Starting phenix.real_space_refine
on Fri Sep 11 01:13:49 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6vrl_21370/09_2026/6vrl_21370.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrl_21370/09_2026/6vrl_21370.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6vrl_21370/09_2026/6vrl_21370.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6vrl_21370/09_2026/6vrl_21370.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vrl_21370/09_2026/6vrl_21370.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrl_21370/09_2026/6vrl_21370.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrl_21370/09_2026/6vrl_21370.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrl_21370/09_2026/6vrl_21370.cif"
  }
  resolution = 3.8
  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=   0.971
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
     I       1     10.91       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 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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, 'RFY': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.33, per 1000 atoms: 0.22
  Number of scatterers: 6141
  At special positions: 0
  Unit cell: (95.256, 104.328, 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)
     I       1     52.95
     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: 0.52
  Conformation dependent library (CDL) restraints added in 366.7 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:
      32 helices and 7 sheets defined
      53.8% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 3.540A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 102
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 113 through 116
    Processing helix  chain 'A' and resid 117 through 128
    Processing helix  chain 'A' and resid 128 through 144
      removed outlier: 4.110A  pdb=" N   LEU A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 4.256A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.589A  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 253 through 271
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 3.721A  pdb=" N   LYS A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 300
      removed outlier: 3.665A  pdb=" N   ILE A 290 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 314
      removed outlier: 4.080A  pdb=" N   VAL A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 321
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 4.094A  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: 3.531A  pdb=" N   ASP A 360 " --> pdb=" O   ASN A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 397
    Processing helix  chain 'A' and resid 403 through 408
    Processing helix  chain 'A' and resid 408 through 417
    Processing helix  chain 'A' and resid 419 through 454
      removed outlier: 4.039A  pdb=" N   PHE A 423 " --> pdb=" O   ALA A 419 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 478
    Processing helix  chain 'A' and resid 479 through 481
      No H-bonds generated for 'chain 'A' and resid 479 through 481'
    Processing helix  chain 'A' and resid 484 through 496
      removed outlier: 3.832A  pdb=" N   VAL A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 514
    Processing helix  chain 'A' and resid 517 through 530
    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 587
      removed outlier: 4.254A  pdb=" N   SER A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   PHE A 586 " --> pdb=" O   GLY A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 596
    Processing helix  chain 'A' and resid 603 through 611
    Processing helix  chain 'B' and resid 81 through 84
      removed outlier: 4.011A  pdb=" N   LYS B  84 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 81 through 84'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565
      removed outlier: 3.666A  pdb=" N   LEU A 565 " --> pdb=" O   TYR A 568 " (cutoff:3.500A)
    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 39 through 41
    Processing sheet with id=AA4, first strand: chain 'C' and resid 73 through 74
      removed outlier: 6.797A  pdb=" N   TRP C  55 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   TYR C  69 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   VAL C  53 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 25
    Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 39
      removed outlier: 3.811A  pdb=" N   VAL B  37 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B 102 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE B  39 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   MET B 100 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79
      removed outlier: 6.649A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   ASN B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   MET B  53 " --> pdb=" O   ASN B  69 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   VAL B 112 " --> pdb=" O   GLN B  58 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    888 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: 0.71

