Starting phenix.real_space_refine
on Thu Jul 24 22:52:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v84_31789/07_2025/7v84_31789.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v84_31789/07_2025/7v84_31789.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v84_31789/07_2025/7v84_31789.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v84_31789/07_2025/7v84_31789.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v84_31789/07_2025/7v84_31789.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v84_31789/07_2025/7v84_31789.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4238      2.51       5
     N    1083      2.21       5
     O    1278      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6636
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1592
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "F"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.43, per 1000 atoms: 0.82
  Number of scatterers: 6636
  At special positions: 0
  Unit cell: (102.3, 74.8, 126.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1278      8.00
     N    1083      7.00
     C    4238      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 133 " - pdb=" SG  CYS F 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 344 " - pdb=" SG  CYS F 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 530 " - pdb=" SG  CYS F 542 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A 331 "
      " NAG B   1 " - " ASN A 343 "
      " NAG C   1 " - " ASN F  90 "
      " NAG D   1 " - " ASN F 103 "
      " NAG E   1 " - " ASN F 322 "
      " NAG F2001 " - " ASN F  53 "
      " NAG F2002 " - " ASN F 432 "
      " NAG G   1 " - " ASN F 546 "
  Time building additional restraints: 2.08
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      52.7% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.507A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.367A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.722A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 53
      removed outlier: 4.030A  pdb=" N   LYS F  26 " --> pdb=" O   GLU F  22 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   THR F  27 " --> pdb=" O   GLU F  23 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE F  28 " --> pdb=" O   GLN F  24 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU F  35 " --> pdb=" O   LYS F  31 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ASP F  38 " --> pdb=" O   HIS F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 56 through 81
      removed outlier: 4.342A  pdb=" N   GLN F  60 " --> pdb=" O   GLU F  56 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ASN F  61 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   MET F  62 " --> pdb=" O   ASN F  58 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   LYS F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER F  77 " --> pdb=" O   LEU F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 90 through 101
      removed outlier: 3.648A  pdb=" N   ALA F  99 " --> pdb=" O   LEU F  95 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU F 100 " --> pdb=" O   GLN F  96 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 109 through 128
    Processing helix  chain 'F' and resid 147 through 152
      removed outlier: 4.084A  pdb=" N   MET F 152 " --> pdb=" O   LEU F 148 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 158 through 172
    Processing helix  chain 'F' and resid 175 through 193
      removed outlier: 4.252A  pdb=" N   LEU F 179 " --> pdb=" O   GLN F 175 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU F 182 " --> pdb=" O   PRO F 178 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   VAL F 185 " --> pdb=" O   GLU F 181 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 198 through 205
      removed outlier: 3.901A  pdb=" N   TYR F 202 " --> pdb=" O   ASP F 198 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 206 through 208
      No H-bonds generated for 'chain 'F' and resid 206 through 208'
    Processing helix  chain 'F' and resid 218 through 229
      removed outlier: 3.887A  pdb=" N   LEU F 222 " --> pdb=" O   SER F 218 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ILE F 223 " --> pdb=" O   ARG F 219 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLU F 224 " --> pdb=" O   GLY F 220 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLU F 227 " --> pdb=" O   ILE F 223 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   HIS F 228 " --> pdb=" O   GLU F 224 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   THR F 229 " --> pdb=" O   ASP F 225 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 252
      removed outlier: 3.728A  pdb=" N   HIS F 239 " --> pdb=" O   PRO F 235 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU F 240 " --> pdb=" O   LEU F 236 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 275 through 279
    Processing helix  chain 'F' and resid 293 through 300
