Starting phenix.real_space_refine
on Sun Apr 27 18:54:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dzz_8943/04_2025/6dzz_8943.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dzz_8943/04_2025/6dzz_8943.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dzz_8943/04_2025/6dzz_8943.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dzz_8943/04_2025/6dzz_8943.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dzz_8943/04_2025/6dzz_8943.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dzz_8943/04_2025/6dzz_8943.cif"
  }
  resolution = 3.6
  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=   0.036 sd=   1.351
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      34      5.16       5
     C    4046      2.51       5
     N     965      2.21       5
     O    1096      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-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6141
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4314
          Classifications: {'peptide': 540}
          Link IDs: {'PTRANS': 23, 'TRANS': 516}
    Chain: "B"
      Number of atoms: 912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 912
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
    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: "A"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 58
          Unusual residues: {'HJM': 1, 'LMT': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.07, per 1000 atoms: 0.83
  Number of scatterers: 6141
  At special positions: 0
  Unit cell: (81.477, 79.008, 115.22, 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      34     16.00
     O    1096      8.00
     N     965      7.00
     C    4046      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 112 " 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 D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 208 "
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 934.0 milliseconds
  

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1402

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 5 sheets defined
      48.3% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 81 through 97
      removed outlier: 3.726A  pdb=" N   LYS A  85 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ASP A  87 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU A  90 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   SER A  91 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY A  94 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR A  95 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 112
      removed outlier: 4.029A  pdb=" N   TYR A 107 " --> pdb=" O   TRP A 103 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ASN A 112 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 128
      removed outlier: 3.676A  pdb=" N   ILE A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ILE A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 144
      removed outlier: 3.744A  pdb=" N   GLU A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LEU A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   HIS A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 154
    Processing helix  chain 'A' and resid 159 through 176
      removed outlier: 3.673A  pdb=" N   TYR A 171 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER A 174 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 189
      removed outlier: 3.614A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR A 186 " --> pdb=" O   TRP A 182 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 187 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 234
      removed outlier: 3.975A  pdb=" N   TYR A 232 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG A 234 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 268
      removed outlier: 3.540A  pdb=" N   LEU A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   CYS A 258 " --> pdb=" O   GLN A 254 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   MET A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ILE A 262 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 285
      removed outlier: 4.265A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 293
    Processing helix  chain 'A' and resid 294 through 302
    Processing helix  chain 'A' and resid 310 through 314
      removed outlier: 4.079A  pdb=" N   LYS A 314 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 337
    Processing helix  chain 'A' and resid 343 through 351
      removed outlier: 3.924A  pdb=" N   SER A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASN A 351 " --> pdb=" O   PHE A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 390
      removed outlier: 3.864A  pdb=" N   LEU A 362 " --> pdb=" O   TYR A 358 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   VAL A 363 " --> pdb=" O   GLN A 359 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS A 369 " --> pdb=" O   SER A 365 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   SER A 375 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ILE A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   PHE A 380 " --> pdb=" O   GLY A 376 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR A 381 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TYR A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   MET A 389 " --> pdb=" O   TYR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 416
      removed outlier: 4.325A  pdb=" N   ALA A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE A 414 " --> pdb=" O   TYR A 410 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ALA A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 441
      removed outlier: 3.630A  pdb=" N   ALA A 424 " --> pdb=" O   SER A 420 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE A 425 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 428 " --> pdb=" O   ALA A 424 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU A 431 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASP A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR A 439 " --> pdb=" O   GLY A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 448
      removed outlier: 3.517A  pdb=" N   THR A 448 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 453
      removed outlier: 3.758A  pdb=" N   ASP A 452 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLU A 453 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 449 through 453'
    Processing helix  chain 'A' and resid 464 through 476
      removed outlier: 3.719A  pdb=" N   VAL A 470 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 490
    Processing helix  chain 'A' and resid 490 through 495
      removed outlier: 3.535A  pdb=" N   TYR A 495 " --> pdb=" O   LEU A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
      removed outlier: 3.567A  pdb=" N   LEU A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A 512 " --> pdb=" O   GLU A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 529
      removed outlier: 3.756A  pdb=" N   PHE A 521 " --> pdb=" O   GLY A 517 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ARG A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LYS A 526 " --> pdb=" O   CYS A 522 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLU A 527 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   MET A 528 " --> pdb=" O   ASP A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 539
      removed outlier: 3.848A  pdb=" N   ILE A 539 " --> pdb=" O   TRP A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 559
      removed outlier: 3.692A  pdb=" N   ILE A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   MET A 558 " --> pdb=" O   CYS A 554 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER A 559 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 583
      removed outlier: 4.040A  pdb=" N   ILE A 576 " --> pdb=" O   TYR A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 596
      removed outlier: 3.530A  pdb=" N   THR A 591 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TYR A 592 " --> pdb=" O   CYS A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 613
      removed outlier: 3.952A  pdb=" N   ILE A 608 " --> pdb=" O   PHE A 604 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ILE A 609 " --> pdb=" O   LYS A 605 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 3.800A  pdb=" N   TYR B  50 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   SER B  51 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 47 through 51'
    Processing helix  chain 'C' and resid 103 through 107
      removed outlier: 3.747A  pdb=" N   THR C 107 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 25
      removed outlier: 3.752A  pdb=" N   ILE B  39 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   MET B 100 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   THR B  97 " --> pdb=" O   ASP B  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79
      removed outlier: 4.059A  pdb=" N   ASP B  76 " --> pdb=" O   TYR B  71 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR B 113 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 30 through 31
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.942A  pdb=" N   TYR C  73 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   TRP C  59 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLN C 113 " --> pdb=" O   ASN C  58 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   PHE C  60 " --> pdb=" O   PHE C 111 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90

    207 hydrogen bonds defined for protein.
