Starting phenix.real_space_refine
on Tue Mar  3 15:04:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vrk_21369/03_2026/6vrk_21369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrk_21369/03_2026/6vrk_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrk_21369/03_2026/6vrk_21369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrk_21369/03_2026/6vrk_21369.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vrk_21369/03_2026/6vrk_21369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrk_21369/03_2026/6vrk_21369.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.15, per 1000 atoms: 0.19
  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: 0.47
  Conformation dependent library (CDL) restraints added in 221.2 milliseconds
  

  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: 0.14
  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: 0.79

  Time building geometry restraints manager: 0.62 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:             5.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.540
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.920
-------------------------------------------------------------------------------
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 : 10.65
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG A 152 
 TYR   0.014   0.001   TYR B 123 
 PHE   0.021   0.001   PHE A 548 
 TRP   0.007   0.001   TRP A 103 
 HIS   0.005   0.001   HIS C 111 

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

*********************** 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  : 0.226 
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: 0.0712
  time to fit residues: 20.5154
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  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0170
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0970
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7418

-------------------------------------------------------------------------------
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 = 0.4251 r_free = 0.4251 target = 0.185838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.165529 restraints weight = 11805.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.170196 restraints weight = 7199.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.173484 restraints weight = 4849.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.175890 restraints weight = 3501.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.177550 restraints weight = 2645.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6331  Z= 0.123
  Angle     :  0.619  13.838   8631  Z= 0.313
  Chirality :  0.040   0.156    966
  Planarity :  0.004   0.077   1048
  Dihedral  :  8.129  62.992    961
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.77 %
    Favored  : 94.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.29), residues: 758
  helix: -0.07 (0.26), residues: 367
  sheet: -2.51 (0.47), residues: 86
  loop : -2.56 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 152 
 TYR   0.015   0.001   TYR B 124 
 PHE   0.026   0.001   PHE A 536 
 TRP   0.033   0.001   TRP A 541 
 HIS   0.002   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6326)
  covalent geometry    : angle       0.61729 ( 8619)
  SS BOND              : bond        0.00565 (    3)
  SS BOND              : angle       1.98575 (    6)
  hydrogen bonds       : bond        0.03751 (  304)
  hydrogen bonds       : angle       4.87113 (  855)
  link_NAG-ASN         : bond        0.00561 (    2)
  link_NAG-ASN         : angle       0.70100 (    6)

*********************** 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: 2
    poor density    : 182
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7657 (tmtt) cc_final: 0.7345 (tptp)
REVERT: A  107 TYR cc_start: 0.7805 (t80) cc_final: 0.7451 (t80)
REVERT: A  180 MET cc_start: 0.8790 (mmp) cc_final: 0.8500 (mmp)
REVERT: A  187 LEU cc_start: 0.8878 (tp) cc_final: 0.8669 (tp)
REVERT: A  229 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8385 (tm-30)
REVERT: A  238 GLN cc_start: 0.6351 (tp40) cc_final: 0.6045 (mm-40)
REVERT: A  242 SER cc_start: 0.8385 (p) cc_final: 0.8164 (t)
REVERT: A  410 TYR cc_start: 0.8458 (t80) cc_final: 0.8035 (t80)
REVERT: A  417 MET cc_start: 0.6438 (mtm) cc_final: 0.5888 (mtm)
REVERT: A  493 GLU cc_start: 0.6460 (tt0) cc_final: 0.6099 (mt-10)
REVERT: A  563 LEU cc_start: 0.8432 (pt) cc_final: 0.7379 (tt)
REVERT: B  109 ASP cc_start: 0.7331 (m-30) cc_final: 0.7022 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 183
  average time/residue: 0.0646
  time to fit residues: 16.2831
Evaluate side-chains
  152 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 34 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 55 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 111 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.187848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.167070 restraints weight = 11594.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.171843 restraints weight = 6985.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.175233 restraints weight = 4687.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.177655 restraints weight = 3365.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.179328 restraints weight = 2554.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6839
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6331  Z= 0.119
  Angle     :  0.632  13.935   8631  Z= 0.317
  Chirality :  0.040   0.152    966
  Planarity :  0.004   0.079   1048
  Dihedral  :  7.789  61.036    961
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.30), residues: 758
  helix:  0.25 (0.27), residues: 369
  sheet: -2.37 (0.48), residues: 93
  loop : -2.28 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 390 
 TYR   0.019   0.001   TYR B 114 
 PHE   0.038   0.002   PHE A 373 
 TRP   0.016   0.001   TRP A 458 
 HIS   0.002   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6326)
  covalent geometry    : angle       0.62875 ( 8619)
  SS BOND              : bond        0.00503 (    3)
  SS BOND              : angle       2.30404 (    6)
  hydrogen bonds       : bond        0.03523 (  304)
  hydrogen bonds       : angle       4.71737 (  855)
  link_NAG-ASN         : bond        0.00226 (    2)
  link_NAG-ASN         : angle       0.83938 (    6)

