Starting phenix.real_space_refine
on Thu Jul 24 16:45:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vrk_21369/07_2025/6vrk_21369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrk_21369/07_2025/6vrk_21369.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vrk_21369/07_2025/6vrk_21369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrk_21369/07_2025/6vrk_21369.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrk_21369/07_2025/6vrk_21369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrk_21369/07_2025/6vrk_21369.cif"
  }
  resolution = 4.1
  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=  -0.001 sd=   0.975
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Br      1      7.06       5
     S      34      5.16       5
     C    4045      2.51       5
     N     958      2.21       5
     O    1103      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6141
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4311
          Classifications: {'peptide': 541}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 23, 'TRANS': 517}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100}
    Chain: "B"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 924
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 5, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 87
          Unusual residues: {'LMT': 1, 'NAG': 2, 'RFS': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 11.13, per 1000 atoms: 1.81
  Number of scatterers: 6141
  At special positions: 0
  Unit cell: (97.2, 102.384, 82.296, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Br      1     34.99
     S      34     16.00
     O    1103      8.00
     N     958      7.00
     C    4045      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 C  43 " - pdb=" SG  CYS C 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " 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
    NAG-ASN
      " NAG A 701 " - " ASN A 208 "
      " NAG A 702 " - " ASN A 217 "
  Time building additional restraints: 3.62
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 7 sheets defined
      56.3% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 4.271A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A  89 " --> pdb=" O   LYS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 112
      removed outlier: 4.976A  pdb=" N   PHE A 105 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 113 through 116
    Processing helix  chain 'A' and resid 117 through 129
    Processing helix  chain 'A' and resid 129 through 144
    Processing helix  chain 'A' and resid 148 through 154
      removed outlier: 4.000A  pdb=" N   TRP A 151 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 4.016A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 252 through 271
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 4.056A  pdb=" N   LYS A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   TRP A 282 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 300
      removed outlier: 3.724A  pdb=" N   ILE A 290 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 314
      removed outlier: 3.945A  pdb=" N   GLY A 308 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 321
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 4.064A  pdb=" N   TRP A 326 " --> pdb=" O   GLU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 349
    Processing helix  chain 'A' and resid 356 through 390
      removed outlier: 3.653A  pdb=" N   VAL A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 398
      removed outlier: 3.921A  pdb=" N   VAL A 397 " --> pdb=" O   ASP A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 408
    Processing helix  chain 'A' and resid 408 through 416
    Processing helix  chain 'A' and resid 419 through 454
      removed outlier: 4.170A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 478
      removed outlier: 3.538A  pdb=" N   VAL A 469 " --> pdb=" O   PHE A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 495
      removed outlier: 4.287A  pdb=" N   VAL A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 515
    Processing helix  chain 'A' and resid 517 through 529
    Processing helix  chain 'A' and resid 534 through 543
    Processing helix  chain 'A' and resid 543 through 557
    Processing helix  chain 'A' and resid 571 through 584
    Processing helix  chain 'A' and resid 587 through 600
      removed outlier: 4.044A  pdb=" N   THR A 591 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   TYR A 592 " --> pdb=" O   CYS A 588 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE A 593 " --> pdb=" O   ILE A 589 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU A 597 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ILE A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A 599 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR A 600 " --> pdb=" O   ARG A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 613
      removed outlier: 3.653A  pdb=" N   ARG A 607 " --> pdb=" O   THR A 603 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   THR A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 3.978A  pdb=" N   TYR B  51 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 96
    Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565
    Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 26
    Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 41
      removed outlier: 3.646A  pdb=" N   ASP C  90 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 73 through 74
      removed outlier: 6.794A  pdb=" N   TRP C  55 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   TYR C  69 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   VAL C  53 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR C 107 " --> pdb=" O   TYR C  56 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN C  58 " --> pdb=" O   VAL C 105 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL C 105 " --> pdb=" O   GLN C  58 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 30
      removed outlier: 5.743A  pdb=" N   GLU B  29 " --> pdb=" O   THR B 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 38
    Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 68
      removed outlier: 6.627A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER B 118 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL B  56 " --> pdb=" O   TYR B 114 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR B 114 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)

    304 hydrogen bonds defined for protein.