    585 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: 1.52

  Time building geometry restraints manager: 1.70 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: 1783
        1.34 -     1.46: 1438
        1.46 -     1.58: 3054
        1.58 -     1.69: 2
        1.69 -     1.81: 49
  Bond restraints: 6326
  Sorted by residual:
  bond pdb=" C2  HJM A 701 "
       pdb=" C8  HJM A 701 "
    ideal  model  delta    sigma   weight residual
    1.490  1.593 -0.103 2.00e-02 2.50e+03 2.63e+01
  bond pdb=" C7  HJM A 701 "
       pdb=" N1  HJM A 701 "
    ideal  model  delta    sigma   weight residual
    1.472  1.566 -0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" C9  HJM A 701 "
       pdb=" N1  HJM A 701 "
    ideal  model  delta    sigma   weight residual
    1.467  1.558 -0.091 2.00e-02 2.50e+03 2.06e+01
  bond pdb=" C18 HJM A 701 "
       pdb=" C19 HJM A 701 "
    ideal  model  delta    sigma   weight residual
    1.407  1.492 -0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" O   HJM A 701 "
       pdb=" C18 HJM A 701 "
    ideal  model  delta    sigma   weight residual
    1.374  1.430 -0.056 2.00e-02 2.50e+03 7.83e+00
  ... (remaining 6321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 8412
        2.38 -     4.75: 155
        4.75 -     7.13: 36
        7.13 -     9.50: 8
        9.50 -    11.88: 3
  Bond angle restraints: 8614
  Sorted by residual:
  angle pdb=" C   ASP A 216 "
        pdb=" N   ASN A 217 "
        pdb=" CA  ASN A 217 "
      ideal   model   delta    sigma   weight residual
     122.46  129.63   -7.17 1.41e+00 5.03e-01 2.58e+01
  angle pdb=" N   GLY A 338 "
        pdb=" CA  GLY A 338 "
        pdb=" C   GLY A 338 "
      ideal   model   delta    sigma   weight residual
     112.34  120.92   -8.58 2.04e+00 2.40e-01 1.77e+01
  angle pdb=" C   GLY B 121 "
        pdb=" N   SER B 122 "
        pdb=" CA  SER B 122 "
      ideal   model   delta    sigma   weight residual
     120.63  127.40   -6.77 1.61e+00 3.86e-01 1.77e+01
  angle pdb=" C   ASN A 569 "
        pdb=" N   TYR A 570 "
        pdb=" CA  TYR A 570 "
      ideal   model   delta    sigma   weight residual
     121.80  131.99  -10.19 2.44e+00 1.68e-01 1.74e+01
  angle pdb=" N   SER B 122 "
        pdb=" CA  SER B 122 "
        pdb=" C   SER B 122 "
      ideal   model   delta    sigma   weight residual
     112.34  117.67   -5.33 1.30e+00 5.92e-01 1.68e+01
  ... (remaining 8609 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.47: 3664
       35.47 -    70.93: 25
       70.93 -   106.40: 8
      106.40 -   141.86: 0
      141.86 -   177.33: 3
  Dihedral angle restraints: 3700
    sinusoidal: 1491
      harmonic: 2209
  Sorted by residual:
  dihedral pdb=" CB  CYS C  43 "
           pdb=" SG  CYS C  43 "
           pdb=" SG  CYS C 112 "
           pdb=" CB  CYS C 112 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  132.33  -39.33     1      1.00e+01 1.00e-02 2.17e+01
  dihedral pdb=" C16 HJM A 701 "
           pdb=" O   HJM A 701 "
           pdb=" C18 HJM A 701 "
           pdb=" C20 HJM A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.78   -1.45 -177.33     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C19 HJM A 701 "
           pdb=" O   HJM A 701 "
           pdb=" C18 HJM A 701 "
           pdb=" C20 HJM A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
       1.28  173.41 -172.13     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 3697 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 843
       0.073 -    0.146: 105
       0.146 -    0.219: 7
       0.219 -    0.292: 2
       0.292 -    0.365: 2
  Chirality restraints: 959
  Sorted by residual:
  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   -2.13   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" C2  HJM A 701 "
            pdb=" C1  HJM A 701 "
            pdb=" C5  HJM A 701 "
            pdb=" C8  HJM A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.28   -0.34 2.00e-01 2.50e+01 2.81e+00
  chirality pdb=" CB  ILE C  99 "
            pdb=" CA  ILE C  99 "
            pdb=" CG1 ILE C  99 "
            pdb=" CG2 ILE C  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.89   -0.24 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 956 not shown)

  Planarity restraints: 1051
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" O   HJM A 701 "   -0.042 2.00e-02 2.50e+03   7.19e-02 1.55e+02
        pdb=" C11 HJM A 701 "    0.051 2.00e-02 2.50e+03
        pdb=" C12 HJM A 701 "    0.086 2.00e-02 2.50e+03
        pdb=" C13 HJM A 701 "   -0.014 2.00e-02 2.50e+03
        pdb=" C15 HJM A 701 "    0.005 2.00e-02 2.50e+03
        pdb=" C16 HJM A 701 "   -0.129 2.00e-02 2.50e+03
        pdb=" C17 HJM A 701 "    0.068 2.00e-02 2.50e+03
        pdb=" C18 HJM A 701 "    0.005 2.00e-02 2.50e+03
        pdb=" C19 HJM A 701 "    0.105 2.00e-02 2.50e+03
        pdb=" C2  HJM A 701 "   -0.018 2.00e-02 2.50e+03
        pdb=" C8  HJM A 701 "    0.013 2.00e-02 2.50e+03
        pdb=" N2  HJM A 701 "   -0.131 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 498 "    0.042 5.00e-02 4.00e+02   6.37e-02 6.50e+00
        pdb=" N   PRO A 499 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 499 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 499 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 560 "    0.041 5.00e-02 4.00e+02   6.18e-02 6.11e+00
        pdb=" N   PRO A 561 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 561 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 561 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1048 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 4
        2.35 -     2.99: 2788
        2.99 -     3.63: 8594
        3.63 -     4.26: 13473
        4.26 -     4.90: 21533
  Nonbonded interactions: 46392