*********************** 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
  174 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7683 (tmtt) cc_final: 0.7376 (tptp)
REVERT: A  107 TYR cc_start: 0.7854 (t80) cc_final: 0.7524 (t80)
REVERT: A  152 ARG cc_start: 0.6851 (ttp-110) cc_final: 0.6097 (ttm-80)
REVERT: A  180 MET cc_start: 0.8699 (mmp) cc_final: 0.8331 (mmp)
REVERT: A  187 LEU cc_start: 0.8835 (tp) cc_final: 0.8621 (tp)
REVERT: A  229 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8494 (tm-30)
REVERT: A  238 GLN cc_start: 0.6450 (tp40) cc_final: 0.6146 (mm-40)
REVERT: A  242 SER cc_start: 0.8431 (p) cc_final: 0.8093 (t)
REVERT: A  306 TRP cc_start: 0.7011 (p-90) cc_final: 0.6661 (m-10)
REVERT: A  313 LEU cc_start: 0.8533 (mm) cc_final: 0.8009 (tp)
REVERT: A  410 TYR cc_start: 0.8402 (t80) cc_final: 0.8012 (t80)
REVERT: A  493 GLU cc_start: 0.6400 (tt0) cc_final: 0.6081 (mt-10)
REVERT: A  563 LEU cc_start: 0.8305 (pt) cc_final: 0.7282 (tt)
REVERT: C  107 TYR cc_start: 0.6792 (m-80) cc_final: 0.6537 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0703
  time to fit residues: 16.2834
Evaluate side-chains
  145 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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**
C 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.184585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.163460 restraints weight = 11981.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.168193 restraints weight = 7305.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.171595 restraints weight = 4957.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.173977 restraints weight = 3592.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.175616 restraints weight = 2747.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.3059

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= 0.138
  Angle     :  0.666  18.082   8631  Z= 0.328
  Chirality :  0.041   0.266    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  7.815  70.974    961
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.30), residues: 758
  helix:  0.38 (0.27), residues: 364
  sheet: -2.34 (0.47), residues: 101
  loop : -2.04 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 307 
 TYR   0.018   0.001   TYR B 114 
 PHE   0.038   0.002   PHE C 118 
 TRP   0.021   0.001   TRP A 306 
 HIS   0.007   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6326)
  covalent geometry    : angle       0.66512 ( 8619)
  SS BOND              : bond        0.00582 (    3)
  SS BOND              : angle       1.60743 (    6)
  hydrogen bonds       : bond        0.03519 (  304)
  hydrogen bonds       : angle       4.67376 (  855)
  link_NAG-ASN         : bond        0.00161 (    2)
  link_NAG-ASN         : angle       0.77890 (    6)