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.23 -     1.40: 2681
        1.40 -     1.58: 3595
        1.58 -     1.75: 0
        1.75 -     1.93: 49
        1.93 -     2.11: 1
  Bond restraints: 6326
  Sorted by residual:
  bond pdb=" C06 RFY A 704 "
       pdb=" C07 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.511  1.576 -0.065 2.00e-02 2.50e+03 1.06e+01
  bond pdb=" C05 RFY A 704 "
       pdb=" C06 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.543  1.493  0.050 2.00e-02 2.50e+03 6.30e+00
  bond pdb=" C17 RFY A 704 "
       pdb=" C18 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.370  1.418 -0.048 2.00e-02 2.50e+03 5.81e+00
  bond pdb=" C19 RFY A 704 "
       pdb=" C20 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.371  1.416 -0.045 2.00e-02 2.50e+03 5.11e+00
  bond pdb=" C01 RFY A 704 "
       pdb=" C06 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.542  1.498  0.044 2.00e-02 2.50e+03 4.95e+00
  ... (remaining 6321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 8430
        1.79 -     3.57: 150
        3.57 -     5.36: 25
        5.36 -     7.15: 10
        7.15 -     8.94: 4
  Bond angle restraints: 8619
  Sorted by residual:
  angle pdb=" N   VAL A 397 "
        pdb=" CA  VAL A 397 "
        pdb=" C   VAL A 397 "
      ideal   model   delta    sigma   weight residual
     113.42  109.33    4.09 1.17e+00 7.31e-01 1.22e+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  117.12   -7.31 2.21e+00 2.05e-01 1.09e+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  108.15    8.94 3.00e+00 1.11e-01 8.87e+00
  angle pdb=" C10 LMT A 703 "
        pdb=" C9  LMT A 703 "
        pdb=" C8  LMT A 703 "
      ideal   model   delta    sigma   weight residual
     116.03  107.32    8.71 3.00e+00 1.11e-01 8.43e+00
  angle pdb=" C   VAL B 120 "
        pdb=" N   ARG B 121 "
        pdb=" CA  ARG B 121 "
      ideal   model   delta    sigma   weight residual
     121.80  128.79   -6.99 2.44e+00 1.68e-01 8.20e+00
  ... (remaining 8614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 3220
       17.53 -    35.07: 315
       35.07 -    52.60: 51
       52.60 -    70.14: 10
       70.14 -    87.67: 4
  Dihedral angle restraints: 3600
    sinusoidal: 1386
      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  128.14   51.86     0      5.00e+00 4.00e-02 1.08e+02
  dihedral pdb=" CB  CYS A 200 "
           pdb=" SG  CYS A 200 "
           pdb=" SG  CYS A 209 "
           pdb=" CB  CYS A 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  133.61  -40.61     1      1.00e+01 1.00e-02 2.31e+01
  dihedral pdb=" CA  CYS A 209 "
           pdb=" C   CYS A 209 "
           pdb=" N   THR A 210 "
           pdb=" CA  THR A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 3597 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 714
       0.042 -    0.083: 207
       0.083 -    0.125: 40
       0.125 -    0.166: 1
       0.166 -    0.208: 4
  Chirality restraints: 966
  Sorted by residual:
  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    0.21 2.00e-01 2.50e+01 1.08e+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    0.21 2.00e-01 2.50e+01 1.07e+00
  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 1.07e+00
  ... (remaining 963 not shown)

  Planarity restraints: 1050
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 121 "   -0.044 5.00e-02 4.00e+02   6.70e-02 7.18e+00
        pdb=" N   PRO B 122 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 122 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 122 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 465 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.90e+00
        pdb=" C   PHE A 465 "    0.034 2.00e-02 2.50e+03
        pdb=" O   PHE A 465 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 466 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 589 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO A 590 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 590 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 590 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1047 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.72: 256
        2.72 -     3.28: 6880
        3.28 -     3.84: 11030
        3.84 -     4.40: 13024
        4.40 -     4.96: 22133
  Nonbonded interactions: 53323
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  83 "
            pdb=" O   THR C  94 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OG  SER B 110 "
            pdb=" O   LEU B 134 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   THR A 221 "
            pdb=" OG  SER A 224 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ASP C 102 "
            pdb=" OH  TYR C 106 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   SER A 559 "
            pdb=" O6' LMT A 703 "
     model   vdw
     2.267 3.040
  ... (remaining 53318 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:             5.110