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 107 "
            pdb=" OE2 GLU A 493 "
     model   vdw
     1.715 3.040
  nonbonded pdb=" OH  TYR A 107 "
            pdb=" CD  GLU A 493 "
     model   vdw
     1.910 3.270
  nonbonded pdb=" OH  TYR A 107 "
            pdb=" OE1 GLU A 493 "
     model   vdw
     2.001 3.040
  nonbonded pdb=" CZ  TYR A 107 "
            pdb=" OE2 GLU A 493 "
     model   vdw
     2.262 3.260
  nonbonded pdb=" O5' LMT A 704 "
            pdb=" O6' LMT A 704 "
     model   vdw
     2.358 2.432
  ... (remaining 46387 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.270
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.090
  Find NCS groups from input model:        0.060
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6604
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      :  0.005   0.103   6331  Z= 0.249
  Angle     :  0.851  11.877   8626  Z= 0.428
  Chirality :  0.052   0.365    959
  Planarity :  0.008   0.072   1050
  Dihedral  : 11.997 177.328   2289
  Min Nonbonded Distance : 1.715

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.40 %
    Favored  : 98.45 %
  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: -5.28 (0.22), residues: 762
  helix: -4.59 (0.10), residues: 301
  sheet: -2.47 (0.50), residues: 94
  loop : -2.71 (0.28), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 130 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.035   0.001   PHE A 454 
 TYR   0.015   0.002   TYR C  73 
 ARG   0.012   0.001   ARG A 234 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00546 (    1)
  link_NAG-ASN         : angle       4.85078 (    3)
  link_BETA1-4         : bond        0.00886 (    1)
  link_BETA1-4         : angle       1.48718 (    3)
  hydrogen bonds       : bond        0.33019 (  207)
  hydrogen bonds       : angle       9.64043 (  585)
  SS BOND              : bond        0.00307 (    3)
  SS BOND              : angle       0.93679 (    6)
  covalent geometry    : bond        0.00497 ( 6326)
  covalent geometry    : angle       0.84645 ( 8614)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 217
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 TYR cc_start: 0.8563 (t80) cc_final: 0.8339 (t80)
REVERT: A  145 ASN cc_start: 0.8176 (m110) cc_final: 0.7690 (m-40)
REVERT: A  272 LYS cc_start: 0.6303 (mmtt) cc_final: 0.5992 (pttt)
REVERT: A  326 TRP cc_start: 0.7372 (m-10) cc_final: 0.7098 (m-10)
REVERT: A  385 TYR cc_start: 0.8146 (t80) cc_final: 0.7512 (t80)
REVERT: A  558 MET cc_start: 0.4587 (tpt) cc_final: 0.3420 (mtt)
REVERT: B   50 TYR cc_start: 0.4382 (t80) cc_final: 0.4068 (t80)
REVERT: B  101 GLN cc_start: 0.6951 (mt0) cc_final: 0.6228 (tm-30)
REVERT: B  102 LEU cc_start: 0.8568 (mt) cc_final: 0.8270 (tt)
REVERT: B  108 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7515 (mt-10)
REVERT: B  127 MET cc_start: 0.5917 (mtp) cc_final: 0.5629 (mtm)
REVERT: B  129 TYR cc_start: 0.7339 (m-10) cc_final: 0.6536 (m-80)
REVERT: C   22 ILE cc_start: 0.7416 (mt) cc_final: 0.7206 (mp)
REVERT: C  112 CYS cc_start: 0.4762 (t) cc_final: 0.4471 (t)
REVERT: C  116 LYS cc_start: 0.7015 (tttt) cc_final: 0.6421 (mttt)
  outliers start: 1
  outliers final: 1
  residues processed: 218
  average time/residue: 0.1822
  time to fit residues: 51.2346
Evaluate side-chains
  133 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.0870
   chunk 57 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0020
   chunk 38 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    2.0172

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
A 202 ASN
A 254 GLN
B  25 GLN
C  51 ASN
C 100 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.153450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.134182 restraints weight = 13069.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.138105 restraints weight = 6864.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.140788 restraints weight = 4341.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6946
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6331  Z= 0.163
  Angle     :  0.707  12.547   8626  Z= 0.350
  Chirality :  0.045   0.253    959
  Planarity :  0.006   0.050   1050
  Dihedral  : 10.537 148.626    974
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  :  9.61 %
    Favored  : 85.89 %
  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: -3.84 (0.26), residues: 762
  helix: -2.67 (0.21), residues: 338
  sheet: -2.19 (0.52), residues: 92
  loop : -2.34 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 130 
 HIS   0.004   0.001   HIS C 100 
 PHE   0.033   0.002   PHE A 454 
 TYR   0.019   0.002   TYR A 495 
 ARG   0.005   0.001   ARG A 104 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00391 (    1)
  link_NAG-ASN         : angle       3.92530 (    3)
  link_BETA1-4         : bond        0.00726 (    1)
  link_BETA1-4         : angle       0.91986 (    3)
  hydrogen bonds       : bond        0.04862 (  207)
  hydrogen bonds       : angle       5.42353 (  585)
  SS BOND              : bond        0.00120 (    3)
  SS BOND              : angle       2.12869 (    6)
  covalent geometry    : bond        0.00349 ( 6326)
  covalent geometry    : angle       0.70076 ( 8614)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 TYR cc_start: 0.8506 (t80) cc_final: 0.8011 (t80)
REVERT: A  272 LYS cc_start: 0.6368 (mmtt) cc_final: 0.6007 (pttt)
REVERT: A  526 LYS cc_start: 0.7822 (mttt) cc_final: 0.7323 (ttmm)
REVERT: A  535 TRP cc_start: 0.5795 (t60) cc_final: 0.5574 (t-100)
REVERT: A  558 MET cc_start: 0.4530 (tpt) cc_final: 0.3557 (mtt)
REVERT: A  597 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8763 (pt)
REVERT: B  101 GLN cc_start: 0.7303 (mt0) cc_final: 0.6867 (pt0)
REVERT: B  102 LEU cc_start: 0.8396 (mt) cc_final: 0.8141 (tt)