*********************** 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
  166 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7668 (tmtt) cc_final: 0.7310 (tptp)
REVERT: A   88 PHE cc_start: 0.8246 (t80) cc_final: 0.8023 (t80)
REVERT: A  152 ARG cc_start: 0.6977 (ttp-110) cc_final: 0.6111 (ttm-80)
REVERT: A  180 MET cc_start: 0.8777 (mmp) cc_final: 0.8298 (mmp)
REVERT: A  229 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8546 (tm-30)
REVERT: A  242 SER cc_start: 0.8502 (p) cc_final: 0.8228 (t)
REVERT: A  313 LEU cc_start: 0.8473 (mm) cc_final: 0.8095 (tp)
REVERT: A  410 TYR cc_start: 0.8543 (t80) cc_final: 0.7923 (t80)
REVERT: A  493 GLU cc_start: 0.6507 (tt0) cc_final: 0.6165 (tt0)
REVERT: A  494 GLU cc_start: 0.8231 (tp30) cc_final: 0.7781 (tt0)
REVERT: A  528 MET cc_start: 0.7284 (ttm) cc_final: 0.7031 (ttm)
REVERT: A  558 MET cc_start: 0.6743 (mtp) cc_final: 0.6518 (mtt)
REVERT: A  563 LEU cc_start: 0.8403 (pt) cc_final: 0.6447 (tt)
REVERT: B  108 GLU cc_start: 0.7906 (pp20) cc_final: 0.7624 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0609
  time to fit residues: 13.9105
Evaluate side-chains
  137 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 16 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 49 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 56 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 69 optimal weight:   20.0000
   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 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 = 0.4260 r_free = 0.4260 target = 0.186302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.165930 restraints weight = 12015.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.170516 restraints weight = 7532.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.173717 restraints weight = 5163.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.176025 restraints weight = 3783.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.177637 restraints weight = 2909.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6331  Z= 0.115
  Angle     :  0.619  12.339   8631  Z= 0.310
  Chirality :  0.040   0.165    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  7.763  77.529    961
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.30), residues: 758
  helix:  0.52 (0.27), residues: 368
  sheet: -2.26 (0.47), residues: 101
  loop : -1.88 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 117 
 TYR   0.014   0.001   TYR A 358 
 PHE   0.025   0.001   PHE C 118 
 TRP   0.018   0.001   TRP C  55 
 HIS   0.005   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6326)
  covalent geometry    : angle       0.61780 ( 8619)
  SS BOND              : bond        0.00289 (    3)
  SS BOND              : angle       1.41597 (    6)
  hydrogen bonds       : bond        0.03362 (  304)
  hydrogen bonds       : angle       4.60066 (  855)
  link_NAG-ASN         : bond        0.00212 (    2)
  link_NAG-ASN         : angle       0.81636 (    6)

*********************** 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
  173 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7614 (tmtt) cc_final: 0.7255 (tptp)
REVERT: A   88 PHE cc_start: 0.8301 (t80) cc_final: 0.8070 (t80)
REVERT: A  107 TYR cc_start: 0.7929 (t80) cc_final: 0.7694 (t80)
REVERT: A  180 MET cc_start: 0.8848 (mmp) cc_final: 0.8317 (mmp)
REVERT: A  187 LEU cc_start: 0.8854 (tp) cc_final: 0.8632 (tp)
REVERT: A  229 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: A  242 SER cc_start: 0.8625 (p) cc_final: 0.8285 (t)
REVERT: A  313 LEU cc_start: 0.8446 (mm) cc_final: 0.7981 (tp)
REVERT: A  314 LYS cc_start: 0.7190 (tttm) cc_final: 0.6823 (mtpt)
REVERT: A  410 TYR cc_start: 0.8478 (t80) cc_final: 0.7913 (t80)
REVERT: A  528 MET cc_start: 0.7402 (ttm) cc_final: 0.7080 (ttm)
REVERT: A  563 LEU cc_start: 0.8400 (pt) cc_final: 0.7440 (tt)
REVERT: B  133 THR cc_start: 0.7749 (p) cc_final: 0.7495 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0599
  time to fit residues: 14.3489
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  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0370
   chunk 51 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.7662

-------------------------------------------------------------------------------
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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.185593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.165916 restraints weight = 11354.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.170411 restraints weight = 7077.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.173525 restraints weight = 4841.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.175671 restraints weight = 3532.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.177351 restraints weight = 2727.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.3638

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= 0.116
  Angle     :  0.623  12.079   8631  Z= 0.313
  Chirality :  0.040   0.151    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  7.898  87.196    961
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.31), residues: 758
  helix:  0.59 (0.27), residues: 368
  sheet: -2.18 (0.47), residues: 101
  loop : -1.84 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 117 
 TYR   0.015   0.001   TYR A 185 
 PHE   0.018   0.001   PHE A 536 
 TRP   0.039   0.002   TRP A 271 
 HIS   0.010   0.002   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6326)
  covalent geometry    : angle       0.62103 ( 8619)
  SS BOND              : bond        0.00460 (    3)
  SS BOND              : angle       1.48191 (    6)
  hydrogen bonds       : bond        0.03342 (  304)
  hydrogen bonds       : angle       4.62991 (  855)
  link_NAG-ASN         : bond        0.00126 (    2)
  link_NAG-ASN         : angle       1.13398 (    6)