    855 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: 4.53

  Time building geometry restraints manager: 3.96 seconds

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

  Histogram of bond lengths:
        1.23 -     1.36: 1822
        1.36 -     1.49: 1931
        1.49 -     1.63: 2523
        1.63 -     1.76: 0
        1.76 -     1.89: 50
  Bond restraints: 6326
  Sorted by residual:
  bond pdb=" C06 RFS A 704 "
       pdb=" C07 RFS A 704 "
    ideal  model  delta    sigma   weight residual
    1.511  1.602 -0.091 2.00e-02 2.50e+03 2.07e+01
  bond pdb=" C14 RFS A 704 "
       pdb=" O15 RFS A 704 "
    ideal  model  delta    sigma   weight residual
    1.432  1.499 -0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" C16 RFS A 704 "
       pdb=" O15 RFS A 704 "
    ideal  model  delta    sigma   weight residual
    1.362  1.426 -0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" C07 RFS A 704 "
       pdb=" C08 RFS A 704 "
    ideal  model  delta    sigma   weight residual
    1.394  1.456 -0.062 2.00e-02 2.50e+03 9.53e+00
  bond pdb=" C19 RFS A 704 "
       pdb=" C20 RFS A 704 "
    ideal  model  delta    sigma   weight residual
    1.376  1.437 -0.061 2.00e-02 2.50e+03 9.17e+00
  ... (remaining 6321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 8493
        2.32 -     4.64: 98
        4.64 -     6.97: 18
        6.97 -     9.29: 9
        9.29 -    11.61: 1
  Bond angle restraints: 8619
  Sorted by residual:
  angle pdb=" C   VAL B 120 "
        pdb=" N   ARG B 121 "
        pdb=" CA  ARG B 121 "
      ideal   model   delta    sigma   weight residual
     121.80  133.41  -11.61 2.44e+00 1.68e-01 2.26e+01
  angle pdb=" N   ILE A 587 "
        pdb=" CA  ILE A 587 "
        pdb=" C   ILE A 587 "
      ideal   model   delta    sigma   weight residual
     112.98  107.67    5.31 1.25e+00 6.40e-01 1.81e+01
  angle pdb=" N   ARG B 121 "
        pdb=" CA  ARG B 121 "
        pdb=" C   ARG B 121 "
      ideal   model   delta    sigma   weight residual
     109.81  117.87   -8.06 2.21e+00 2.05e-01 1.33e+01
  angle pdb=" C2  LMT A 703 "
        pdb=" C3  LMT A 703 "
        pdb=" C4  LMT A 703 "
      ideal   model   delta    sigma   weight residual
     117.09  107.89    9.20 3.00e+00 1.11e-01 9.40e+00
  angle pdb=" C   TRP A 458 "
        pdb=" N   ALA A 459 "
        pdb=" CA  ALA A 459 "
      ideal   model   delta    sigma   weight residual
     121.54  127.20   -5.66 1.91e+00 2.74e-01 8.78e+00
  ... (remaining 8614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 3320
       17.44 -    34.87: 300
       34.87 -    52.31: 51
       52.31 -    69.75: 12
       69.75 -    87.18: 9
  Dihedral angle restraints: 3692
    sinusoidal: 1478
      harmonic: 2214
  Sorted by residual:
  dihedral pdb=" CA  ARG B 121 "
           pdb=" C   ARG B 121 "
           pdb=" N   PRO B 122 "
           pdb=" CA  PRO B 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.50   44.50     0      5.00e+00 4.00e-02 7.92e+01
  dihedral pdb=" CB  CYS C  43 "
           pdb=" SG  CYS C  43 "
           pdb=" SG  CYS C 108 "
           pdb=" CB  CYS C 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -33.27  -52.73     1      1.00e+01 1.00e-02 3.79e+01
  dihedral pdb=" CA  TYR B 123 "
           pdb=" C   TYR B 123 "
           pdb=" N   TYR B 124 "
           pdb=" CA  TYR B 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.46   18.54     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 3689 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 724
       0.042 -    0.083: 196
       0.083 -    0.125: 40
       0.125 -    0.167: 2
       0.167 -    0.208: 4
  Chirality restraints: 966
  Sorted by residual:
  chirality pdb=" C5' LMT A 703 "
            pdb=" C4' LMT A 703 "
            pdb=" C6' LMT A 703 "
            pdb=" O5' LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.30   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" C3B LMT A 703 "
            pdb=" C2B LMT A 703 "
            pdb=" C4B LMT A 703 "
            pdb=" O3B LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.29    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" C4' LMT A 703 "
            pdb=" C3' LMT A 703 "
            pdb=" C5' LMT A 703 "
            pdb=" O1B LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.76    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 963 not shown)

  Planarity restraints: 1050
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 121 "   -0.043 5.00e-02 4.00e+02   6.48e-02 6.72e+00
        pdb=" N   PRO B 122 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B 122 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 122 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 548 "    0.012 2.00e-02 2.50e+03   9.45e-03 1.56e+00