REVERT: B  129 TYR cc_start: 0.7643 (m-10) cc_final: 0.7191 (m-10)
REVERT: C   44 ARG cc_start: 0.6291 (mmt-90) cc_final: 0.6081 (mmm160)
REVERT: C   61 GLN cc_start: 0.7636 (mt0) cc_final: 0.7157 (mt0)
REVERT: C   69 LYS cc_start: 0.7029 (tmtt) cc_final: 0.6686 (tmtt)
REVERT: C   71 LEU cc_start: 0.8593 (tp) cc_final: 0.8296 (mt)
REVERT: C   86 PHE cc_start: 0.5743 (m-80) cc_final: 0.5269 (m-10)
REVERT: C  116 LYS cc_start: 0.7145 (tttt) cc_final: 0.6356 (ptpt)
  outliers start: 29
  outliers final: 24
  residues processed: 146
  average time/residue: 0.1621
  time to fit residues: 31.8673
Evaluate side-chains
  133 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  360 ASP
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  452 ASP
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  537 TRP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 52 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 71 optimal weight:   10.0000
   chunk 31 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0770
   chunk 46 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   overall best weight:    0.9340

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

Flipped N/Q/H residues before XYZ refinement:
B  24 GLN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.153371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.134206 restraints weight = 13499.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.138123 restraints weight = 7086.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.140821 restraints weight = 4530.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6331  Z= 0.114
  Angle     :  0.628  10.619   8626  Z= 0.306
  Chirality :  0.042   0.269    959
  Planarity :  0.005   0.053   1050
  Dihedral  :  9.972 173.693    974
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 12.71 %
    Favored  : 82.64 %
  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: -2.80 (0.29), residues: 762
  helix: -1.63 (0.25), residues: 342
  sheet: -1.64 (0.54), residues: 90
  loop : -2.04 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 282 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.023   0.001   PHE A 454 
 TYR   0.013   0.001   TYR C  73 
 ARG   0.002   0.000   ARG A 298 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00280 (    1)
  link_NAG-ASN         : angle       3.45632 (    3)
  link_BETA1-4         : bond        0.00383 (    1)
  link_BETA1-4         : angle       0.58267 (    3)
  hydrogen bonds       : bond        0.03902 (  207)
  hydrogen bonds       : angle       4.61423 (  585)
  SS BOND              : bond        0.00161 (    3)
  SS BOND              : angle       1.99673 (    6)
  covalent geometry    : bond        0.00255 ( 6326)
  covalent geometry    : angle       0.62250 ( 8614)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 LYS cc_start: 0.6435 (mmtt) cc_final: 0.5757 (pttt)
REVERT: A  526 LYS cc_start: 0.7874 (mttt) cc_final: 0.7268 (tmtt)
REVERT: A  535 TRP cc_start: 0.5909 (t60) cc_final: 0.5625 (t-100)
REVERT: A  548 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7595 (t80)
REVERT: A  558 MET cc_start: 0.4536 (tpt) cc_final: 0.3567 (mtt)
REVERT: A  597 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8758 (pt)
REVERT: B   38 ARG cc_start: 0.7914 (ttt90) cc_final: 0.7705 (tpt170)
REVERT: B  101 GLN cc_start: 0.7382 (mt0) cc_final: 0.7033 (pt0)
REVERT: B  102 LEU cc_start: 0.8452 (mt) cc_final: 0.8180 (tt)
REVERT: B  125 PHE cc_start: 0.4767 (p90) cc_final: 0.4558 (p90)
REVERT: B  129 TYR cc_start: 0.7582 (m-10) cc_final: 0.6723 (m-80)
REVERT: C   44 ARG cc_start: 0.6321 (mmt-90) cc_final: 0.6088 (mmm160)
REVERT: C   61 GLN cc_start: 0.7706 (mt0) cc_final: 0.7301 (mt0)
REVERT: C   69 LYS cc_start: 0.6988 (tmtt) cc_final: 0.6647 (tmtt)
REVERT: C   71 LEU cc_start: 0.8605 (tp) cc_final: 0.8304 (mt)
REVERT: C   86 PHE cc_start: 0.5841 (m-80) cc_final: 0.5447 (m-10)
REVERT: C  116 LYS cc_start: 0.7066 (tttt) cc_final: 0.6402 (ptpt)
  outliers start: 30
  outliers final: 19
  residues processed: 136
  average time/residue: 0.1672
  time to fit residues: 31.0503
Evaluate side-chains
  125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  211 ASN
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  360 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  452 ASP
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  537 TRP
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:    0.0870
   chunk 1 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 254 GLN
** C  62 GLN ** 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 = 0.4133 r_free = 0.4133 target = 0.154120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.135058 restraints weight = 13636.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.138946 restraints weight = 7103.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.141648 restraints weight = 4536.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.4309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6331  Z= 0.103
  Angle     :  0.583   9.437   8626  Z= 0.286
  Chirality :  0.041   0.268    959
  Planarity :  0.004   0.041   1050
  Dihedral  :  9.468 169.685    974
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 14.26 %
    Favored  : 81.55 %
  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: -2.15 (0.30), residues: 762
  helix: -0.92 (0.28), residues: 329
  sheet: -1.32 (0.53), residues: 91
  loop : -1.89 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 282 
 HIS   0.002   0.001   HIS C 100 
 PHE   0.018   0.001   PHE A 454 
 TYR   0.011   0.001   TYR C  73 
 ARG   0.003   0.000   ARG A 298 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00344 (    1)
  link_NAG-ASN         : angle       3.26705 (    3)
