 SER cc_start: 0.9061 (m) cc_final: 0.8097 (p)
REVERT: B  503 MET cc_start: 0.8561 (mmm) cc_final: 0.8336 (mmm)
  outliers start: 38
  outliers final: 22
  residues processed: 134
  average time/residue: 0.0676
  time to fit residues: 14.0666
Evaluate side-chains
  120 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  597 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  542 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 300 GLN
A 422 GLN
A 479 ASN
A 516 GLN
B 408 HIS
B 451 ASN
B 491 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.104715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.080694 restraints weight = 23693.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.083297 restraints weight = 13941.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.085111 restraints weight = 9911.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.086369 restraints weight = 7786.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.087257 restraints weight = 6600.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3286
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8355  Z= 0.136
  Angle     :  0.622   8.310  11367  Z= 0.309
  Chirality :  0.042   0.163   1342
  Planarity :  0.004   0.046   1431
  Dihedral  :  7.030  66.582   1195
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 14.99 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.26), residues: 1049
  helix:  1.10 (0.23), residues: 492
  sheet: -0.63 (0.36), residues: 210
  loop : -1.73 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 381 
 TYR   0.013   0.001   TYR B 479 
 PHE   0.020   0.002   PHE A 458 
 TRP   0.014   0.002   TRP B  22 
 HIS   0.005   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8355)
  covalent geometry    : angle       0.62247 (11367)
  hydrogen bonds       : bond        0.04159 (  461)
  hydrogen bonds       : angle       4.46688 ( 1326)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 107
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6958 (pp)
REVERT: A  203 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.6531 (t80)
REVERT: A  341 MET cc_start: 0.8215 (tpp) cc_final: 0.7868 (tpt)
REVERT: A  399 TYR cc_start: 0.7085 (m-80) cc_final: 0.6877 (m-80)
REVERT: A  471 VAL cc_start: 0.7830 (t) cc_final: 0.7566 (m)
REVERT: A  479 ASN cc_start: 0.7046 (OUTLIER) cc_final: 0.6711 (p0)
REVERT: A  607 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7762 (t80)
REVERT: B   61 LEU cc_start: 0.8244 (pt) cc_final: 0.7933 (tt)
REVERT: B  106 ASP cc_start: 0.8640 (t0) cc_final: 0.8165 (t0)
REVERT: B  119 SER cc_start: 0.9165 (m) cc_final: 0.8224 (p)
REVERT: B  503 MET cc_start: 0.8527 (mmm) cc_final: 0.8316 (mmm)
  outliers start: 43
  outliers final: 27
  residues processed: 143
  average time/residue: 0.0656
  time to fit residues: 14.4058
Evaluate side-chains
  126 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  422 GLN
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  597 PHE
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  357 GLU
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  542 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0770
   chunk 18 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.3342