        pdb=" CG  PHE A 548 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 548 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 548 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 548 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 548 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 548 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 130 "    0.020 5.00e-02 4.00e+02   3.08e-02 1.51e+00
        pdb=" N   PRO A 131 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 131 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 131 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1047 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1363
        2.78 -     3.31: 6145
        3.31 -     3.84: 10436
        3.84 -     4.37: 11804
        4.37 -     4.90: 20067
  Nonbonded interactions: 49815
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 596 "
            pdb=" OG1 THR A 600 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG1 THR C  51 "
            pdb=" O   SER C  70 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR A 385 "
            pdb=" OD1 ASN A 416 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG1 THR C  83 "
            pdb=" O   THR C  94 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG1 THR A 210 "
            pdb=" OG  SER A 224 "
     model   vdw
     2.268 3.040
  ... (remaining 49810 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:             586.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          15.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     38.530
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.090
  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:             0.010
  Load rotamer database and sin/cos tables:4.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  645.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091   6331  Z= 0.200
  Angle     :  0.688  11.612   8631  Z= 0.351
  Chirality :  0.040   0.208    966
  Planarity :  0.004   0.065   1048
  Dihedral  : 13.927  87.184   2277
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -3.10 (0.27), residues: 758
  helix: -1.01 (0.23), residues: 359
  sheet: -3.09 (0.42), residues: 89
  loop : -2.93 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 103 
 HIS   0.005   0.001   HIS C 111 
 PHE   0.021   0.001   PHE A 548 
 TYR   0.014   0.001   TYR B 123 
 ARG   0.002   0.000   ARG A 152 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00170 (    2)
  link_NAG-ASN         : angle       0.72521 (    6)
  hydrogen bonds       : bond        0.15893 (  304)
  hydrogen bonds       : angle       6.33585 (  855)
  SS BOND              : bond        0.00144 (    3)
  SS BOND              : angle       2.27138 (    6)
  covalent geometry    : bond        0.00392 ( 6326)
  covalent geometry    : angle       0.68599 ( 8619)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7388 (tptp)
REVERT: A  135 MET cc_start: 0.9118 (tmm) cc_final: 0.8871 (tmm)
REVERT: A  152 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6490 (ttm-80)
REVERT: A  229 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8683 (tm-30)
REVERT: A  417 MET cc_start: 0.6445 (mtm) cc_final: 0.5830 (mtm)
REVERT: A  432 ILE cc_start: 0.8960 (mt) cc_final: 0.8707 (mt)
REVERT: A  493 GLU cc_start: 0.6717 (tt0) cc_final: 0.6314 (tt0)
REVERT: A  494 GLU cc_start: 0.8033 (tp30) cc_final: 0.7783 (tt0)
REVERT: A  563 LEU cc_start: 0.8343 (pt) cc_final: 0.6023 (tt)
REVERT: C   48 ASP cc_start: 0.7048 (t0) cc_final: 0.6770 (t0)
REVERT: C   99 GLN cc_start: 0.6118 (mt0) cc_final: 0.5802 (mt0)
REVERT: B   58 GLN cc_start: 0.6535 (tm-30) cc_final: 0.6331 (tm-30)
REVERT: B  109 ASP cc_start: 0.7275 (m-30) cc_final: 0.6728 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.3825
  time to fit residues: 107.5722
Evaluate side-chains
  159 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 31 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 30 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 238 GLN
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.184759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.164315 restraints weight = 11611.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.169042 restraints weight = 6994.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.172413 restraints weight = 4683.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.2280

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= 0.130
  Angle     :  0.630  13.930   8631  Z= 0.320
  Chirality :  0.040   0.152    966
  Planarity :  0.004   0.075   1048
  Dihedral  :  8.165  63.387    961
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  4.77 %
    Favored  : 94.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -2.01 (0.29), residues: 758
  helix: -0.09 (0.26), residues: 368
  sheet: -2.59 (0.46), residues: 89
  loop : -2.47 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 541 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.028   0.002   PHE A 536 
 TYR   0.016   0.001   TYR B  52 