  link_BETA1-4         : bond        0.00381 (    1)
  link_BETA1-4         : angle       0.47112 (    3)
  hydrogen bonds       : bond        0.03254 (  207)
  hydrogen bonds       : angle       4.31976 (  585)
  SS BOND              : bond        0.00112 (    3)
  SS BOND              : angle       1.90142 (    6)
  covalent geometry    : bond        0.00237 ( 6326)
  covalent geometry    : angle       0.57790 ( 8614)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6303 (mpp)
REVERT: A  215 GLU cc_start: 0.7056 (mp0) cc_final: 0.6342 (pm20)
REVERT: A  526 LYS cc_start: 0.7892 (mttt) cc_final: 0.7238 (tmtt)
REVERT: A  535 TRP cc_start: 0.6005 (t60) cc_final: 0.5672 (t-100)
REVERT: A  548 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7558 (t80)
REVERT: A  558 MET cc_start: 0.4546 (tpt) cc_final: 0.3627 (mtt)
REVERT: A  597 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8677 (pt)
REVERT: B   76 ASP cc_start: 0.7626 (m-30) cc_final: 0.6615 (m-30)
REVERT: B  101 GLN cc_start: 0.7294 (mt0) cc_final: 0.6879 (pt0)
REVERT: B  102 LEU cc_start: 0.8524 (mt) cc_final: 0.8193 (tt)
REVERT: B  125 PHE cc_start: 0.4652 (p90) cc_final: 0.4443 (p90)
REVERT: C   44 ARG cc_start: 0.6249 (mmt-90) cc_final: 0.6013 (mmm160)
REVERT: C   69 LYS cc_start: 0.6936 (tmtt) cc_final: 0.6598 (tmtt)
REVERT: C   71 LEU cc_start: 0.8583 (tp) cc_final: 0.8178 (mt)
REVERT: C  116 LYS cc_start: 0.6991 (tttt) cc_final: 0.6312 (ptpt)
  outliers start: 27
  outliers final: 16
  residues processed: 126
  average time/residue: 0.1638
  time to fit residues: 27.6903
Evaluate side-chains
  124 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  211 ASN
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  360 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  452 ASP
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  579 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   chunk 62 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 114 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.148043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.129746 restraints weight = 12957.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.133509 restraints weight = 6504.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.136108 restraints weight = 4065.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.4815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6331  Z= 0.128
  Angle     :  0.621  10.820   8626  Z= 0.304
  Chirality :  0.042   0.277    959
  Planarity :  0.004   0.042   1050
  Dihedral  :  9.363 167.556    974
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 14.57 %
    Favored  : 80.31 %
  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: -1.79 (0.30), residues: 762
  helix: -0.61 (0.28), residues: 332
  sheet: -0.82 (0.56), residues: 85
  loop : -1.80 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 541 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.014   0.001   PHE A 133 
 TYR   0.011   0.001   TYR A 570 
 ARG   0.003   0.000   ARG A 298 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00070 (    1)
  link_NAG-ASN         : angle       3.47828 (    3)
  link_BETA1-4         : bond        0.00343 (    1)
  link_BETA1-4         : angle       0.69272 (    3)
  hydrogen bonds       : bond        0.03318 (  207)
  hydrogen bonds       : angle       4.22141 (  585)
  SS BOND              : bond        0.00157 (    3)
  SS BOND              : angle       1.80859 (    6)
  covalent geometry    : bond        0.00296 ( 6326)
  covalent geometry    : angle       0.61605 ( 8614)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6366 (mpp)
REVERT: A  215 GLU cc_start: 0.6952 (mp0) cc_final: 0.6553 (mp0)
REVERT: A  475 PHE cc_start: 0.6357 (m-80) cc_final: 0.6027 (m-80)
REVERT: A  526 LYS cc_start: 0.7885 (mttt) cc_final: 0.7260 (tmtt)
REVERT: A  528 MET cc_start: 0.7820 (pmm) cc_final: 0.7543 (pmm)
REVERT: A  548 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7586 (t80)
REVERT: A  558 MET cc_start: 0.4573 (tpt) cc_final: 0.3578 (mtt)
REVERT: B   76 ASP cc_start: 0.7530 (m-30) cc_final: 0.6850 (m-30)
REVERT: B  101 GLN cc_start: 0.7420 (mt0) cc_final: 0.7184 (pt0)
REVERT: B  102 LEU cc_start: 0.8524 (mt) cc_final: 0.8243 (tt)
REVERT: B  125 PHE cc_start: 0.5131 (p90) cc_final: 0.4896 (p90)
REVERT: C   44 ARG cc_start: 0.6183 (mmt-90) cc_final: 0.5928 (mmm-85)
REVERT: C   69 LYS cc_start: 0.7139 (tmtt) cc_final: 0.6827 (tmtt)
REVERT: C   71 LEU cc_start: 0.8614 (tp) cc_final: 0.8310 (mt)
REVERT: C  116 LYS cc_start: 0.7185 (tttt) cc_final: 0.6376 (ptpt)
  outliers start: 33
  outliers final: 23
  residues processed: 133
  average time/residue: 0.1607
  time to fit residues: 29.0161
Evaluate side-chains
  128 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  211 ASN
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  360 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  452 ASP
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  537 TRP
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  579 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue  102 MET
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 54 optimal weight:   20.0000
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 68 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 72 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    2.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 101 GLN
** C  62 GLN ** 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 = 0.4103 r_free = 0.4103 target = 0.147790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.129952 restraints weight = 13295.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.133592 restraints weight = 7008.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.136168 restraints weight = 4505.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.5431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6331  Z= 0.148
  Angle     :  0.659  13.103   8626  Z= 0.322