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.700
  Find NCS groups from input model:        0.030
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
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   0.065   6331  Z= 0.185
  Angle     :  0.634   8.936   8631  Z= 0.327
  Chirality :  0.040   0.208    966
  Planarity :  0.004   0.067   1048
  Dihedral  : 13.881  87.674   2185
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  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: -3.12 (0.27), residues: 758
  helix: -0.96 (0.24), residues: 360
  sheet: -3.12 (0.42), residues: 99
  loop : -3.02 (0.32), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 121 
 TYR   0.013   0.001   TYR B 123 
 PHE   0.015   0.001   PHE A 311 
 TRP   0.007   0.001   TRP A 151 
 HIS   0.001   0.000   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.19 ( 6326)
  covalent geometry    : angle       0.63334 /  0.33 ( 8619)
  SS BOND              : bond        0.00176 /  0.09 (    3)
  SS BOND              : angle       0.83461 /  0.40 (    6)
  hydrogen bonds       : bond        0.16879 / 10.85 (  312)
  hydrogen bonds       : angle       6.71669 /  5.06 (  888)
  link_NAG-ASN         : bond        0.00214 /  0.13 (    2)
  link_NAG-ASN         : angle       0.89954 /  0.51 (    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
  206 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TRP cc_start: 0.8013 (m100) cc_final: 0.7796 (m100)
REVERT: A  134 TYR cc_start: 0.7064 (t80) cc_final: 0.6846 (t80)
REVERT: A  135 MET cc_start: 0.7156 (ttm) cc_final: 0.6387 (ttm)
REVERT: A  136 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6437 (mm-30)
REVERT: A  151 TRP cc_start: 0.7688 (m100) cc_final: 0.7140 (m100)
REVERT: A  179 ILE cc_start: 0.8985 (mm) cc_final: 0.8530 (mt)
REVERT: A  234 ARG cc_start: 0.6268 (ttm-80) cc_final: 0.5843 (mtt-85)
REVERT: A  373 PHE cc_start: 0.8209 (t80) cc_final: 0.7918 (t80)
REVERT: A  408 ILE cc_start: 0.8773 (mt) cc_final: 0.8554 (mt)
REVERT: A  494 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6567 (mm-30)
REVERT: A  553 ILE cc_start: 0.9055 (pt) cc_final: 0.8833 (pt)
REVERT: C   47 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7393 (tm-30)
REVERT: C   67 LEU cc_start: 0.6982 (mm) cc_final: 0.6741 (mm)
REVERT: C  114 ILE cc_start: 0.8801 (pt) cc_final: 0.8582 (mp)
REVERT: B   42 LYS cc_start: 0.6139 (mttt) cc_final: 0.5449 (tptt)
REVERT: B   53 MET cc_start: 0.8867 (tpp) cc_final: 0.8515 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0675
  time to fit residues: 18.9775
Evaluate side-chains
  148 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0010
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 ASN
A 202 ASN
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.183087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.166173 restraints weight = 11168.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.170329 restraints weight = 6794.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.173217 restraints weight = 4498.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.174475 restraints weight = 3230.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.176380 restraints weight = 2616.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6331  Z= 0.124
  Angle     :  0.624  10.212   8631  Z= 0.312
  Chirality :  0.041   0.245    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  6.257  78.062    869
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.54 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z 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: -1.75 (0.30), residues: 758
  helix:  0.25 (0.26), residues: 363
  sheet: -2.54 (0.46), residues: 100
  loop : -2.43 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 116 
 TYR   0.018   0.001   TYR B 123 
 PHE   0.018   0.001   PHE A 423 
 TRP   0.016   0.001   TRP A 220 
 HIS   0.005   0.001   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 6326)
  covalent geometry    : angle       0.62337 /  0.31 ( 8619)
  SS BOND              : bond        0.00126 /  0.08 (    3)
  SS BOND              : angle       1.01989 /  0.53 (    6)
  hydrogen bonds       : bond        0.04135 /  2.76 (  312)
  hydrogen bonds       : angle       5.07887 /  3.77 (  888)
  link_NAG-ASN         : bond        0.00225 /  0.13 (    2)
  link_NAG-ASN         : angle       0.76181 /  0.44 (    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
  181 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 166
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6421 (mm-30)
REVERT: A  151 TRP cc_start: 0.7767 (m100) cc_final: 0.7129 (m100)
REVERT: A  240 HIS cc_start: 0.6967 (p90) cc_final: 0.6638 (m170)
REVERT: A  373 PHE cc_start: 0.8283 (t80) cc_final: 0.7828 (t80)
REVERT: A  553 ILE cc_start: 0.9034 (pt) cc_final: 0.8830 (pt)
REVERT: B   42 LYS cc_start: 0.6296 (mttt) cc_final: 0.5839 (tptt)
REVERT: B   53 MET cc_start: 0.9022 (tpp) cc_final: 0.8765 (tpt)
REVERT: B  100 MET cc_start: 0.3556 (ppp) cc_final: 0.3239 (ppp)