 ARG   0.005   0.001   ARG A 152 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00549 (    2)
  link_NAG-ASN         : angle       0.69237 (    6)
  hydrogen bonds       : bond        0.03605 (  304)
  hydrogen bonds       : angle       4.84389 (  855)
  SS BOND              : bond        0.00744 (    3)
  SS BOND              : angle       1.91065 (    6)
  covalent geometry    : bond        0.00284 ( 6326)
  covalent geometry    : angle       0.62816 ( 8619)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 181
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7693 (tmtt) cc_final: 0.7374 (tptp)
REVERT: A  107 TYR cc_start: 0.7821 (t80) cc_final: 0.7467 (t80)
REVERT: A  180 MET cc_start: 0.8804 (mmp) cc_final: 0.8492 (mmp)
REVERT: A  229 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8482 (tm-30)
REVERT: A  238 GLN cc_start: 0.6382 (tp40) cc_final: 0.6060 (mm-40)
REVERT: A  242 SER cc_start: 0.8466 (p) cc_final: 0.8241 (t)
REVERT: A  417 MET cc_start: 0.6486 (mtm) cc_final: 0.5904 (mtm)
REVERT: A  493 GLU cc_start: 0.6514 (tt0) cc_final: 0.6053 (mt-10)
REVERT: A  563 LEU cc_start: 0.8510 (pt) cc_final: 0.7426 (tt)
REVERT: C  117 THR cc_start: 0.8094 (p) cc_final: 0.7856 (p)
REVERT: B  109 ASP cc_start: 0.7384 (m-30) cc_final: 0.7049 (m-30)
  outliers start: 3
  outliers final: 1
  residues processed: 182
  average time/residue: 0.3031
  time to fit residues: 77.4457
Evaluate side-chains
  148 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 46 optimal weight:    0.2980
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
C  28 HIS
C 109 GLN
** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.182655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.162461 restraints weight = 11876.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.166734 restraints weight = 7440.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.169846 restraints weight = 5150.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6331  Z= 0.147
  Angle     :  0.649  13.801   8631  Z= 0.329
  Chirality :  0.041   0.169    966
  Planarity :  0.004   0.068   1048
  Dihedral  :  8.014  57.471    961
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.70 (0.30), residues: 758
  helix:  0.14 (0.26), residues: 369
  sheet: -2.63 (0.45), residues: 101
  loop : -2.17 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 541 
 HIS   0.002   0.001   HIS C 111 
 PHE   0.032   0.002   PHE A 373 
 TYR   0.018   0.002   TYR A 121 
 ARG   0.003   0.000   ARG C 116 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00107 (    2)
  link_NAG-ASN         : angle       0.93959 (    6)
  hydrogen bonds       : bond        0.03742 (  304)
  hydrogen bonds       : angle       4.76982 (  855)
  SS BOND              : bond        0.00513 (    3)
  SS BOND              : angle       2.27909 (    6)
  covalent geometry    : bond        0.00328 ( 6326)
  covalent geometry    : angle       0.64601 ( 8619)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7715 (tmtt) cc_final: 0.7438 (tptp)
REVERT: A  107 TYR cc_start: 0.7945 (t80) cc_final: 0.7598 (t80)
REVERT: A  152 ARG cc_start: 0.7098 (ttp-110) cc_final: 0.6125 (ttm-80)
REVERT: A  180 MET cc_start: 0.8829 (mmp) cc_final: 0.8459 (mmp)
REVERT: A  187 LEU cc_start: 0.8909 (tp) cc_final: 0.8691 (tp)
REVERT: A  229 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8546 (tm-30)
REVERT: A  242 SER cc_start: 0.8661 (p) cc_final: 0.8342 (t)
REVERT: A  306 TRP cc_start: 0.7197 (p-90) cc_final: 0.6689 (m-10)
REVERT: A  410 TYR cc_start: 0.8559 (t80) cc_final: 0.7837 (t80)
REVERT: A  417 MET cc_start: 0.6561 (mtm) cc_final: 0.6177 (mtm)
REVERT: A  493 GLU cc_start: 0.6500 (tt0) cc_final: 0.6201 (tt0)
REVERT: A  563 LEU cc_start: 0.8510 (pt) cc_final: 0.7414 (tt)
REVERT: A  570 TYR cc_start: 0.7969 (m-80) cc_final: 0.7676 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1735
  time to fit residues: 39.9555
Evaluate side-chains
  146 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 109 GLN
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.180781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.161128 restraints weight = 11978.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.165459 restraints weight = 7525.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.168545 restraints weight = 5161.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6331  Z= 0.147
  Angle     :  0.657  13.187   8631  Z= 0.334
  Chirality :  0.041   0.164    966
  Planarity :  0.004   0.070   1048
  Dihedral  :  7.953  68.237    961
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.71 (0.30), residues: 758
  helix:  0.13 (0.26), residues: 371
  sheet: -2.51 (0.46), residues: 101
  loop : -2.24 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 306 
 HIS   0.006   0.001   HIS C 111 
 PHE   0.037   0.002   PHE C 118 
 TYR   0.019   0.002   TYR B 114 
 ARG   0.005   0.001   ARG A 307 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00194 (    2)