  Chirality :  0.043   0.284    959
  Planarity :  0.004   0.040   1050
  Dihedral  :  9.649 172.868    974
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 15.66 %
    Favored  : 78.91 %
  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: -1.82 (0.30), residues: 762
  helix: -0.66 (0.27), residues: 342
  sheet: -0.91 (0.52), residues: 99
  loop : -1.81 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 151 
 HIS   0.001   0.000   HIS C 100 
 PHE   0.012   0.001   PHE A 566 
 TYR   0.012   0.001   TYR C  52 
 ARG   0.004   0.001   ARG A 564 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00101 (    1)
  link_NAG-ASN         : angle       3.61362 (    3)
  link_BETA1-4         : bond        0.00274 (    1)
  link_BETA1-4         : angle       0.59907 (    3)
  hydrogen bonds       : bond        0.03368 (  207)
  hydrogen bonds       : angle       4.36409 (  585)
  SS BOND              : bond        0.00171 (    3)
  SS BOND              : angle       1.95865 (    6)
  covalent geometry    : bond        0.00346 ( 6326)
  covalent geometry    : angle       0.65370 ( 8614)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 113
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.6354 (mpp)
REVERT: A  215 GLU cc_start: 0.6918 (mp0) cc_final: 0.6578 (mp0)
REVERT: A  254 GLN cc_start: 0.7491 (tt0) cc_final: 0.6492 (tp-100)
REVERT: A  318 GLN cc_start: 0.6114 (tp40) cc_final: 0.5434 (tp40)
REVERT: A  465 PHE cc_start: 0.7359 (p90) cc_final: 0.7095 (p90)
REVERT: A  526 LYS cc_start: 0.7957 (mttt) cc_final: 0.7343 (tmtt)
REVERT: A  548 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7636 (t80)
REVERT: A  558 MET cc_start: 0.4564 (tpt) cc_final: 0.3693 (mtt)
REVERT: B   76 ASP cc_start: 0.7327 (m-30) cc_final: 0.6700 (m-30)
REVERT: C   44 ARG cc_start: 0.6090 (mmt-90) cc_final: 0.5855 (mmm160)
REVERT: C   61 GLN cc_start: 0.7953 (mt0) cc_final: 0.7724 (mt0)
REVERT: C   69 LYS cc_start: 0.7155 (tmtt) cc_final: 0.6928 (tmtt)
REVERT: C   71 LEU cc_start: 0.8645 (tp) cc_final: 0.8340 (mt)
REVERT: C  116 LYS cc_start: 0.7332 (tttt) cc_final: 0.6578 (ptpt)
  outliers start: 35
  outliers final: 29
  residues processed: 135
  average time/residue: 0.1580
  time to fit residues: 29.1028
Evaluate side-chains
  136 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  211 ASN
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  360 ASP
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  452 ASP
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  537 TRP
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  579 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 60 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 64 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 101 GLN
** C  62 GLN ** 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 = 0.4101 r_free = 0.4101 target = 0.147255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.129509 restraints weight = 13439.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.133164 restraints weight = 7041.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.135700 restraints weight = 4510.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.5709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6331  Z= 0.143
  Angle     :  0.662  10.465   8626  Z= 0.321
  Chirality :  0.043   0.283    959
  Planarity :  0.005   0.082   1050
  Dihedral  :  9.895 179.416    974
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 17.21 %
    Favored  : 76.90 %
  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: -1.69 (0.30), residues: 762
  helix: -0.56 (0.28), residues: 343
  sheet: -0.86 (0.51), residues: 97
  loop : -1.73 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 151 
 HIS   0.003   0.001   HIS C 100 
 PHE   0.012   0.001   PHE C  95 
 TYR   0.013   0.001   TYR A 289 
 ARG   0.004   0.000   ARG A 234 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00059 (    1)
  link_NAG-ASN         : angle       3.62696 (    3)
  link_BETA1-4         : bond        0.00532 (    1)
  link_BETA1-4         : angle       0.76734 (    3)
  hydrogen bonds       : bond        0.03286 (  207)
  hydrogen bonds       : angle       4.26480 (  585)
  SS BOND              : bond        0.00187 (    3)
  SS BOND              : angle       1.83166 (    6)
  covalent geometry    : bond        0.00332 ( 6326)
  covalent geometry    : angle       0.65700 ( 8614)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 108
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.6303 (mpp)
REVERT: A  215 GLU cc_start: 0.6841 (mp0) cc_final: 0.6578 (mp0)
REVERT: A  254 GLN cc_start: 0.7464 (tt0) cc_final: 0.6455 (tp-100)
REVERT: A  318 GLN cc_start: 0.6208 (tp40) cc_final: 0.5510 (tp40)
REVERT: A  465 PHE cc_start: 0.7500 (p90) cc_final: 0.7247 (p90)
REVERT: A  526 LYS cc_start: 0.8035 (mttt) cc_final: 0.7390 (tmtt)
REVERT: A  548 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7620 (t80)
REVERT: A  558 MET cc_start: 0.4546 (tpt) cc_final: 0.3634 (mtt)
REVERT: A  570 TYR cc_start: 0.6336 (OUTLIER) cc_final: 0.5033 (m-80)
REVERT: B   76 ASP cc_start: 0.7360 (m-30) cc_final: 0.6697 (m-30)
REVERT: C   61 GLN cc_start: 0.7979 (mt0) cc_final: 0.7776 (mt0)
REVERT: C   69 LYS cc_start: 0.7128 (tmtt) cc_final: 0.6905 (tmtt)
REVERT: C   71 LEU cc_start: 0.8620 (tp) cc_final: 0.8363 (mt)
REVERT: C  116 LYS cc_start: 0.7318 (tttt) cc_final: 0.6599 (ptpt)
  outliers start: 38
  outliers final: 28
  residues processed: 134
  average time/residue: 0.1570
  time to fit residues: 28.7582
Evaluate side-chains
  134 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  211 ASN