*********************** 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
  168 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7618 (tmtt) cc_final: 0.7333 (tptp)
REVERT: A  107 TYR cc_start: 0.7937 (t80) cc_final: 0.7707 (t80)
REVERT: A  180 MET cc_start: 0.8870 (mmp) cc_final: 0.8316 (mmp)
REVERT: A  187 LEU cc_start: 0.8868 (tp) cc_final: 0.8663 (tp)
REVERT: A  229 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8582 (tm-30)
REVERT: A  242 SER cc_start: 0.8606 (p) cc_final: 0.8295 (t)
REVERT: A  313 LEU cc_start: 0.8488 (mm) cc_final: 0.8019 (tp)
REVERT: A  314 LYS cc_start: 0.7200 (tttm) cc_final: 0.6815 (mtpt)
REVERT: A  410 TYR cc_start: 0.8225 (t80) cc_final: 0.7614 (t80)
REVERT: A  528 MET cc_start: 0.7450 (ttm) cc_final: 0.7053 (ttm)
REVERT: A  563 LEU cc_start: 0.8512 (pt) cc_final: 0.7355 (tt)
REVERT: C  109 GLN cc_start: 0.7273 (tt0) cc_final: 0.6369 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0661
  time to fit residues: 15.2750
Evaluate side-chains
  147 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 7 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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
** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.186937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.167062 restraints weight = 11733.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.171395 restraints weight = 7537.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.174463 restraints weight = 5283.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.176746 restraints weight = 3930.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.178219 restraints weight = 3047.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6331  Z= 0.113
  Angle     :  0.628  12.531   8631  Z= 0.315
  Chirality :  0.041   0.179    966
  Planarity :  0.004   0.078   1048
  Dihedral  :  7.485  80.437    961
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.31), residues: 758
  helix:  0.67 (0.27), residues: 367
  sheet: -2.06 (0.47), residues: 101
  loop : -1.68 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  79 
 TYR   0.018   0.001   TYR A 267 
 PHE   0.018   0.001   PHE A 536 
 TRP   0.018   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 6326)
  covalent geometry    : angle       0.62671 ( 8619)
  SS BOND              : bond        0.00426 (    3)
  SS BOND              : angle       1.60602 (    6)
  hydrogen bonds       : bond        0.03278 (  304)
  hydrogen bonds       : angle       4.63423 (  855)
  link_NAG-ASN         : bond        0.00306 (    2)
  link_NAG-ASN         : angle       0.95242 (    6)

*********************** 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
  168 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A   85 LYS cc_start: 0.7638 (tmtt) cc_final: 0.7257 (tptp)
REVERT: A  107 TYR cc_start: 0.7903 (t80) cc_final: 0.7691 (t80)
REVERT: A  180 MET cc_start: 0.8773 (mmp) cc_final: 0.8184 (mmp)
REVERT: A  187 LEU cc_start: 0.8837 (tp) cc_final: 0.8615 (tp)
REVERT: A  229 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8564 (tm-30)
REVERT: A  242 SER cc_start: 0.8568 (p) cc_final: 0.8241 (t)
REVERT: A  313 LEU cc_start: 0.8507 (mm) cc_final: 0.8007 (tp)
REVERT: A  314 LYS cc_start: 0.7252 (tttm) cc_final: 0.6838 (mtpt)
REVERT: A  410 TYR cc_start: 0.8202 (t80) cc_final: 0.7655 (t80)
REVERT: A  432 ILE cc_start: 0.8710 (mt) cc_final: 0.8436 (mt)
REVERT: A  528 MET cc_start: 0.7386 (ttm) cc_final: 0.6981 (ttm)
REVERT: A  563 LEU cc_start: 0.8469 (pt) cc_final: 0.7338 (tt)
REVERT: C  109 GLN cc_start: 0.7234 (tt0) cc_final: 0.6274 (tt0)
REVERT: B   96 THR cc_start: 0.5634 (t) cc_final: 0.5387 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0601
  time to fit residues: 13.9968
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  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0050
   chunk 41 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 59 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.8996

-------------------------------------------------------------------------------
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  26 GLN ** 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 = 0.4261 r_free = 0.4261 target = 0.187084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.167012 restraints weight = 11879.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.171234 restraints weight = 7635.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.174301 restraints weight = 5358.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.176523 restraints weight = 3992.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.177909 restraints weight = 3120.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6833
moved from start:          0.3970