  link_NAG-ASN         : angle       0.92683 (    6)
  hydrogen bonds       : bond        0.03767 (  304)
  hydrogen bonds       : angle       4.79963 (  855)
  SS BOND              : bond        0.00967 (    3)
  SS BOND              : angle       1.59856 (    6)
  covalent geometry    : bond        0.00321 ( 6326)
  covalent geometry    : angle       0.65584 ( 8619)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7741 (tmtt) cc_final: 0.7458 (tptp)
REVERT: A  180 MET cc_start: 0.8807 (mmp) cc_final: 0.8379 (mmp)
REVERT: A  187 LEU cc_start: 0.8864 (tp) cc_final: 0.8644 (tp)
REVERT: A  229 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8558 (tm-30)
REVERT: A  242 SER cc_start: 0.8706 (p) cc_final: 0.8443 (t)
REVERT: A  313 LEU cc_start: 0.8476 (mm) cc_final: 0.8248 (tp)
REVERT: A  314 LYS cc_start: 0.7323 (tttm) cc_final: 0.6886 (mtpt)
REVERT: A  410 TYR cc_start: 0.8486 (t80) cc_final: 0.7678 (t80)
REVERT: A  437 ASP cc_start: 0.7907 (p0) cc_final: 0.7693 (p0)
REVERT: A  493 GLU cc_start: 0.6561 (tt0) cc_final: 0.6239 (tt0)
REVERT: A  528 MET cc_start: 0.7368 (ttm) cc_final: 0.7157 (ttm)
REVERT: A  563 LEU cc_start: 0.8525 (pt) cc_final: 0.7572 (tt)
REVERT: A  570 TYR cc_start: 0.7938 (m-80) cc_final: 0.7681 (m-80)
REVERT: C  111 HIS cc_start: 0.8100 (m-70) cc_final: 0.7862 (m-70)
REVERT: B  108 GLU cc_start: 0.7865 (pp20) cc_final: 0.7639 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1591
  time to fit residues: 36.2564
Evaluate side-chains
  142 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 69 optimal weight:   10.0000
   chunk 25 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 109 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.183344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.163411 restraints weight = 11752.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.167831 restraints weight = 7285.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.170999 restraints weight = 4970.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6331  Z= 0.117
  Angle     :  0.622  10.385   8631  Z= 0.316
  Chirality :  0.040   0.160    966
  Planarity :  0.004   0.070   1048
  Dihedral  :  7.714  74.819    961
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.27 (0.31), residues: 758
  helix:  0.42 (0.27), residues: 367
  sheet: -2.36 (0.46), residues: 101
  loop : -1.86 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 271 
 HIS   0.005   0.001   HIS C 111 
 PHE   0.023   0.001   PHE C 118 
 TYR   0.017   0.001   TYR B 114 
 ARG   0.002   0.000   ARG B 117 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00204 (    2)
  link_NAG-ASN         : angle       0.83901 (    6)
  hydrogen bonds       : bond        0.03456 (  304)
  hydrogen bonds       : angle       4.75296 (  855)
  SS BOND              : bond        0.00314 (    3)
  SS BOND              : angle       1.45889 (    6)
  covalent geometry    : bond        0.00253 ( 6326)
  covalent geometry    : angle       0.62055 ( 8619)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7670 (tmtt) cc_final: 0.7391 (tptp)
REVERT: A  107 TYR cc_start: 0.8055 (t80) cc_final: 0.7790 (t80)
REVERT: A  180 MET cc_start: 0.8840 (mmp) cc_final: 0.8291 (mmp)
REVERT: A  187 LEU cc_start: 0.8858 (tp) cc_final: 0.8647 (tp)
REVERT: A  229 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8579 (tm-30)
REVERT: A  242 SER cc_start: 0.8648 (p) cc_final: 0.8364 (t)
REVERT: A  313 LEU cc_start: 0.8366 (mm) cc_final: 0.8122 (tp)
REVERT: A  314 LYS cc_start: 0.7317 (tttm) cc_final: 0.6911 (mtpt)
REVERT: A  410 TYR cc_start: 0.8397 (t80) cc_final: 0.7916 (t80)
REVERT: A  494 GLU cc_start: 0.8159 (tp30) cc_final: 0.7717 (tt0)
REVERT: A  528 MET cc_start: 0.7393 (ttm) cc_final: 0.7115 (ttm)
REVERT: A  563 LEU cc_start: 0.8594 (pt) cc_final: 0.6615 (tt)
REVERT: B  108 GLU cc_start: 0.7751 (pp20) cc_final: 0.7541 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1603
  time to fit residues: 37.2171
Evaluate side-chains
  139 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 34 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.183998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.164064 restraints weight = 11555.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.168510 restraints weight = 7141.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.171656 restraints weight = 4869.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          0.3588

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= 0.117
  Angle     :  0.619  10.380   8631  Z= 0.314
  Chirality :  0.040   0.153    966
  Planarity :  0.004   0.070   1048
  Dihedral  :  7.704  78.364    961
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.13 (0.31), residues: 758
  helix:  0.51 (0.27), residues: 368
  sheet: -2.36 (0.44), residues: 101
  loop : -1.71 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  55 