  outliers start: 15
  outliers final: 8
  residues processed: 169
  average time/residue: 0.0592
  time to fit residues: 13.7493
Evaluate side-chains
  148 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 140
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 17 optimal weight:    0.0070
   chunk 34 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.7200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 416 ASN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  24 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.185708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.168816 restraints weight = 11073.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.172776 restraints weight = 6785.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.175585 restraints weight = 4501.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.177924 restraints weight = 3300.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.179334 restraints weight = 2382.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6331  Z= 0.119
  Angle     :  0.623  11.670   8631  Z= 0.309
  Chirality :  0.041   0.222    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  6.186  76.932    869
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 20.00 %
    Favored  : 77.69 %
  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: -1.11 (0.31), residues: 758
  helix:  0.82 (0.27), residues: 353
  sheet: -2.41 (0.47), residues: 96
  loop : -2.02 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  81 
 TYR   0.020   0.001   TYR A 134 
 PHE   0.020   0.001   PHE A 423 
 TRP   0.014   0.001   TRP A 103 
 HIS   0.004   0.001   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 6326)
  covalent geometry    : angle       0.62304 /  0.31 ( 8619)
  SS BOND              : bond        0.00150 /  0.09 (    3)
  SS BOND              : angle       0.86980 /  0.45 (    6)
  hydrogen bonds       : bond        0.03721 /  2.48 (  312)
  hydrogen bonds       : angle       4.78923 /  3.56 (  888)
  link_NAG-ASN         : bond        0.00243 /  0.15 (    2)
  link_NAG-ASN         : angle       0.78864 /  0.46 (    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
  164 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6672 (mm-30)
REVERT: A  151 TRP cc_start: 0.7838 (m100) cc_final: 0.7236 (m100)
REVERT: A  417 MET cc_start: 0.6271 (mtm) cc_final: 0.5563 (mtm)
REVERT: A  494 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6444 (mm-30)
REVERT: A  553 ILE cc_start: 0.9052 (pt) cc_final: 0.8812 (pt)
REVERT: B   42 LYS cc_start: 0.6234 (mttt) cc_final: 0.5821 (tptt)
REVERT: B  100 MET cc_start: 0.3559 (ppp) cc_final: 0.3351 (ppp)
  outliers start: 15
  outliers final: 10
  residues processed: 154
  average time/residue: 0.0597
  time to fit residues: 12.7599
Evaluate side-chains
  146 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 136
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  311 PHE
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0980
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 62 optimal weight:    9.9990
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 562 GLN
C  57 GLN
B  24 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.183241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.166412 restraints weight = 11268.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.170276 restraints weight = 6953.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.173076 restraints weight = 4715.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.175230 restraints weight = 3371.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.176757 restraints weight = 2510.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6331  Z= 0.133
  Angle     :  0.624  10.166   8631  Z= 0.312
  Chirality :  0.041   0.191    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  6.210  77.744    869
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.15 %
    Favored  : 74.77 %
  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: -1.08 (0.30), residues: 758
  helix:  0.76 (0.27), residues: 356
  sheet: -2.32 (0.45), residues: 100
  loop : -1.91 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C  81 
 TYR   0.029   0.002   TYR A 134 
 PHE   0.018   0.001   PHE A 428 
 TRP   0.026   0.002   TRP B  55 
 HIS   0.004   0.001   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.13 ( 6326)
  covalent geometry    : angle       0.62314 /  0.31 ( 8619)
  SS BOND              : bond        0.00256 /  0.14 (    3)
  SS BOND              : angle       1.13455 /  0.58 (    6)
  hydrogen bonds       : bond        0.03689 /  2.47 (  312)
  hydrogen bonds       : angle       4.76620 /  3.52 (  888)
  link_NAG-ASN         : bond        0.00133 /  0.08 (    2)
  link_NAG-ASN         : angle       0.87657 /  0.52 (    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
  159 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6759 (mm-30)
REVERT: A  494 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6555 (mm-30)