    Processing helix  chain 'F' and resid 303 through 319
      removed outlier: 3.683A  pdb=" N   ILE F 307 " --> pdb=" O   ASP F 303 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE F 308 " --> pdb=" O   ALA F 304 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE F 315 " --> pdb=" O   ALA F 311 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 326 through 331
      removed outlier: 3.580A  pdb=" N   SER F 331 " --> pdb=" O   PHE F 327 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 365 through 385
      removed outlier: 3.904A  pdb=" N   TYR F 385 " --> pdb=" O   TYR F 381 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 389 through 393
      removed outlier: 3.716A  pdb=" N   ARG F 393 " --> pdb=" O   PHE F 390 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 397 through 412
      removed outlier: 4.542A  pdb=" N   HIS F 401 " --> pdb=" O   ASN F 397 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   GLU F 402 " --> pdb=" O   GLU F 398 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA F 403 " --> pdb=" O   GLY F 399 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   MET F 408 " --> pdb=" O   VAL F 404 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   SER F 409 " --> pdb=" O   GLY F 405 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 414 through 421
    Processing helix  chain 'F' and resid 431 through 444
      removed outlier: 3.517A  pdb=" N   GLU F 435 " --> pdb=" O   ASP F 431 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 449 through 466
    Processing helix  chain 'F' and resid 473 through 485
      removed outlier: 3.590A  pdb=" N   TRP F 477 " --> pdb=" O   TRP F 473 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TRP F 478 " --> pdb=" O   MET F 474 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU F 483 " --> pdb=" O   GLU F 479 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 498 through 502
    Processing helix  chain 'F' and resid 503 through 508
      removed outlier: 3.637A  pdb=" N   SER F 507 " --> pdb=" O   LEU F 503 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ASN F 508 " --> pdb=" O   PHE F 504 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 503 through 508'
    Processing helix  chain 'F' and resid 513 through 532
      removed outlier: 3.864A  pdb=" N   THR F 519 " --> pdb=" O   TYR F 515 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU F 520 " --> pdb=" O   TYR F 516 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 538 through 542
      removed outlier: 3.532A  pdb=" N   LYS F 541 " --> pdb=" O   PRO F 538 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 548 through 559
      removed outlier: 3.606A  pdb=" N   LYS F 553 " --> pdb=" O   GLU F 549 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU F 554 " --> pdb=" O   ALA F 550 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   MET F 557 " --> pdb=" O   LYS F 553 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ARG F 559 " --> pdb=" O   PHE F 555 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 565 through 570
    Processing helix  chain 'F' and resid 582 through 588
      removed outlier: 3.552A  pdb=" N   ASN F 586 " --> pdb=" O   ARG F 582 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 588 through 599
      removed outlier: 3.782A  pdb=" N   ASP F 597 " --> pdb=" O   THR F 593 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.598A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'F' and resid 132 through 133
      removed outlier: 3.663A  pdb=" N   VAL F 132 " --> pdb=" O   LEU F 142 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 347 through 352
      removed outlier: 5.981A  pdb=" N   ASP F 355 " --> pdb=" O   LEU F 351 " (cutoff:3.500A)

    261 hydrogen bonds defined for protein.
    735 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: 1.95

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2101
        1.34 -     1.46: 1769
        1.46 -     1.58: 2891
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6819
  Sorted by residual:
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.471 -0.065 2.00e-02 2.50e+03 1.05e+01
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.84e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.06e+00
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.02e+00
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.98e+00
  ... (remaining 6814 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 9059
        1.54 -     3.08: 169
        3.08 -     4.62: 30
        4.62 -     6.15: 9
        6.15 -     7.69: 1
  Bond angle restraints: 9268
  Sorted by residual:
  angle pdb=" N   GLY F 326 "
        pdb=" CA  GLY F 326 "
        pdb=" C   GLY F 326 "
      ideal   model   delta    sigma   weight residual
     113.58  110.08    3.50 1.07e+00 8.73e-01 1.07e+01
  angle pdb=" CA  MET F 557 "
        pdb=" CB  MET F 557 "
        pdb=" CG  MET F 557 "