 HIS   0.004   0.001   HIS A 143 
 PHE   0.018   0.001   PHE A 536 
 TYR   0.016   0.001   TYR A 267 
 ARG   0.003   0.000   ARG B 117 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00217 (    2)
  link_NAG-ASN         : angle       0.89167 (    6)
  hydrogen bonds       : bond        0.03504 (  304)
  hydrogen bonds       : angle       4.65230 (  855)
  SS BOND              : bond        0.00417 (    3)
  SS BOND              : angle       1.17839 (    6)
  covalent geometry    : bond        0.00254 ( 6326)
  covalent geometry    : angle       0.61862 ( 8619)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7658 (tmtt) cc_final: 0.7382 (tptp)
REVERT: A  107 TYR cc_start: 0.8015 (t80) cc_final: 0.7754 (t80)
REVERT: A  180 MET cc_start: 0.8840 (mmp) cc_final: 0.8293 (mmp)
REVERT: A  187 LEU cc_start: 0.8862 (tp) cc_final: 0.8660 (tp)
REVERT: A  229 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: A  242 SER cc_start: 0.8611 (p) cc_final: 0.8346 (t)
REVERT: A  313 LEU cc_start: 0.8382 (mm) cc_final: 0.8119 (tp)
REVERT: A  314 LYS cc_start: 0.7318 (tttm) cc_final: 0.6898 (mtpt)
REVERT: A  410 TYR cc_start: 0.8248 (t80) cc_final: 0.7904 (t80)
REVERT: A  437 ASP cc_start: 0.7776 (p0) cc_final: 0.7545 (p0)
REVERT: A  493 GLU cc_start: 0.6974 (tt0) cc_final: 0.5932 (tt0)
REVERT: A  494 GLU cc_start: 0.8360 (tp30) cc_final: 0.7745 (tt0)
REVERT: A  528 MET cc_start: 0.7503 (ttm) cc_final: 0.7209 (ttm)
REVERT: A  563 LEU cc_start: 0.8705 (pt) cc_final: 0.6720 (tt)
REVERT: C   75 TYR cc_start: 0.8094 (t80) cc_final: 0.7849 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1688
  time to fit residues: 38.1924
Evaluate side-chains
  141 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0070
   chunk 63 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.0800

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.182506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.162367 restraints weight = 11939.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.166793 restraints weight = 7432.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.169962 restraints weight = 5078.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6331  Z= 0.129
  Angle     :  0.649  10.553   8631  Z= 0.329
  Chirality :  0.041   0.163    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  7.750  78.677    961
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: 758
  helix:  0.51 (0.27), residues: 367
  sheet: -2.43 (0.43), residues: 101
  loop : -1.63 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP A 541 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.023   0.001   PHE A 536 
 TYR   0.014   0.001   TYR A 358 
 ARG   0.004   0.000   ARG A 307 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00164 (    2)
  link_NAG-ASN         : angle       1.14403 (    6)
  hydrogen bonds       : bond        0.03508 (  304)
  hydrogen bonds       : angle       4.84918 (  855)
  SS BOND              : bond        0.00337 (    3)
  SS BOND              : angle       1.48955 (    6)
  covalent geometry    : bond        0.00287 ( 6326)
  covalent geometry    : angle       0.64777 ( 8619)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7648 (tmtt) cc_final: 0.7308 (tptp)
REVERT: A  107 TYR cc_start: 0.7995 (t80) cc_final: 0.7781 (t80)
REVERT: A  180 MET cc_start: 0.8870 (mmp) cc_final: 0.8284 (mmp)
REVERT: A  187 LEU cc_start: 0.8889 (tp) cc_final: 0.8685 (tp)
REVERT: A  229 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8628 (tm-30)
REVERT: A  242 SER cc_start: 0.8633 (p) cc_final: 0.8383 (t)
REVERT: A  313 LEU cc_start: 0.8460 (mm) cc_final: 0.8142 (tp)
REVERT: A  314 LYS cc_start: 0.7303 (tttm) cc_final: 0.7009 (ttpp)
REVERT: A  410 TYR cc_start: 0.8229 (t80) cc_final: 0.7831 (t80)
REVERT: A  432 ILE cc_start: 0.8777 (mt) cc_final: 0.8530 (mt)
REVERT: A  493 GLU cc_start: 0.6981 (tt0) cc_final: 0.5916 (tt0)
REVERT: A  494 GLU cc_start: 0.8414 (tp30) cc_final: 0.7790 (tt0)
REVERT: A  528 MET cc_start: 0.7512 (ttm) cc_final: 0.7196 (ttm)
REVERT: A  563 LEU cc_start: 0.8688 (pt) cc_final: 0.6694 (tt)
REVERT: C   75 TYR cc_start: 0.8116 (t80) cc_final: 0.7889 (t80)
REVERT: C  111 HIS cc_start: 0.7842 (m-70) cc_final: 0.7635 (m90)
REVERT: B  133 THR cc_start: 0.7844 (p) cc_final: 0.7571 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1517
  time to fit residues: 33.8061
Evaluate side-chains
  140 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 9 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 38 optimal weight:    0.1980
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** 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 = 0.4241 r_free = 0.4241 target = 0.184771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.165105 restraints weight = 11739.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.169340 restraints weight = 7412.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.172371 restraints weight = 5131.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.3946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6331  Z= 0.114