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  360 ASP
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  452 ASP
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  537 TRP
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  570 TYR
Chi-restraints excluded: chain A residue  579 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  102 MET
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.146585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.129466 restraints weight = 12979.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.133290 restraints weight = 6458.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.135834 restraints weight = 3951.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.5919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6331  Z= 0.136
  Angle     :  0.645  10.198   8626  Z= 0.314
  Chirality :  0.042   0.282    959
  Planarity :  0.005   0.076   1050
  Dihedral  :  9.640 174.601    972
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 18.29 %
    Favored  : 76.59 %
  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: -1.52 (0.30), residues: 762
  helix: -0.33 (0.28), residues: 340
  sheet: -1.01 (0.49), residues: 101
  loop : -1.67 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 541 
 HIS   0.005   0.001   HIS C 100 
 PHE   0.026   0.001   PHE A 341 
 TYR   0.010   0.001   TYR C  52 
 ARG   0.003   0.000   ARG A 298 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00108 (    1)
  link_NAG-ASN         : angle       3.58601 (    3)
  link_BETA1-4         : bond        0.00272 (    1)
  link_BETA1-4         : angle       0.62546 (    3)
  hydrogen bonds       : bond        0.03216 (  207)
  hydrogen bonds       : angle       4.16912 (  585)
  SS BOND              : bond        0.00206 (    3)
  SS BOND              : angle       1.80776 (    6)
  covalent geometry    : bond        0.00317 ( 6326)
  covalent geometry    : angle       0.64058 ( 8614)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 110
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6225 (mpp)
REVERT: A  215 GLU cc_start: 0.6987 (mp0) cc_final: 0.6696 (mp0)
REVERT: A  254 GLN cc_start: 0.7412 (tt0) cc_final: 0.6398 (tp-100)
REVERT: A  318 GLN cc_start: 0.6368 (tp40) cc_final: 0.5628 (tp40)
REVERT: A  465 PHE cc_start: 0.7433 (p90) cc_final: 0.7111 (p90)
REVERT: A  526 LYS cc_start: 0.8066 (mttt) cc_final: 0.7370 (tmtt)
REVERT: A  548 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7605 (t80)
REVERT: A  558 MET cc_start: 0.4572 (tpt) cc_final: 0.3737 (mtt)
REVERT: B   76 ASP cc_start: 0.7355 (m-30) cc_final: 0.6670 (m-30)
REVERT: C   44 ARG cc_start: 0.5937 (mmm-85) cc_final: 0.5348 (mmm160)
REVERT: C   61 GLN cc_start: 0.7961 (mt0) cc_final: 0.7757 (mt0)
REVERT: C   71 LEU cc_start: 0.8632 (tp) cc_final: 0.8347 (mt)
REVERT: C  116 LYS cc_start: 0.7175 (tttt) cc_final: 0.6433 (ptpt)
  outliers start: 33
  outliers final: 27
  residues processed: 132
  average time/residue: 0.1589
  time to fit residues: 28.8123
Evaluate side-chains
  134 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  211 ASN
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  360 ASP
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  452 ASP
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  537 TRP
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  579 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  102 MET
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 101 GLN
** C  62 GLN ** 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 = 0.4101 r_free = 0.4101 target = 0.147119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.130073 restraints weight = 13065.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.133905 restraints weight = 6509.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.136450 restraints weight = 3985.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.6065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6331  Z= 0.123
  Angle     :  0.650  10.270   8626  Z= 0.317
  Chirality :  0.043   0.278    959
  Planarity :  0.005   0.089   1050
  Dihedral  :  9.234 163.839    972
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 19.07 %
    Favored  : 75.66 %
  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: -1.25 (0.31), residues: 762
  helix: -0.12 (0.28), residues: 336
  sheet: -0.83 (0.50), residues: 101
  loop : -1.50 (0.37), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 458 
 HIS   0.004   0.001   HIS C 100 
 PHE   0.024   0.001   PHE A 341 
 TYR   0.013   0.001   TYR A 289 
 ARG   0.003   0.000   ARG A 298 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00153 (    1)
  link_NAG-ASN         : angle       3.51286 (    3)
  link_BETA1-4         : bond        0.00513 (    1)
  link_BETA1-4         : angle       0.71403 (    3)
  hydrogen bonds       : bond        0.03082 (  207)
  hydrogen bonds       : angle       4.10404 (  585)
  SS BOND              : bond        0.00184 (    3)
  SS BOND              : angle       1.77336 (    6)
  covalent geometry    : bond        0.00288 ( 6326)
  covalent geometry    : angle       0.64576 ( 8614)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 109
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6134 (mpp)
REVERT: A  215 GLU cc_start: 0.6870 (mp0) cc_final: 0.6609 (mp0)
REVERT: A  254 GLN cc_start: 0.7337 (tt0) cc_final: 0.6310 (tp-100)
REVERT: A  318 GLN cc_start: 0.6376 (tp40) cc_final: 0.5721 (tp40)
REVERT: A  465 PHE cc_start: 0.7434 (p90) cc_final: 0.7150 (p90)
REVERT: A  526 LYS cc_start: 0.8029 (mttt) cc_final: 0.7359 (tmtt)
REVERT: A  548 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7614 (t80)
REVERT: A  558 MET cc_start: 0.4599 (tpt) cc_final: 0.3742 (mtt)