      ideal   model   delta    sigma   weight residual
     114.10  119.57   -5.47 2.00e+00 2.50e-01 7.48e+00
  angle pdb=" CB  MET F 557 "
        pdb=" CG  MET F 557 "
        pdb=" SD  MET F 557 "
      ideal   model   delta    sigma   weight residual
     112.70  120.39   -7.69 3.00e+00 1.11e-01 6.58e+00
  angle pdb=" C1  NAG B   2 "
        pdb=" O5  NAG B   2 "
        pdb=" C5  NAG B   2 "
      ideal   model   delta    sigma   weight residual
     113.21  118.73   -5.52 3.00e+00 1.11e-01 3.39e+00
  angle pdb=" N   ASP F 335 "
        pdb=" CA  ASP F 335 "
        pdb=" C   ASP F 335 "
      ideal   model   delta    sigma   weight residual
     109.81  113.87   -4.06 2.21e+00 2.05e-01 3.37e+00
  ... (remaining 9263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.59: 3897
       23.59 -    47.17: 245
       47.17 -    70.76: 26
       70.76 -    94.35: 10
       94.35 -   117.94: 15
  Dihedral angle restraints: 4193
    sinusoidal: 1854
      harmonic: 2339
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   43.92   49.08     1      1.00e+01 1.00e-02 3.31e+01
  dihedral pdb=" CB  CYS F 133 "
           pdb=" SG  CYS F 133 "
           pdb=" SG  CYS F 141 "
           pdb=" CB  CYS F 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -120.26   34.26     1      1.00e+01 1.00e-02 1.67e+01
  dihedral pdb=" CA  PRO F 146 "
           pdb=" C   PRO F 146 "
           pdb=" N   GLY F 147 "
           pdb=" CA  GLY F 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.78  -20.22     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 4190 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 988
       0.106 -    0.212: 19
       0.212 -    0.318: 1
       0.318 -    0.424: 0
       0.424 -    0.530: 1
  Chirality restraints: 1009
  Sorted by residual:
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN F 546 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.87   -0.53 2.00e-01 2.50e+01 7.02e+00
  chirality pdb=" C2  NAG B   2 "
            pdb=" C1  NAG B   2 "
            pdb=" C3  NAG B   2 "
            pdb=" N2  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.27   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" C2  NAG D   1 "
            pdb=" C1  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" N2  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.18 2.00e-01 2.50e+01 7.83e-01
  ... (remaining 1006 not shown)

  Planarity restraints: 1190
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE F  72 "   -0.006 2.00e-02 2.50e+03   1.29e-02 1.68e+00
        pdb=" C   PHE F  72 "    0.022 2.00e-02 2.50e+03
        pdb=" O   PHE F  72 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LEU F  73 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F 283 "   -0.021 5.00e-02 4.00e+02   3.12e-02 1.56e+00
        pdb=" N   PRO F 284 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO F 284 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO F 284 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 234 "   -0.019 5.00e-02 4.00e+02   2.96e-02 1.41e+00
        pdb=" N   PRO F 235 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO F 235 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO F 235 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1187 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 462
        2.74 -     3.28: 6514
        3.28 -     3.82: 10579
        3.82 -     4.36: 12110
        4.36 -     4.90: 21228
  Nonbonded interactions: 50893
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F  20 "
            pdb=" OE1 GLU F  23 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG  SER A 349 "
            pdb=" O   LEU A 452 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NE1 TRP F 271 "
            pdb=" O   SER F 502 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" NH1 ARG F 161 "
            pdb=" O   HIS F 265 "
     model   vdw
     2.335 3.120
  ... (remaining 50888 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.100
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:17.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6839  Z= 0.151
  Angle     :  0.560   9.242   9321  Z= 0.271
  Chirality :  0.045   0.530   1009
  Planarity :  0.003   0.031   1182
  Dihedral  : 16.314 117.936   2672
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.29), residues: 793
  helix:  0.79 (0.29), residues: 343
  sheet:  1.04 (0.79), residues: 47
  loop : -1.35 (0.27), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 165 
 HIS   0.005   0.001   HIS F 378 
 PHE   0.008   0.001   PHE F 369 
 TYR   0.006   0.001   TYR F  50 
 ARG   0.007   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00417 (    8)
  link_NAG-ASN         : angle       2.81682 (   24)
  link_BETA1-4         : bond        0.00684 (    5)
  link_BETA1-4         : angle       1.47524 (   15)
  hydrogen bonds       : bond        0.16960 (  261)
