Starting phenix.real_space_refine
on Tue Feb 11 22:32:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v84_31789/02_2025/7v84_31789.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v84_31789/02_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_31789/02_2025/7v84_31789.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v84_31789/02_2025/7v84_31789.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v84_31789/02_2025/7v84_31789.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v84_31789/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.83, per 1000 atoms: 0.73
  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: 1.76
  Conformation dependent library (CDL) restraints added in 962.9 milliseconds
  

  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: 0.64
  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: 1.72

  Time building geometry restraints manager: 2.04 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:             4.810
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.620
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:12.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.480
-------------------------------------------------------------------------------
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   6819  Z= 0.197
  Angle     :  0.538   7.693   9268  Z= 0.266
  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 

*********************** 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  : 0.733 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 1.3960
  time to fit residues: 73.6645
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  : 0.779 
-------------------------------------------------------------------------------
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:    0.6980
   overall best weight:    0.9900

-------------------------------------------------------------------------------
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 = 0.3061 r_free = 0.3061 target = 0.058819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.047663 restraints weight = 19829.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 3.48
r_work: 0.2655 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6819  Z= 0.225
  Angle     :  0.599   9.897   9268  Z= 0.285
  Chirality :  0.046   0.422   1009
  Planarity :  0.004   0.032   1182
  Dihedral  : 10.752 104.172   1139
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.29 %
    Favored  : 91.86 %
  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: -0.18 (0.29), residues: 793
  helix:  0.85 (0.29), residues: 356
  sheet:  1.04 (0.79), residues: 47
  loop : -1.19 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F  69 
 HIS   0.005   0.001   HIS F 505 
 PHE   0.011   0.001   PHE F 369 
 TYR   0.011   0.001   TYR F 385 
 ARG   0.002   0.000   ARG F 460 

*********************** 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: 0.8729 (pmm-80) cc_final: 0.8299 (pmm-80)
REVERT: A  386 LYS cc_start: 0.9113 (tppp) cc_final: 0.8459 (tmmm)
  outliers start: 6
  outliers final: 2
  residues processed: 43
  average time/residue: 1.5955
  time to fit residues: 72.1300
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  : 0.815 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.058670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.047470 restraints weight = 20011.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 3.53
r_work: 0.2644 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6819  Z= 0.194
  Angle     :  0.553   9.566   9268  Z= 0.264
  Chirality :  0.043   0.401   1009
  Planarity :  0.003   0.027   1182
  Dihedral  :  8.084 100.380   1139
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.29 %
    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: -0.07 (0.29), residues: 793
  helix:  1.03 (0.29), residues: 349
  sheet:  1.06 (0.79), residues: 47
  loop : -1.20 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 477 
 HIS   0.004   0.001   HIS F 401 
 PHE   0.010   0.001   PHE F 369 
 TYR   0.011   0.001   TYR F  50 
 ARG   0.003   0.000   ARG F 460 

*********************** 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
  43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9117 (tppp) cc_final: 0.8459 (tmmm)
  outliers start: 5
  outliers final: 1
  residues processed: 42
  average time/residue: 1.6607
  time to fit residues: 73.2749
Evaluate side-chains
  39 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0050
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0060
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.4210

-------------------------------------------------------------------------------
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 = 0.3065 r_free = 0.3065 target = 0.059123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.048184 restraints weight = 20018.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 3.43
r_work: 0.2676 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6819  Z= 0.139
  Angle     :  0.527   9.602   9268  Z= 0.248
  Chirality :  0.042   0.381   1009
  Planarity :  0.003   0.025   1182
  Dihedral  :  7.296  90.757   1139
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.86 %
    Favored  : 87.43 %
  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:  1.16 (0.29), residues: 354
  sheet:  1.08 (0.79), residues: 47
  loop : -1.09 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   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   0.002   0.000   ARG A 346 