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
A 479 ASN
B 408 HIS
B 491 HIS
** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.103252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.081201 restraints weight = 34614.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.081792 restraints weight = 24056.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.082745 restraints weight = 18791.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.084885 restraints weight = 12335.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.085117 restraints weight = 9173.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   8355  Z= 0.166
  Angle     :  0.640   9.956  11367  Z= 0.317
  Chirality :  0.042   0.171   1342
  Planarity :  0.004   0.045   1431
  Dihedral  :  6.543  64.095   1193
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 14.76 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.26), residues: 1049
  helix:  1.19 (0.23), residues: 489
  sheet: -0.40 (0.37), residues: 200
  loop : -1.78 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 381 
 TYR   0.012   0.001   TYR B 569 
 PHE   0.019   0.002   PHE A 458 
 TRP   0.011   0.002   TRP B  22 
 HIS   0.013   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8355)
  covalent geometry    : angle       0.63995 (11367)
  hydrogen bonds       : bond        0.04189 (  461)
  hydrogen bonds       : angle       4.43485 ( 1326)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 95
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7068 (pp)
REVERT: A  203 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.6588 (t80)
REVERT: A  399 TYR cc_start: 0.7258 (m-80) cc_final: 0.6977 (m-80)
REVERT: A  471 VAL cc_start: 0.8051 (t) cc_final: 0.7827 (m)
REVERT: A  607 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7774 (t80)
REVERT: B   61 LEU cc_start: 0.8379 (pt) cc_final: 0.8087 (tt)
REVERT: B  106 ASP cc_start: 0.8690 (t0) cc_final: 0.8146 (t0)
REVERT: B  119 SER cc_start: 0.9126 (m) cc_final: 0.8201 (p)
REVERT: B  338 LEU cc_start: 0.9067 (mt) cc_final: 0.8741 (mt)
REVERT: B  503 MET cc_start: 0.8499 (mmm) cc_final: 0.8247 (mmm)
  outliers start: 48
  outliers final: 36
  residues processed: 135
  average time/residue: 0.0675
  time to fit residues: 14.0819
Evaluate side-chains
  133 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 94
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  422 GLN
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  478 SER
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  597 PHE
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  357 GLU
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  542 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
B 491 HIS
** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.104036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.081517 restraints weight = 26264.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.083443 restraints weight = 17763.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.084092 restraints weight = 12668.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.084487 restraints weight = 9693.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.084978 restraints weight = 9301.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8355  Z= 0.130
  Angle     :  0.613   9.131  11367  Z= 0.302
  Chirality :  0.042   0.242   1342
  Planarity :  0.004   0.045   1431
  Dihedral  :  6.479  64.291   1193
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 16.17 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.26), residues: 1049
  helix:  1.28 (0.23), residues: 491
  sheet: -0.44 (0.36), residues: 210
  loop : -1.66 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 381 
 TYR   0.012   0.001   TYR B 479 
 PHE   0.017   0.002   PHE A 458 
 TRP   0.011   0.002   TRP B  22 
 HIS   0.012   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8355)
  covalent geometry    : angle       0.61345 (11367)
  hydrogen bonds       : bond        0.03992 (  461)
  hydrogen bonds       : angle       4.33875 ( 1326)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 96
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6641 (t80)
REVERT: A  399 TYR cc_start: 0.7253 (m-80) cc_final: 0.6981 (m-80)
REVERT: A  607 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7750 (t80)
REVERT: B   61 LEU cc_start: 0.8374 (pt) cc_final: 0.8134 (tt)
  outliers start: 41
  outliers final: 30
  residues processed: 131
  average time/residue: 0.0663
  time to fit residues: 13.3883
Evaluate side-chains
  122 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 90
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  422 GLN
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  357 GLU
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  542 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 56 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0980
   chunk 90 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0060
   chunk 63 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
B 491 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.104650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.082634 restraints weight = 32207.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.083440 restraints weight = 21343.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.084386 restraints weight = 16645.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.086415 restraints weight = 10909.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.086642 restraints weight = 8580.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3277
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3277
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8355  Z= 0.118
  Angle     :  0.617  10.751  11367  Z= 0.301
  Chirality :  0.042   0.342   1342
  Planarity :  0.004   0.044   1431
  Dihedral  :  6.442  65.355   1193
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 16.53 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.26), residues: 1049
  helix:  1.25 (0.23), residues: 497
  sheet: -0.35 (0.37), residues: 210
  loop : -1.58 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 381 
 TYR   0.011   0.001   TYR B 479 
 PHE   0.016   0.002   PHE A 141 
 TRP   0.010   0.002   TRP B  22 
 HIS   0.011   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8355)
  covalent geometry    : angle       0.61664 (11367)
  hydrogen bonds       : bond        0.03895 (  461)
  hydrogen bonds       : angle       4.32624 ( 1326)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 97
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6969 (OUTLIER) cc_final: 0.6652 (t80)
REVERT: A  607 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7672 (t80)
REVERT: B  106 ASP cc_start: 0.8687 (t0) cc_final: 0.8166 (t0)
  outliers start: 43
  outliers final: 34
  residues processed: 132
  average time/residue: 0.0682
  time to fit residues: 13.9375
Evaluate side-chains
  127 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 91
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  422 GLN
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  597 PHE
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  357 GLU
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  542 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
B 346 HIS
B 419 ASN
B 491 HIS
** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.104326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.082982 restraints weight = 23350.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.084172 restraints weight = 16191.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.084990 restraints weight = 13629.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.085993 restraints weight = 9503.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.086212 restraints weight = 8268.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3263
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.4035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8355  Z= 0.130
  Angle     :  0.618  11.251  11367  Z= 0.303
  Chirality :  0.042   0.219   1342
  Planarity :  0.004   0.046   1431
  Dihedral  :  6.399  63.550   1193
  Min Nonbonded Distance : 1.820

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 17.00 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.26), residues: 1049
  helix:  1.28 (0.23), residues: 497
  sheet: -0.22 (0.37), residues: 210
  loop : -1.55 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 381 
 TYR   0.013   0.001   TYR A 372 
 PHE   0.015   0.002   PHE A 458 
 TRP   0.009   0.002   TRP B  22 
 HIS   0.011   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8355)
  covalent geometry    : angle       0.61790 (11367)
  hydrogen bonds       : bond        0.03880 (  461)
  hydrogen bonds       : angle       4.31502 ( 1326)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 94
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6653 (t80)
REVERT: A  399 TYR cc_start: 0.7324 (m-80) cc_final: 0.7059 (m-80)
REVERT: A  607 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7642 (t80)
REVERT: B  330 LEU cc_start: 0.9078 (mt) cc_final: 0.8787 (tp)
  outliers start: 39
  outliers final: 34
  residues processed: 125
  average time/residue: 0.0701
  time to fit residues: 13.4182
Evaluate side-chains
  128 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 92
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  422 GLN
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  597 PHE
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  357 GLU
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 86 optimal weight:    0.0870
   chunk 50 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 99 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
B 346 HIS
B 491 HIS
** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.104314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.081922 restraints weight = 34552.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.083156 restraints weight = 22007.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.083752 restraints weight = 17925.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.085897 restraints weight = 11327.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.086039 restraints weight = 8250.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.172   8355  Z= 0.172
  Angle     :  0.951  59.180  11367  Z= 0.542
  Chirality :  0.043   0.364   1342
  Planarity :  0.005   0.090   1431
  Dihedral  :  6.455  63.577   1193
  Min Nonbonded Distance : 1.598