  hydrogen bonds       : angle       6.01990 (  735)
  SS BOND              : bond        0.00329 (    7)
  SS BOND              : angle       0.94537 (   14)
  covalent geometry    : bond        0.00304 ( 6819)
  covalent geometry    : angle       0.53821 ( 9268)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.032 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 1.2966
  time to fit residues: 68.5787
Evaluate side-chains
  38 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 20 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0570
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 71 optimal weight:    0.1980
   overall best weight:    0.8900

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS
** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.059120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.047943 restraints weight = 19796.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 3.48
r_work: 0.2660 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.0982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6839  Z= 0.144
  Angle     :  0.616  10.116   9321  Z= 0.288
  Chirality :  0.046   0.415   1009
  Planarity :  0.004   0.032   1182
  Dihedral  : 10.660 103.989   1139
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.14 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.29), residues: 793
  helix:  0.86 (0.29), residues: 356
  sheet:  1.04 (0.79), residues: 47
  loop : -1.18 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F  69 
 HIS   0.005   0.001   HIS F 378 
 PHE   0.010   0.001   PHE A 347 
 TYR   0.011   0.001   TYR F 385 
 ARG   0.002   0.000   ARG F 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00431 (    8)
  link_NAG-ASN         : angle       2.71307 (   24)
  link_BETA1-4         : bond        0.00723 (    5)
  link_BETA1-4         : angle       1.47333 (   15)
  hydrogen bonds       : bond        0.04970 (  261)
  hydrogen bonds       : angle       4.44577 (  735)
  SS BOND              : bond        0.00377 (    7)
  SS BOND              : angle       1.04116 (   14)
  covalent geometry    : bond        0.00325 ( 6819)
  covalent geometry    : angle       0.59786 ( 9268)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.845 
Fit side-chains
REVERT: A  346 ARG cc_start: 0.8722 (pmm-80) cc_final: 0.8292 (pmm-80)
REVERT: A  386 LYS cc_start: 0.9112 (tppp) cc_final: 0.8466 (tmmm)
  outliers start: 6
  outliers final: 2
  residues processed: 43
  average time/residue: 1.5031
  time to fit residues: 68.0426
Evaluate side-chains
  40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  144 LEU
Chi-restraints excluded: chain F residue  522 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.057417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.046264 restraints weight = 20123.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 3.52
r_work: 0.2610 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6839  Z= 0.182
  Angle     :  0.606   9.648   9321  Z= 0.288
  Chirality :  0.045   0.426   1009
  Planarity :  0.003   0.030   1182
  Dihedral  :  8.241 100.742   1139
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 10.43 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.29), residues: 793
  helix:  0.85 (0.28), residues: 362
  sheet:  0.88 (0.77), residues: 49
  loop : -1.25 (0.28), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 477 
 HIS   0.005   0.001   HIS F 505 
 PHE   0.012   0.001   PHE F 369 
 TYR   0.012   0.001   TYR F 385 
 ARG   0.003   0.000   ARG F 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00344 (    8)
  link_NAG-ASN         : angle       2.76272 (   24)
  link_BETA1-4         : bond        0.00723 (    5)
  link_BETA1-4         : angle       1.65014 (   15)
  hydrogen bonds       : bond        0.05287 (  261)
  hydrogen bonds       : angle       4.26996 (  735)
  SS BOND              : bond        0.00463 (    7)
  SS BOND              : angle       1.14593 (   14)
  covalent geometry    : bond        0.00425 ( 6819)
  covalent geometry    : angle       0.58567 ( 9268)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9150 (tppp) cc_final: 0.8482 (tmmm)
  outliers start: 4
  outliers final: 2
  residues processed: 44
  average time/residue: 1.4766
  time to fit residues: 68.5964
Evaluate side-chains
  41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  144 LEU
Chi-restraints excluded: chain F residue  522 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0470
   chunk 78 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    0.3980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS
F 442 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.058419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.047564 restraints weight = 20093.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 3.43
r_work: 0.2655 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6839  Z= 0.105
  Angle     :  0.559   9.569   9321  Z= 0.260