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= 0.121
  Angle     :  0.634  12.755   8631  Z= 0.320
  Chirality :  0.041   0.164    966
  Planarity :  0.004   0.078   1048
  Dihedral  :  7.068  72.033    961
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.31), residues: 758
  helix:  0.67 (0.27), residues: 366
  sheet: -2.06 (0.47), residues: 101
  loop : -1.64 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 538 
 TYR   0.034   0.002   TYR B  52 
 PHE   0.036   0.002   PHE A 373 
 TRP   0.061   0.002   TRP A 541 
 HIS   0.006   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6326)
  covalent geometry    : angle       0.63309 ( 8619)
  SS BOND              : bond        0.00447 (    3)
  SS BOND              : angle       1.46195 (    6)
  hydrogen bonds       : bond        0.03376 (  304)
  hydrogen bonds       : angle       4.72426 (  855)
  link_NAG-ASN         : bond        0.00211 (    2)
  link_NAG-ASN         : angle       0.95346 (    6)

*********************** 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  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7686 (tmtt) cc_final: 0.7296 (tptp)
REVERT: A  180 MET cc_start: 0.8801 (mmp) cc_final: 0.8205 (mmp)
REVERT: A  185 TYR cc_start: 0.7374 (t80) cc_final: 0.7145 (t80)
REVERT: A  187 LEU cc_start: 0.8867 (tp) cc_final: 0.8639 (tp)
REVERT: A  229 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8595 (tm-30)
REVERT: A  242 SER cc_start: 0.8576 (p) cc_final: 0.8265 (t)
REVERT: A  313 LEU cc_start: 0.8354 (mm) cc_final: 0.8073 (tp)
REVERT: A  314 LYS cc_start: 0.7296 (tttm) cc_final: 0.7081 (ttpp)
REVERT: A  410 TYR cc_start: 0.8125 (t80) cc_final: 0.7527 (t80)
REVERT: A  432 ILE cc_start: 0.8746 (mt) cc_final: 0.8500 (mt)
REVERT: A  528 MET cc_start: 0.7380 (ttm) cc_final: 0.7030 (ttm)
REVERT: A  563 LEU cc_start: 0.8493 (pt) cc_final: 0.7365 (tt)
REVERT: C   75 TYR cc_start: 0.8006 (t80) cc_final: 0.7801 (t80)
REVERT: C  109 GLN cc_start: 0.7174 (tt0) cc_final: 0.6373 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0651
  time to fit residues: 14.7516
Evaluate side-chains
  143 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 50 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   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 111 GLN
A 112 ASN
A 240 HIS
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 GLN
B  25 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.182767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.163327 restraints weight = 11751.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.167527 restraints weight = 7540.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.170450 restraints weight = 5293.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.172748 restraints weight = 3966.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.174363 restraints weight = 3067.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6814
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6331  Z= 0.117
  Angle     :  0.633  12.732   8631  Z= 0.318
  Chirality :  0.041   0.154    966
  Planarity :  0.004   0.075   1048
  Dihedral  :  6.612  60.398    961
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.31), residues: 758
  helix:  0.75 (0.27), residues: 368
  sheet: -1.97 (0.48), residues: 101
  loop : -1.56 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 117 
 TYR   0.026   0.001   TYR A 267 
 PHE   0.020   0.001   PHE A 521 
 TRP   0.056   0.002   TRP A 541 
 HIS   0.011   0.002   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6326)
  covalent geometry    : angle       0.63183 ( 8619)
  SS BOND              : bond        0.00372 (    3)
  SS BOND              : angle       1.23773 (    6)
  hydrogen bonds       : bond        0.03250 (  304)
  hydrogen bonds       : angle       4.63243 (  855)
  link_NAG-ASN         : bond        0.00225 (    2)
  link_NAG-ASN         : angle       0.94407 (    6)