  Angle     :  0.627  10.996   8631  Z= 0.317
  Chirality :  0.041   0.164    966
  Planarity :  0.004   0.071   1048
  Dihedral  :  7.685  81.015    961
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.31), residues: 758
  helix:  0.69 (0.27), residues: 368
  sheet: -2.35 (0.44), residues: 100
  loop : -1.45 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 541 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.029   0.002   PHE A 287 
 TYR   0.021   0.001   TYR A 267 
 ARG   0.002   0.000   ARG A 307 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00361 (    2)
  link_NAG-ASN         : angle       1.05305 (    6)
  hydrogen bonds       : bond        0.03332 (  304)
  hydrogen bonds       : angle       4.76939 (  855)
  SS BOND              : bond        0.00310 (    3)
  SS BOND              : angle       1.59867 (    6)
  covalent geometry    : bond        0.00247 ( 6326)
  covalent geometry    : angle       0.62546 ( 8619)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7634 (tmtt) cc_final: 0.7243 (tptp)
REVERT: A  180 MET cc_start: 0.8861 (mmp) cc_final: 0.8279 (mmp)
REVERT: A  229 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8588 (tm-30)
REVERT: A  242 SER cc_start: 0.8554 (p) cc_final: 0.8302 (t)
REVERT: A  313 LEU cc_start: 0.8347 (mm) cc_final: 0.8054 (tp)
REVERT: A  314 LYS cc_start: 0.7317 (tttm) cc_final: 0.7009 (ttpp)
REVERT: A  410 TYR cc_start: 0.8116 (t80) cc_final: 0.7527 (t80)
REVERT: A  432 ILE cc_start: 0.8796 (mt) cc_final: 0.8593 (mt)
REVERT: A  437 ASP cc_start: 0.7662 (p0) cc_final: 0.7407 (p0)
REVERT: A  493 GLU cc_start: 0.6991 (tt0) cc_final: 0.5975 (tt0)
REVERT: A  494 GLU cc_start: 0.8355 (tp30) cc_final: 0.7851 (tt0)
REVERT: A  528 MET cc_start: 0.7391 (ttm) cc_final: 0.7153 (ttm)
REVERT: A  563 LEU cc_start: 0.8621 (pt) cc_final: 0.6641 (tt)
REVERT: C   75 TYR cc_start: 0.8111 (t80) cc_final: 0.7886 (t80)
REVERT: B   57 LYS cc_start: 0.7000 (tttt) cc_final: 0.6794 (ttmt)
REVERT: B  108 GLU cc_start: 0.7638 (pp20) cc_final: 0.7412 (pp20)
REVERT: B  133 THR cc_start: 0.7849 (p) cc_final: 0.7608 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.1477
  time to fit residues: 33.2444
Evaluate side-chains
  146 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 50 optimal weight:   10.0000
   chunk 61 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.185421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.165575 restraints weight = 11753.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.169847 restraints weight = 7416.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.172937 restraints weight = 5143.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.4104

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= 0.119
  Angle     :  0.650  11.336   8631  Z= 0.324
  Chirality :  0.041   0.155    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  7.597  86.988    961
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.15 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.31), residues: 758
  helix:  0.65 (0.27), residues: 368
  sheet: -2.30 (0.45), residues: 101
  loop : -1.47 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 143 
 PHE   0.026   0.002   PHE A 287 
 TYR   0.026   0.002   TYR B  51 
 ARG   0.007   0.000   ARG B 117 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00226 (    2)
  link_NAG-ASN         : angle       1.03431 (    6)
  hydrogen bonds       : bond        0.03380 (  304)
  hydrogen bonds       : angle       4.77300 (  855)
  SS BOND              : bond        0.00334 (    3)
  SS BOND              : angle       1.39151 (    6)
  covalent geometry    : bond        0.00262 ( 6326)
  covalent geometry    : angle       0.64840 ( 8619)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7617 (tmtt) cc_final: 0.7212 (tptp)
REVERT: A  180 MET cc_start: 0.8852 (mmp) cc_final: 0.8258 (mmp)
REVERT: A  187 LEU cc_start: 0.8868 (tp) cc_final: 0.8660 (tp)
REVERT: A  229 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8597 (tm-30)
REVERT: A  238 GLN cc_start: 0.6161 (tp40) cc_final: 0.5703 (mm-40)
REVERT: A  242 SER cc_start: 0.8525 (p) cc_final: 0.8243 (t)
REVERT: A  313 LEU cc_start: 0.8420 (mm) cc_final: 0.8044 (tp)
REVERT: A  314 LYS cc_start: 0.7278 (tttm) cc_final: 0.6947 (ttpp)
REVERT: A  410 TYR cc_start: 0.7906 (t80) cc_final: 0.7094 (t80)
REVERT: A  432 ILE cc_start: 0.8764 (mt) cc_final: 0.8555 (mt)
REVERT: A  493 GLU cc_start: 0.6946 (tt0) cc_final: 0.6089 (tt0)
REVERT: A  494 GLU cc_start: 0.8374 (tp30) cc_final: 0.7838 (tt0)
REVERT: A  528 MET cc_start: 0.7450 (ttm) cc_final: 0.7180 (ttm)
REVERT: A  563 LEU cc_start: 0.8620 (pt) cc_final: 0.6635 (tt)
REVERT: C   75 TYR cc_start: 0.8048 (t80) cc_final: 0.7830 (t80)
REVERT: C  109 GLN cc_start: 0.7139 (mm110) cc_final: 0.6769 (tp40)