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 16.53 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.26), residues: 1049
  helix:  1.34 (0.23), residues: 494
  sheet: -0.21 (0.37), residues: 210
  loop : -1.57 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 381 
 TYR   0.011   0.001   TYR B 479 
 PHE   0.021   0.002   PHE B 457 
 TRP   0.008   0.001   TRP B  22 
 HIS   0.010   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8355)
  covalent geometry    : angle       0.95103 (11367)
  hydrogen bonds       : bond        0.03909 (  461)
  hydrogen bonds       : angle       4.31347 ( 1326)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 92
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6668 (t80)
REVERT: A  399 TYR cc_start: 0.7356 (m-80) cc_final: 0.7070 (m-80)
REVERT: A  607 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7656 (t80)
REVERT: B  106 ASP cc_start: 0.8703 (t0) cc_final: 0.8122 (t0)
  outliers start: 42
  outliers final: 37
  residues processed: 127
  average time/residue: 0.0687
  time to fit residues: 13.3857
Evaluate side-chains
  130 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 91
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  505 MET
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  597 PHE
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  357 GLU
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 346 HIS
B 491 HIS
** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.104351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.081888 restraints weight = 27061.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.084148 restraints weight = 18163.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.084694 restraints weight = 12611.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.085049 restraints weight = 9497.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.085490 restraints weight = 8972.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3253
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3253
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.250   8355  Z= 0.215
  Angle     :  0.922  47.003  11367  Z= 0.618
  Chirality :  0.044   0.534   1342
  Planarity :  0.005   0.096   1431
  Dihedral  :  6.455  63.577   1193
  Min Nonbonded Distance : 1.599

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 16.88 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.26), residues: 1049
  helix:  1.34 (0.23), residues: 494
  sheet: -0.21 (0.37), residues: 210
  loop : -1.57 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 381 
 TYR   0.011   0.001   TYR B 479 
 PHE   0.021   0.002   PHE B 457 
 TRP   0.008   0.001   TRP B  22 
 HIS   0.010   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 8355)
  covalent geometry    : angle       0.92245 (11367)
  hydrogen bonds       : bond        0.03909 (  461)
  hydrogen bonds       : angle       4.31347 ( 1326)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 91
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6674 (t80)
REVERT: A  399 TYR cc_start: 0.7361 (m-80) cc_final: 0.7070 (m-80)
REVERT: A  607 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7662 (t80)
REVERT: B  106 ASP cc_start: 0.8744 (t0) cc_final: 0.8166 (t0)
  outliers start: 39
  outliers final: 36
  residues processed: 123
  average time/residue: 0.0663
  time to fit residues: 12.5375
Evaluate side-chains
  129 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 91
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  505 MET
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  597 PHE
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  357 GLU
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  542 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 81 optimal weight:    0.2980
   chunk 24 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0470
   chunk 97 optimal weight:    0.0980
   chunk 47 optimal weight:    0.0040
   chunk 43 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.1068

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

Flipped N/Q/H residues before XYZ refinement:
B 346 HIS
B 491 HIS
** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.104409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.082946 restraints weight = 22602.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.084621 restraints weight = 14430.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.085208 restraints weight = 12159.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.085656 restraints weight = 8195.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.086048 restraints weight = 7615.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8355  Z= 0.156
  Angle     :  0.950  59.192  11367  Z= 0.524
  Chirality :  0.042   0.265   1342
  Planarity :  0.004   0.066   1431
  Dihedral  :  6.406  63.616   1193
  Min Nonbonded Distance : 1.818

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 16.77 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.26), residues: 1049
  helix:  1.35 (0.23), residues: 494
  sheet: -0.20 (0.37), residues: 210
  loop : -1.57 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 381 
 TYR   0.011   0.001   TYR B 479 
 PHE   0.021   0.002   PHE B 457 
 TRP   0.007   0.001   TRP B  22 
 HIS   0.010   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8355)
  covalent geometry    : angle       0.94977 (11367)
  hydrogen bonds       : bond        0.03908 (  461)
  hydrogen bonds       : angle       4.31445 ( 1326)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1542.22 seconds
wall clock time: 27 minutes 22.57 seconds (1642.57 seconds total)