REVERT: A  553 ILE cc_start: 0.9078 (pt) cc_final: 0.8833 (pt)
REVERT: B   42 LYS cc_start: 0.6028 (mttt) cc_final: 0.5806 (tptt)
  outliers start: 20
  outliers final: 15
  residues processed: 148
  average time/residue: 0.0595
  time to fit residues: 12.5327
Evaluate side-chains
  151 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 56 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   chunk 69 optimal weight:    6.9990
   overall best weight:    0.6980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.189416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.172263 restraints weight = 10988.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.176083 restraints weight = 6728.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.178756 restraints weight = 4520.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.179860 restraints weight = 3342.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.181924 restraints weight = 2745.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.4239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6331  Z= 0.114
  Angle     :  0.610  10.297   8631  Z= 0.305
  Chirality :  0.041   0.253    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  6.304  77.310    869
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.92 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z 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: -0.90 (0.31), residues: 758
  helix:  0.81 (0.27), residues: 356
  sheet: -1.92 (0.49), residues: 96
  loop : -1.82 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  81 
 TYR   0.021   0.001   TYR A 134 
 PHE   0.015   0.001   PHE A 428 
 TRP   0.024   0.001   TRP A 103 
 HIS   0.003   0.001   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.11 ( 6326)
  covalent geometry    : angle       0.61017 /  0.30 ( 8619)
  SS BOND              : bond        0.00221 /  0.12 (    3)
  SS BOND              : angle       0.68262 /  0.33 (    6)
  hydrogen bonds       : bond        0.03469 /  2.32 (  312)
  hydrogen bonds       : angle       4.60173 /  3.38 (  888)
  link_NAG-ASN         : bond        0.00186 /  0.12 (    2)
  link_NAG-ASN         : angle       0.85176 /  0.49 (    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
  157 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6783 (mm-30)
REVERT: A  494 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6467 (mm-30)
REVERT: A  528 MET cc_start: 0.6562 (mtp) cc_final: 0.6234 (mtp)
REVERT: A  553 ILE cc_start: 0.9104 (pt) cc_final: 0.8854 (pt)
REVERT: B   42 LYS cc_start: 0.5989 (mttt) cc_final: 0.5747 (tptt)
REVERT: B   58 GLN cc_start: 0.5063 (OUTLIER) cc_final: 0.4256 (tp40)
  outliers start: 19
  outliers final: 14
  residues processed: 149
  average time/residue: 0.0628
  time to fit residues: 13.2465
Evaluate side-chains
  147 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 69 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 44 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0370
   overall best weight:    1.3462

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 520 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.185330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.167882 restraints weight = 10754.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.170673 restraints weight = 6668.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.174200 restraints weight = 4854.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.176666 restraints weight = 3498.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.177971 restraints weight = 2589.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6331  Z= 0.140
  Angle     :  0.643  12.774   8631  Z= 0.321
  Chirality :  0.043   0.342    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  6.289  73.969    869
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 23.85 %
    Favored  : 72.77 %
  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: -0.91 (0.31), residues: 758
  helix:  0.77 (0.27), residues: 356
  sheet: -2.00 (0.46), residues: 100
  loop : -1.75 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 117 
 TYR   0.024   0.002   TYR A 134 
 PHE   0.028   0.001   PHE A 521 
 TRP   0.036   0.002   TRP A 103 
 HIS   0.005   0.001   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 ( 6326)
  covalent geometry    : angle       0.64303 /  0.32 ( 8619)
  SS BOND              : bond        0.00203 /  0.12 (    3)
  SS BOND              : angle       0.84511 /  0.37 (    6)
  hydrogen bonds       : bond        0.03658 /  2.43 (  312)
  hydrogen bonds       : angle       4.71374 /  3.44 (  888)
  link_NAG-ASN         : bond        0.00150 /  0.09 (    2)
  link_NAG-ASN         : angle       0.88723 /  0.53 (    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
  161 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6849 (mm-30)
REVERT: A  494 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6556 (mm-30)
REVERT: A  553 ILE cc_start: 0.9126 (pt) cc_final: 0.8872 (pt)
REVERT: C   31 MET cc_start: 0.6495 (ppp) cc_final: 0.6251 (tmm)