*********************** 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
  165 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.7581 (tmtt) cc_final: 0.7193 (tptp)
REVERT: A  180 MET cc_start: 0.8814 (mmp) cc_final: 0.8209 (mmp)
REVERT: A  187 LEU cc_start: 0.8821 (tp) cc_final: 0.8601 (tp)
REVERT: A  229 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8569 (tm-30)
REVERT: A  242 SER cc_start: 0.8557 (p) cc_final: 0.8234 (t)
REVERT: A  313 LEU cc_start: 0.8427 (mm) cc_final: 0.7930 (tp)
REVERT: A  314 LYS cc_start: 0.7259 (tttm) cc_final: 0.7013 (ttpp)
REVERT: A  410 TYR cc_start: 0.8126 (t80) cc_final: 0.7602 (t80)
REVERT: A  432 ILE cc_start: 0.8731 (mt) cc_final: 0.8457 (mt)
REVERT: A  528 MET cc_start: 0.7301 (ttm) cc_final: 0.6967 (ttm)
REVERT: A  563 LEU cc_start: 0.8478 (pt) cc_final: 0.7335 (tt)
REVERT: C  109 GLN cc_start: 0.7238 (tt0) cc_final: 0.6319 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0606
  time to fit residues: 13.8399
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  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 52 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   chunk 53 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 GLN
C 111 HIS
B  25 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.188851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.167323 restraints weight = 12024.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.172070 restraints weight = 7552.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.175443 restraints weight = 5222.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.177919 restraints weight = 3829.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.179655 restraints weight = 2935.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6331  Z= 0.113
  Angle     :  0.638  12.043   8631  Z= 0.321
  Chirality :  0.041   0.156    966
  Planarity :  0.004   0.077   1048
  Dihedral  :  6.473  55.535    961
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.31), residues: 758
  helix:  0.82 (0.27), residues: 369
  sheet: -1.89 (0.49), residues: 101
  loop : -1.51 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 117 
 TYR   0.023   0.002   TYR A 107 
 PHE   0.030   0.001   PHE A 287 
 TRP   0.069   0.002   TRP A 541 
 HIS   0.003   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6326)
  covalent geometry    : angle       0.63696 ( 8619)
  SS BOND              : bond        0.00356 (    3)
  SS BOND              : angle       1.18520 (    6)
  hydrogen bonds       : bond        0.03241 (  304)
  hydrogen bonds       : angle       4.64997 (  855)
  link_NAG-ASN         : bond        0.00223 (    2)
  link_NAG-ASN         : angle       0.95178 (    6)

********************** 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
  165 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   85 LYS cc_start: 0.7580 (tmtt) cc_final: 0.7183 (tptp)
REVERT: A  180 MET cc_start: 0.8805 (mmp) cc_final: 0.8582 (mmp)
REVERT: A  187 LEU cc_start: 0.8828 (tp) cc_final: 0.8607 (tp)
REVERT: A  229 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8510 (tm-30)
REVERT: A  242 SER cc_start: 0.8490 (p) cc_final: 0.8181 (t)
REVERT: A  313 LEU cc_start: 0.8479 (mm) cc_final: 0.8017 (tp)
REVERT: A  314 LYS cc_start: 0.7232 (tttm) cc_final: 0.6995 (ttpp)
REVERT: A  410 TYR cc_start: 0.7882 (t80) cc_final: 0.7408 (t80)
REVERT: A  528 MET cc_start: 0.7382 (ttm) cc_final: 0.6959 (ttm)
REVERT: A  563 LEU cc_start: 0.8461 (pt) cc_final: 0.7320 (tt)
REVERT: C  109 GLN cc_start: 0.7249 (tt0) cc_final: 0.6364 (tt0)
REVERT: B   25 GLN cc_start: 0.5294 (pt0) cc_final: 0.5025 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0646
  time to fit residues: 14.8165
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  : 0.230 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0470
   chunk 25 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0870
   chunk 51 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.4856

-------------------------------------------------------------------------------
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  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.186413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.166795 restraints weight = 11575.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.170984 restraints weight = 7528.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.174067 restraints weight = 5297.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.176311 restraints weight = 3939.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.178027 restraints weight = 3058.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.4454

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= 0.109
  Angle     :  0.628  11.970   8631  Z= 0.313
  Chirality :  0.041   0.160    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  6.214  51.842    961
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.31), residues: 758
  helix:  0.91 (0.27), residues: 368
  sheet: -1.77 (0.50), residues: 101
  loop : -1.49 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 117 
 TYR   0.021   0.001   TYR A 267 
 PHE   0.025   0.001   PHE A 536 
 TRP   0.023   0.001   TRP A 458 
 HIS   0.002   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6326)
  covalent geometry    : angle       0.62689 ( 8619)
  SS BOND              : bond        0.00376 (    3)
  SS BOND              : angle       1.12092 (    6)
  hydrogen bonds       : bond        0.03167 (  304)
  hydrogen bonds       : angle       4.55842 (  855)
  link_NAG-ASN         : bond        0.00226 (    2)
  link_NAG-ASN         : angle       0.92151 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1222.68 seconds
wall clock time: 21 minutes 47.92 seconds (1307.92 seconds total)