*********************** 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
  44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.796 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9170 (tppp) cc_final: 0.8405 (tmmm)
REVERT: A  390 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9270 (pt)
  outliers start: 5
  outliers final: 1
  residues processed: 43
  average time/residue: 1.6008
  time to fit residues: 72.3341
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  : 0.802 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 9 optimal weight:    0.1980
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 74 optimal weight:    0.3980
   chunk 24 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.2959 r_free = 0.2959 target = 0.056196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.044947 restraints weight = 20187.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.2676 rms_B_bonded: 3.62
r_work: 0.2545 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6819  Z= 0.277
  Angle     :  0.590  10.230   9268  Z= 0.285
  Chirality :  0.045   0.411   1009
  Planarity :  0.003   0.026   1182
  Dihedral  :  7.397  87.093   1139
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.43 %
    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: -0.05 (0.29), residues: 793
  helix:  0.99 (0.29), residues: 362
  sheet:  0.97 (0.77), residues: 49
  loop : -1.20 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 165 
 HIS   0.005   0.001   HIS F 505 
 PHE   0.013   0.001   PHE F 369 
 TYR   0.013   0.001   TYR F 385 
 ARG   0.003   0.000   ARG A 346 

*********************** 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
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9159 (tppp) cc_final: 0.8404 (tmmm)
REVERT: F  249 MET cc_start: 0.8350 (ttt) cc_final: 0.8100 (mtp)
REVERT: F  332 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8843 (ttp)
  outliers start: 12
  outliers final: 2
  residues processed: 50
  average time/residue: 1.3342
  time to fit residues: 70.6236
Evaluate side-chains
  42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
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  332 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0770
   chunk 10 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.6538

-------------------------------------------------------------------------------
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 = 0.2991 r_free = 0.2991 target = 0.057548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.046307 restraints weight = 19987.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.2699 rms_B_bonded: 3.59
r_work: 0.2566 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6819  Z= 0.172
  Angle     :  0.547   9.871   9268  Z= 0.260
  Chirality :  0.043   0.380   1009
  Planarity :  0.003   0.025   1182
  Dihedral  :  7.161  83.941   1139
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.29 %
    Favored  : 85.71 %
  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:  0.06 (0.29), residues: 793
  helix:  1.11 (0.29), residues: 360
  sheet:  1.09 (0.78), residues: 47
  loop : -1.16 (0.29), residues: 386

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 183 
 ARG   0.002   0.000   ARG A 346 

*********************** 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
  45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9123 (tppp) cc_final: 0.8516 (tmmm)
  outliers start: 7
  outliers final: 2
  residues processed: 43
  average time/residue: 1.4599
  time to fit residues: 66.3061
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  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.0570
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0370
   chunk 34 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.5376

-------------------------------------------------------------------------------
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 = 0.3001 r_free = 0.3001 target = 0.058023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.046758 restraints weight = 20003.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 3.61
r_work: 0.2596 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6819  Z= 0.160
  Angle     :  0.550  10.479   9268  Z= 0.260
  Chirality :  0.043   0.372   1009
  Planarity :  0.003   0.024   1182
  Dihedral  :  7.023  80.515   1139
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 14.14 %
    Favored  : 85.43 %
  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:  0.13 (0.30), residues: 793
  helix:  1.16 (0.29), residues: 360
  sheet:  1.09 (0.78), residues: 47
  loop : -1.10 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 477 
 HIS   0.003   0.001   HIS F 401 
 PHE   0.008   0.001   PHE F 369 
 TYR   0.007   0.001   TYR F  50 
 ARG   0.002   0.000   ARG A 346 

*********************** 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
  42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A  346 ARG cc_start: 0.8588 (pmm-80) cc_final: 0.8098 (pmm-80)
REVERT: A  386 LYS cc_start: 0.9138 (tppp) cc_final: 0.8416 (tmmm)
  outliers start: 3
  outliers final: 3
  residues processed: 42
  average time/residue: 1.4920
  time to fit residues: 66.1847
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  : 0.791 
-------------------------------------------------------------------------------
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  249 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0470
   chunk 51 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.5482

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS
F 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.055698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.044526 restraints weight = 20068.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.2666 rms_B_bonded: 3.58
r_work: 0.2535 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6819  Z= 0.326
  Angle     :  0.613  10.463   9268  Z= 0.297
  Chirality :  0.045   0.402   1009
  Planarity :  0.003   0.027   1182
  Dihedral  :  7.241  80.832   1139
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 14.43 %
    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: -0.10 (0.29), residues: 793
  helix:  0.94 (0.28), residues: 367
  sheet:  0.84 (0.75), residues: 51
  loop : -1.24 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 477 
 HIS   0.006   0.001   HIS F 505 
 PHE   0.014   0.001   PHE F 523 
 TYR   0.014   0.001   TYR F 252 
 ARG   0.002   0.000   ARG F 460 