REVERT: B   42 LYS cc_start: 0.6087 (mttt) cc_final: 0.5865 (tptt)
REVERT: B   58 GLN cc_start: 0.5039 (OUTLIER) cc_final: 0.4227 (tp40)
  outliers start: 22
  outliers final: 19
  residues processed: 151
  average time/residue: 0.0623
  time to fit residues: 13.2821
Evaluate side-chains
  154 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 24 optimal weight:    0.1980
   chunk 21 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.3984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.189333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.171296 restraints weight = 10575.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.175449 restraints weight = 6436.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.178534 restraints weight = 4278.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.180681 restraints weight = 3044.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.181373 restraints weight = 2302.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.4255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6331  Z= 0.143
  Angle     :  0.641   9.658   8631  Z= 0.322
  Chirality :  0.043   0.343    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  6.411  75.805    869
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 24.31 %
    Favored  : 72.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z 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 (0.30), residues: 758
  helix:  0.73 (0.27), residues: 356
  sheet: -1.98 (0.47), residues: 95
  loop : -1.75 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  81 
 TYR   0.024   0.002   TYR B 123 
 PHE   0.020   0.001   PHE A 521 
 TRP   0.027   0.002   TRP A 103 
 HIS   0.004   0.001   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.14 ( 6326)
  covalent geometry    : angle       0.64043 /  0.32 ( 8619)
  SS BOND              : bond        0.00284 /  0.16 (    3)
  SS BOND              : angle       0.83993 /  0.35 (    6)
  hydrogen bonds       : bond        0.03687 /  2.43 (  312)
  hydrogen bonds       : angle       4.69920 /  3.43 (  888)
  link_NAG-ASN         : bond        0.00136 /  0.08 (    2)
  link_NAG-ASN         : angle       0.95509 /  0.56 (    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
  161 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6883 (mm-30)
REVERT: A  494 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6565 (mm-30)
REVERT: A  553 ILE cc_start: 0.9159 (pt) cc_final: 0.8896 (pt)
REVERT: C   74 ARG cc_start: 0.6947 (ptt-90) cc_final: 0.6680 (ptp90)
REVERT: B   42 LYS cc_start: 0.6173 (mttt) cc_final: 0.5761 (tptt)
REVERT: B   58 GLN cc_start: 0.4899 (OUTLIER) cc_final: 0.4082 (tp40)
  outliers start: 23
  outliers final: 17
  residues processed: 153
  average time/residue: 0.0661
  time to fit residues: 14.3498
Evaluate side-chains
  148 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
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:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 64 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0470
   chunk 40 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.8082

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.191953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.174073 restraints weight = 10551.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.178288 restraints weight = 6371.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.181313 restraints weight = 4220.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.183663 restraints weight = 3005.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.185217 restraints weight = 2190.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6331  Z= 0.124
  Angle     :  0.657   9.895   8631  Z= 0.328
  Chirality :  0.042   0.317    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  6.384  75.541    869
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 26.46 %
    Favored  : 70.00 %
  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: -0.80 (0.31), residues: 758
  helix:  0.83 (0.27), residues: 356
  sheet: -1.77 (0.47), residues: 99
  loop : -1.71 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  81 
 TYR   0.023   0.001   TYR B 123 
 PHE   0.023   0.001   PHE A 311 
 TRP   0.021   0.001   TRP A 103 
 HIS   0.004   0.001   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 6326)
  covalent geometry    : angle       0.65637 /  0.33 ( 8619)
  SS BOND              : bond        0.00418 /  0.26 (    3)
  SS BOND              : angle       0.86601 /  0.33 (    6)
  hydrogen bonds       : bond        0.03536 /  2.35 (  312)
  hydrogen bonds       : angle       4.68580 /  3.46 (  888)
  link_NAG-ASN         : bond        0.00067 /  0.04 (    2)
  link_NAG-ASN         : angle       1.00724 /  0.56 (    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
  162 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6860 (mm-30)
REVERT: A  180 MET cc_start: 0.7958 (mmp) cc_final: 0.7425 (mmm)
REVERT: A  417 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5913 (mtm)