REVERT: A  570 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.5316 (m-80)
REVERT: B   76 ASP cc_start: 0.7312 (m-30) cc_final: 0.6616 (m-30)
REVERT: C   44 ARG cc_start: 0.5811 (mmm-85) cc_final: 0.5263 (mmm160)
REVERT: C   69 LYS cc_start: 0.7287 (tmtt) cc_final: 0.6960 (tmtt)
REVERT: C  105 ASP cc_start: 0.8359 (t0) cc_final: 0.8012 (t0)
REVERT: C  116 LYS cc_start: 0.7070 (tttt) cc_final: 0.6363 (ptpt)
  outliers start: 34
  outliers final: 28
  residues processed: 133
  average time/residue: 0.1666
  time to fit residues: 30.3313
Evaluate side-chains
  138 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  211 ASN
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  360 ASP
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  452 ASP
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  570 TYR
Chi-restraints excluded: chain A residue  579 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  102 MET
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0670
   chunk 51 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 17 optimal weight:    0.0970
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8320

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.150505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.132906 restraints weight = 13672.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.136668 restraints weight = 7102.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.139227 restraints weight = 4518.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.6158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6331  Z= 0.108
  Angle     :  0.638  10.357   8626  Z= 0.309
  Chirality :  0.042   0.271    959
  Planarity :  0.005   0.085   1050
  Dihedral  :  8.676 149.648    972
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 20.16 %
    Favored  : 75.66 %
  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: -1.11 (0.31), residues: 762
  helix:  0.04 (0.28), residues: 339
  sheet: -0.83 (0.50), residues: 101
  loop : -1.47 (0.37), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 282 
 HIS   0.005   0.001   HIS C 100 
 PHE   0.019   0.001   PHE A 341 
 TYR   0.010   0.001   TYR C  73 
 ARG   0.003   0.000   ARG A 390 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00282 (    1)
  link_NAG-ASN         : angle       3.28362 (    3)
  link_BETA1-4         : bond        0.00431 (    1)
  link_BETA1-4         : angle       0.61332 (    3)
  hydrogen bonds       : bond        0.02891 (  207)
  hydrogen bonds       : angle       3.92849 (  585)
  SS BOND              : bond        0.00196 (    3)
  SS BOND              : angle       1.75986 (    6)
  covalent geometry    : bond        0.00247 ( 6326)
  covalent geometry    : angle       0.63419 ( 8614)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6088 (mpp)
REVERT: A  254 GLN cc_start: 0.7194 (tt0) cc_final: 0.6135 (tp-100)
REVERT: A  318 GLN cc_start: 0.6333 (tp40) cc_final: 0.5756 (tp40)
REVERT: A  465 PHE cc_start: 0.7374 (p90) cc_final: 0.7074 (p90)
REVERT: A  526 LYS cc_start: 0.8055 (mttt) cc_final: 0.7380 (tmtt)
REVERT: A  548 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7612 (t80)
REVERT: A  558 MET cc_start: 0.4593 (tpt) cc_final: 0.3750 (mtt)
REVERT: B   76 ASP cc_start: 0.7307 (m-30) cc_final: 0.6592 (m-30)
REVERT: C   44 ARG cc_start: 0.5700 (mmm-85) cc_final: 0.5470 (mmm160)
REVERT: C  105 ASP cc_start: 0.8298 (t0) cc_final: 0.8009 (t0)
REVERT: C  116 LYS cc_start: 0.6881 (tttt) cc_final: 0.6316 (ptpt)
  outliers start: 27
  outliers final: 24
  residues processed: 130
  average time/residue: 0.1839
  time to fit residues: 32.8427
Evaluate side-chains
  134 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  211 ASN
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  360 ASP
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  452 ASP
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  579 TYR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   chunk 56 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
B 101 GLN
** C  62 GLN ** 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 = 0.4125 r_free = 0.4125 target = 0.148967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.131382 restraints weight = 13745.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.135141 restraints weight = 7135.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.137635 restraints weight = 4512.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.6259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6331  Z= 0.122
  Angle     :  0.662  10.097   8626  Z= 0.319
  Chirality :  0.042   0.277    959
  Planarity :  0.005   0.084   1050
  Dihedral  :  8.491 144.056    972
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 20.31 %
    Favored  : 75.35 %
  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: -1.00 (0.31), residues: 762
  helix:  0.14 (0.28), residues: 339
  sheet: -0.78 (0.50), residues: 101
  loop : -1.44 (0.37), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 282 
 HIS   0.005   0.001   HIS C 100 
 PHE   0.019   0.001   PHE A 341 
 TYR   0.012   0.001   TYR A 289 
 ARG   0.004   0.000   ARG A 298 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00103 (    1)
  link_NAG-ASN         : angle       3.42224 (    3)
  link_BETA1-4         : bond        0.00316 (    1)
  link_BETA1-4         : angle       0.71435 (    3)
  hydrogen bonds       : bond        0.02944 (  207)
  hydrogen bonds       : angle       3.94853 (  585)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       1.75532 (    6)
  covalent geometry    : bond        0.00285 ( 6326)
  covalent geometry    : angle       0.65761 ( 8614)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3087.19 seconds
wall clock time: 55 minutes 26.77 seconds (3326.77 seconds total)