  Chirality :  0.043   0.390   1009
  Planarity :  0.003   0.027   1182
  Dihedral  :  7.431  92.196   1139
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.86 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.29), residues: 793
  helix:  1.08 (0.29), residues: 353
  sheet:  1.10 (0.79), residues: 47
  loop : -1.16 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 477 
 HIS   0.004   0.001   HIS F 401 
 PHE   0.009   0.001   PHE F 369 
 TYR   0.007   0.001   TYR F 207 
 ARG   0.003   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00361 (    8)
  link_NAG-ASN         : angle       2.64774 (   24)
  link_BETA1-4         : bond        0.00598 (    5)
  link_BETA1-4         : angle       2.04985 (   15)
  hydrogen bonds       : bond        0.04075 (  261)
  hydrogen bonds       : angle       4.03238 (  735)
  SS BOND              : bond        0.00395 (    7)
  SS BOND              : angle       1.18404 (   14)
  covalent geometry    : bond        0.00235 ( 6819)
  covalent geometry    : angle       0.53629 ( 9268)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.783 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9182 (tppp) cc_final: 0.8426 (tmmm)
REVERT: A  390 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9328 (pt)
  outliers start: 6
  outliers final: 1
  residues processed: 44
  average time/residue: 1.5567
  time to fit residues: 72.0773
Evaluate side-chains
  40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 74 optimal weight:    0.3980
   chunk 24 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0870
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.058891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.047634 restraints weight = 20071.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 3.53
r_work: 0.2648 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6839  Z= 0.109
  Angle     :  0.562   9.997   9321  Z= 0.260
  Chirality :  0.043   0.385   1009
  Planarity :  0.003   0.026   1182
  Dihedral  :  7.232  87.446   1139
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.14 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.29), residues: 793
  helix:  1.15 (0.29), residues: 355
  sheet:  1.15 (0.79), residues: 47
  loop : -1.10 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 165 
 HIS   0.004   0.001   HIS F 401 
 PHE   0.009   0.001   PHE F 369 
 TYR   0.007   0.001   TYR F 385 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00334 (    8)
  link_NAG-ASN         : angle       2.60188 (   24)
  link_BETA1-4         : bond        0.00557 (    5)
  link_BETA1-4         : angle       2.02053 (   15)
  hydrogen bonds       : bond        0.03996 (  261)
  hydrogen bonds       : angle       3.94475 (  735)
  SS BOND              : bond        0.00365 (    7)
  SS BOND              : angle       1.06529 (   14)
  covalent geometry    : bond        0.00248 ( 6819)
  covalent geometry    : angle       0.54057 ( 9268)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9184 (tppp) cc_final: 0.8403 (tmmm)
REVERT: A  390 LEU cc_start: 0.9561 (pp) cc_final: 0.9336 (pt)
REVERT: F  175 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8606 (pm20)
REVERT: F  249 MET cc_start: 0.8382 (ttt) cc_final: 0.7592 (tmm)
  outliers start: 13
  outliers final: 2
  residues processed: 52
  average time/residue: 1.3489
  time to fit residues: 74.1248
Evaluate side-chains
  41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain F residue  144 LEU
Chi-restraints excluded: chain F residue  175 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0000
   chunk 65 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS
F  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.057823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.046530 restraints weight = 19960.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 3.60
r_work: 0.2576 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6839  Z= 0.123
  Angle     :  0.575  10.172   9321  Z= 0.267
  Chirality :  0.043   0.385   1009
  Planarity :  0.003   0.027   1182
  Dihedral  :  7.133  84.341   1139
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.14 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.29), residues: 793
  helix:  1.14 (0.29), residues: 355
  sheet:  1.14 (0.79), residues: 47
  loop : -1.13 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 165 
 HIS   0.003   0.001   HIS F 505 
 PHE   0.009   0.001   PHE F 369 
 TYR   0.010   0.001   TYR F  50 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00318 (    8)
  link_NAG-ASN         : angle       2.60370 (   24)
  link_BETA1-4         : bond        0.00524 (    5)
  link_BETA1-4         : angle       2.07379 (   15)
  hydrogen bonds       : bond        0.04126 (  261)
  hydrogen bonds       : angle       3.91099 (  735)
  SS BOND              : bond        0.00397 (    7)
  SS BOND              : angle       1.04005 (   14)