*********************** 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
  46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.9155 (tppp) cc_final: 0.8554 (tmmm)
REVERT: F  249 MET cc_start: 0.8306 (ttt) cc_final: 0.8038 (mtp)
  outliers start: 5
  outliers final: 2
  residues processed: 45
  average time/residue: 1.5515
  time to fit residues: 73.5102
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  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.2974 r_free = 0.2974 target = 0.056911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.045661 restraints weight = 20057.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.2698 rms_B_bonded: 3.60
r_work: 0.2567 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6819  Z= 0.186
  Angle     :  0.570  10.310   9268  Z= 0.272
  Chirality :  0.043   0.374   1009
  Planarity :  0.003   0.045   1182
  Dihedral  :  7.107  78.338   1139
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 14.71 %
    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:  0.07 (0.30), residues: 793
  helix:  1.12 (0.29), residues: 361
  sheet:  1.04 (0.77), residues: 49
  loop : -1.15 (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   0.010   0.001   PHE F 369 
 TYR   0.008   0.001   TYR F  50 
 ARG   0.002   0.000   ARG A 346 

*********************** 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
  41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A  346 ARG cc_start: 0.8658 (pmm-80) cc_final: 0.8192 (pmm-80)
REVERT: A  386 LYS cc_start: 0.9172 (tppp) cc_final: 0.8445 (tmmm)
REVERT: F  249 MET cc_start: 0.8206 (ttt) cc_final: 0.7454 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 41
  average time/residue: 1.5244
  time to fit residues: 65.9997
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  : 0.820 
-------------------------------------------------------------------------------
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 30 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.2933 r_free = 0.2933 target = 0.055230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.044073 restraints weight = 20426.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2653 rms_B_bonded: 3.60
r_work: 0.2521 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6819  Z= 0.320
  Angle     :  0.627  10.793   9268  Z= 0.305
  Chirality :  0.046   0.398   1009
  Planarity :  0.003   0.038   1182
  Dihedral  :  7.345  79.138   1139
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 14.71 %
    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 (0.29), residues: 793
  helix:  0.83 (0.28), residues: 374
  sheet:  0.89 (0.75), residues: 51
  loop : -1.17 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 477 
 HIS   0.006   0.001   HIS F 505 
 PHE   0.013   0.001   PHE F 523 
 TYR   0.012   0.001   TYR F 385 
 ARG   0.003   0.000   ARG F 460 

********************** 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
  40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A  346 ARG cc_start: 0.8669 (pmm-80) cc_final: 0.8170 (pmm-80)
REVERT: A  386 LYS cc_start: 0.9168 (tppp) cc_final: 0.8585 (tmmm)
REVERT: F  249 MET cc_start: 0.8383 (ttt) cc_final: 0.7607 (tmm)
REVERT: F  455 MET cc_start: 0.8755 (tmm) cc_final: 0.8482 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 40
  average time/residue: 1.5768
  time to fit residues: 66.3840
Evaluate side-chains
  39 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 44 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.2968 r_free = 0.2968 target = 0.056706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.045486 restraints weight = 20162.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2692 rms_B_bonded: 3.60
r_work: 0.2560 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6819  Z= 0.182
  Angle     :  0.575  10.524   9268  Z= 0.275
  Chirality :  0.043   0.368   1009
  Planarity :  0.003   0.034   1182
  Dihedral  :  7.151  76.421   1139
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 14.71 %
    Favored  : 84.71 %
  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 (0.30), residues: 793
  helix:  1.02 (0.28), residues: 367
  sheet:  1.07 (0.77), residues: 49
  loop : -1.18 (0.29), residues: 377

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   0.010   0.001   PHE F 369 
 TYR   0.007   0.001   TYR F 385 
 ARG   0.002   0.000   ARG A 346 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3634.04 seconds
wall clock time: 65 minutes 18.72 seconds (3918.72 seconds total)