REVERT: C  111 HIS cc_start: 0.7783 (m-70) cc_final: 0.7492 (m90)
REVERT: B  124 TYR cc_start: 0.8209 (p90) cc_final: 0.7998 (p90)
REVERT: B  133 THR cc_start: 0.7888 (p) cc_final: 0.7626 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 164
  average time/residue: 0.1483
  time to fit residues: 33.7662
Evaluate side-chains
  144 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0770
   chunk 52 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.9140

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.185274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.165480 restraints weight = 11808.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.169823 restraints weight = 7436.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.172964 restraints weight = 5163.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6331  Z= 0.122
  Angle     :  0.644  10.539   8631  Z= 0.325
  Chirality :  0.041   0.155    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  7.507  85.592    961
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.31 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.31), residues: 758
  helix:  0.73 (0.27), residues: 369
  sheet: -2.29 (0.45), residues: 101
  loop : -1.44 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B  55 
 HIS   0.003   0.001   HIS C 111 
 PHE   0.022   0.002   PHE A 427 
 TYR   0.017   0.001   TYR B  52 
 ARG   0.005   0.000   ARG B 117 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00235 (    2)
  link_NAG-ASN         : angle       1.02058 (    6)
  hydrogen bonds       : bond        0.03414 (  304)
  hydrogen bonds       : angle       4.70963 (  855)
  SS BOND              : bond        0.00334 (    3)
  SS BOND              : angle       1.28304 (    6)
  covalent geometry    : bond        0.00272 ( 6326)
  covalent geometry    : angle       0.64288 ( 8619)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7615 (tmtt) cc_final: 0.7225 (tptp)
REVERT: A  124 MET cc_start: 0.7563 (tpt) cc_final: 0.7298 (tpt)
REVERT: A  180 MET cc_start: 0.8858 (mmp) cc_final: 0.8326 (mmt)
REVERT: A  229 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8621 (tm-30)
REVERT: A  242 SER cc_start: 0.8569 (p) cc_final: 0.8292 (t)
REVERT: A  313 LEU cc_start: 0.8476 (mm) cc_final: 0.8059 (tp)
REVERT: A  314 LYS cc_start: 0.7269 (tttm) cc_final: 0.6955 (ttpp)
REVERT: A  410 TYR cc_start: 0.7984 (t80) cc_final: 0.7237 (t80)
REVERT: A  432 ILE cc_start: 0.8762 (mt) cc_final: 0.8425 (mt)
REVERT: A  437 ASP cc_start: 0.7620 (p0) cc_final: 0.7406 (p0)
REVERT: A  493 GLU cc_start: 0.6953 (tt0) cc_final: 0.6203 (tt0)
REVERT: A  494 GLU cc_start: 0.8418 (tp30) cc_final: 0.7857 (tt0)
REVERT: A  528 MET cc_start: 0.7499 (ttm) cc_final: 0.7222 (ttm)
REVERT: A  562 GLN cc_start: 0.6891 (tp-100) cc_final: 0.6688 (tp40)
REVERT: A  563 LEU cc_start: 0.8623 (pt) cc_final: 0.6503 (tt)
REVERT: C   75 TYR cc_start: 0.8032 (t80) cc_final: 0.7807 (t80)
REVERT: C   82 PHE cc_start: 0.5170 (m-80) cc_final: 0.4893 (m-80)
REVERT: B  124 TYR cc_start: 0.8326 (p90) cc_final: 0.8118 (p90)
REVERT: B  133 THR cc_start: 0.7906 (p) cc_final: 0.7637 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1480
  time to fit residues: 33.9597
Evaluate side-chains
  146 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  57 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 = 0.4274 r_free = 0.4274 target = 0.187470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.167548 restraints weight = 11956.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.171960 restraints weight = 7370.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.175145 restraints weight = 5052.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.4139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.4267

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= 0.131
  Angle     :  0.653  10.680   8631  Z= 0.331
  Chirality :  0.041   0.155    966
  Planarity :  0.004   0.071   1048
  Dihedral  :  7.431  85.569    961
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.31), residues: 758
  helix:  0.75 (0.27), residues: 367
  sheet: -2.30 (0.47), residues: 95
  loop : -1.38 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 271 
 HIS   0.005   0.001   HIS A 143 
 PHE   0.026   0.002   PHE A 287 
 TYR   0.018   0.002   TYR B  52 
 ARG   0.006   0.000   ARG B 117 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00206 (    2)
  link_NAG-ASN         : angle       1.07418 (    6)
  hydrogen bonds       : bond        0.03489 (  304)
  hydrogen bonds       : angle       4.77689 (  855)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       1.45118 (    6)
  covalent geometry    : bond        0.00292 ( 6326)
  covalent geometry    : angle       0.65171 ( 8619)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3625.25 seconds
wall clock time: 65 minutes 46.09 seconds (3946.09 seconds total)