  covalent geometry    : bond        0.00284 ( 6819)
  covalent geometry    : angle       0.55376 ( 9268)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9128 (tppp) cc_final: 0.8353 (tmmm)
REVERT: A  390 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9281 (pt)
  outliers start: 7
  outliers final: 2
  residues processed: 45
  average time/residue: 1.4464
  time to fit residues: 68.6426
Evaluate side-chains
  41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 60 optimal weight:    0.0170
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 34 optimal weight:    0.1980
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.8222

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.057411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.046189 restraints weight = 19997.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.2702 rms_B_bonded: 3.59
r_work: 0.2572 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6839  Z= 0.131
  Angle     :  0.591  10.433   9321  Z= 0.275
  Chirality :  0.043   0.383   1009
  Planarity :  0.003   0.026   1182
  Dihedral  :  7.064  81.549   1139
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 13.71 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.29), residues: 793
  helix:  1.10 (0.29), residues: 361
  sheet:  1.12 (0.79), residues: 47
  loop : -1.13 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 477 
 HIS   0.004   0.001   HIS F 505 
 PHE   0.009   0.001   PHE F 369 
 TYR   0.010   0.001   TYR F  50 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00297 (    8)
  link_NAG-ASN         : angle       2.60841 (   24)
  link_BETA1-4         : bond        0.00521 (    5)
  link_BETA1-4         : angle       2.12123 (   15)
  hydrogen bonds       : bond        0.04207 (  261)
  hydrogen bonds       : angle       3.93332 (  735)
  SS BOND              : bond        0.00396 (    7)
  SS BOND              : angle       1.03917 (   14)
  covalent geometry    : bond        0.00304 ( 6819)
  covalent geometry    : angle       0.57008 ( 9268)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9130 (tppp) cc_final: 0.8380 (tmmm)
REVERT: A  390 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9303 (pt)
REVERT: F  249 MET cc_start: 0.8228 (ttt) cc_final: 0.7448 (tmm)
  outliers start: 5
  outliers final: 2
  residues processed: 43
  average time/residue: 1.5281
  time to fit residues: 69.2316
Evaluate side-chains
  41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 57 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.057516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.046268 restraints weight = 19803.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 3.59
r_work: 0.2574 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6839  Z= 0.125
  Angle     :  0.591  10.338   9321  Z= 0.274
  Chirality :  0.043   0.377   1009
  Planarity :  0.003   0.026   1182
  Dihedral  :  7.007  78.969   1139
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 14.57 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.30), residues: 793
  helix:  1.14 (0.29), residues: 361
  sheet:  1.11 (0.79), residues: 47
  loop : -1.13 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 165 
 HIS   0.003   0.001   HIS F 505 
 PHE   0.009   0.001   PHE F 327 
 TYR   0.010   0.001   TYR F  50 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00293 (    8)
  link_NAG-ASN         : angle       2.57695 (   24)
  link_BETA1-4         : bond        0.00517 (    5)
  link_BETA1-4         : angle       2.17667 (   15)
  hydrogen bonds       : bond        0.04109 (  261)
  hydrogen bonds       : angle       3.91196 (  735)
  SS BOND              : bond        0.00394 (    7)
  SS BOND              : angle       1.03003 (   14)
  covalent geometry    : bond        0.00288 ( 6819)
  covalent geometry    : angle       0.56977 ( 9268)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A  346 ARG cc_start: 0.8631 (pmm-80) cc_final: 0.8164 (pmm-80)
REVERT: A  386 LYS cc_start: 0.9116 (tppp) cc_final: 0.8381 (tmmm)
REVERT: A  390 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9293 (pt)
REVERT: F  249 MET cc_start: 0.8198 (ttt) cc_final: 0.7438 (tmm)
  outliers start: 4
  outliers final: 2
  residues processed: 42
  average time/residue: 1.3906
  time to fit residues: 61.7981
Evaluate side-chains
  41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0270
   chunk 15 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0570
   chunk 25 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0050
   overall best weight:    0.2970

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.059904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.048655 restraints weight = 19917.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 3.51
r_work: 0.2682 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6839  Z= 0.094
  Angle     :  0.578  11.414   9321  Z= 0.264
  Chirality :  0.042   0.352   1009
  Planarity :  0.003   0.026   1182
  Dihedral  :  6.711  71.936   1139
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 14.00 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.30), residues: 793
  helix:  1.32 (0.29), residues: 359
  sheet:  1.13 (0.79), residues: 47
  loop : -1.07 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 165 
 HIS   0.005   0.001   HIS A 519 
 PHE   0.007   0.001   PHE F 369 
 TYR   0.007   0.001   TYR F 207 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00384 (    8)
  link_NAG-ASN         : angle       2.43837 (   24)
  link_BETA1-4         : bond        0.00539 (    5)
  link_BETA1-4         : angle       2.31173 (   15)
  hydrogen bonds       : bond        0.03265 (  261)
  hydrogen bonds       : angle       3.82902 (  735)
  SS BOND              : bond        0.00343 (    7)
  SS BOND              : angle       0.96800 (   14)
  covalent geometry    : bond        0.00209 ( 6819)
  covalent geometry    : angle       0.55678 ( 9268)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A  346 ARG cc_start: 0.8626 (pmm-80) cc_final: 0.8173 (pmm-80)
REVERT: A  386 LYS cc_start: 0.9162 (tppp) cc_final: 0.8420 (tmmm)
REVERT: A  390 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9337 (pt)
REVERT: F  249 MET cc_start: 0.8236 (ttt) cc_final: 0.7448 (tmm)
REVERT: F  455 MET cc_start: 0.8752 (tmm) cc_final: 0.8465 (tmm)
  outliers start: 5
  outliers final: 2
  residues processed: 44
  average time/residue: 1.4414
  time to fit residues: 67.0326
Evaluate side-chains
  41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   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 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.055087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.043907 restraints weight = 20445.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.2648 rms_B_bonded: 3.62
r_work: 0.2517 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   6839  Z= 0.238
  Angle     :  0.674  10.144   9321  Z= 0.323
  Chirality :  0.046   0.410   1009
  Planarity :  0.004   0.032   1182
  Dihedral  :  7.195  74.648   1139
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 14.29 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.29), residues: 793
  helix:  0.96 (0.28), residues: 369
  sheet:  0.82 (0.75), residues: 51
  loop : -1.17 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 271 
 HIS   0.008   0.001   HIS F 505 
 PHE   0.015   0.002   PHE F 523 
 TYR   0.016   0.001   TYR F 381 
 ARG   0.003   0.001   ARG F 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00351 (    8)
  link_NAG-ASN         : angle       2.76806 (   24)
  link_BETA1-4         : bond        0.00478 (    5)
  link_BETA1-4         : angle       2.26353 (   15)
  hydrogen bonds       : bond        0.05623 (  261)
  hydrogen bonds       : angle       4.13962 (  735)
  SS BOND              : bond        0.00514 (    7)
  SS BOND              : angle       1.21420 (   14)
  covalent geometry    : bond        0.00555 ( 6819)
  covalent geometry    : angle       0.65316 ( 9268)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9133 (tppp) cc_final: 0.8385 (tmmm)
  outliers start: 5
  outliers final: 2
  residues processed: 43
  average time/residue: 1.4439
  time to fit residues: 65.6231
Evaluate side-chains
  38 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    0.0870
   chunk 44 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.056710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.045563 restraints weight = 20110.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.2696 rms_B_bonded: 3.58
r_work: 0.2565 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6839  Z= 0.123
  Angle     :  0.620  10.845   9321  Z= 0.289
  Chirality :  0.043   0.368   1009
  Planarity :  0.003   0.047   1182
  Dihedral  :  6.981  71.342   1139
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 14.29 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.30), residues: 793
  helix:  1.14 (0.29), residues: 361
  sheet:  0.96 (0.77), residues: 49
  loop : -1.10 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 477 
 HIS   0.003   0.001   HIS F 505 
 PHE   0.011   0.001   PHE F 369 
 TYR   0.008   0.001   TYR A 453 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00291 (    8)
  link_NAG-ASN         : angle       2.62319 (   24)
  link_BETA1-4         : bond        0.00493 (    5)
  link_BETA1-4         : angle       2.32621 (   15)
  hydrogen bonds       : bond        0.04350 (  261)
  hydrogen bonds       : angle       4.01330 (  735)
  SS BOND              : bond        0.00436 (    7)
  SS BOND              : angle       0.87752 (   14)
  covalent geometry    : bond        0.00282 ( 6819)
  covalent geometry    : angle       0.59905 ( 9268)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3899.35 seconds
wall clock time: 67 minutes 47.06 seconds (4067.06 seconds total)