REVERT: A  475 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7960 (m-80)
REVERT: A  494 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6547 (mm-30)
REVERT: A  553 ILE cc_start: 0.9142 (pt) cc_final: 0.8880 (pt)
REVERT: C   74 ARG cc_start: 0.6860 (ptt-90) cc_final: 0.6583 (ptp90)
REVERT: C   81 ARG cc_start: 0.4579 (OUTLIER) cc_final: 0.3723 (ttt-90)
REVERT: B   42 LYS cc_start: 0.6106 (mttt) cc_final: 0.5856 (tptt)
REVERT: B   58 GLN cc_start: 0.4797 (OUTLIER) cc_final: 0.4039 (tp40)
  outliers start: 23
  outliers final: 15
  residues processed: 153
  average time/residue: 0.0633
  time to fit residues: 13.6082
Evaluate side-chains
  151 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue   81 ARG
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0770
   chunk 74 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.6938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.190384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.172432 restraints weight = 10876.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.176823 restraints weight = 6455.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.179917 restraints weight = 4314.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.182183 restraints weight = 2995.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.183224 restraints weight = 2200.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6331  Z= 0.121
  Angle     :  0.654  10.479   8631  Z= 0.325
  Chirality :  0.041   0.308    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  6.335  74.332    869
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 26.62 %
    Favored  : 70.92 %
  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: -0.67 (0.31), residues: 758
  helix:  0.91 (0.27), residues: 356
  sheet: -1.57 (0.48), residues: 95
  loop : -1.68 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  81 
 TYR   0.023   0.001   TYR B 123 
 PHE   0.024   0.001   PHE A 311 
 TRP   0.016   0.001   TRP A 220 
 HIS   0.005   0.001   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 6326)
  covalent geometry    : angle       0.65364 /  0.33 ( 8619)
  SS BOND              : bond        0.00300 /  0.18 (    3)
  SS BOND              : angle       0.98982 /  0.37 (    6)
  hydrogen bonds       : bond        0.03462 /  2.29 (  312)
  hydrogen bonds       : angle       4.63675 /  3.40 (  888)
  link_NAG-ASN         : bond        0.00155 /  0.09 (    2)
  link_NAG-ASN         : angle       0.85253 /  0.49 (    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
  156 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6826 (mm-30)
REVERT: A  151 TRP cc_start: 0.7931 (m100) cc_final: 0.7339 (m100)
REVERT: A  180 MET cc_start: 0.7971 (mmp) cc_final: 0.7518 (mmm)
REVERT: A  417 MET cc_start: 0.6230 (mtm) cc_final: 0.5698 (mtm)
REVERT: A  475 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.8019 (m-80)
REVERT: A  494 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6485 (mm-30)
REVERT: A  553 ILE cc_start: 0.9120 (pt) cc_final: 0.8863 (pt)
REVERT: C   74 ARG cc_start: 0.6785 (ptt-90) cc_final: 0.6504 (ptp90)
REVERT: B   42 LYS cc_start: 0.6163 (mttt) cc_final: 0.5935 (tptt)
REVERT: B   58 GLN cc_start: 0.4799 (OUTLIER) cc_final: 0.3986 (tp40)
  outliers start: 16
  outliers final: 13
  residues processed: 150
  average time/residue: 0.0635
  time to fit residues: 13.2510
Evaluate side-chains
  153 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 68 optimal weight:    0.3980
   chunk 13 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0030
   chunk 9 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.5190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 416 ASN
C 109 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.192524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.175741 restraints weight = 10906.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.179655 restraints weight = 6571.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.182595 restraints weight = 4427.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.184394 restraints weight = 3106.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.184394 restraints weight = 2425.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.3724

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= 0.120
  Angle     :  0.661  10.291   8631  Z= 0.330
  Chirality :  0.042   0.288    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  6.348  73.501    869
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 27.08 %
    Favored  : 70.31 %
  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: -0.58 (0.31), residues: 758
  helix:  0.96 (0.27), residues: 354
  sheet: -1.48 (0.49), residues: 94
  loop : -1.59 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  81 
 TYR   0.022   0.001   TYR B 123 
 PHE   0.024   0.001   PHE A 311 
 TRP   0.047   0.001   TRP B  55 
 HIS   0.003   0.001   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 6326)
  covalent geometry    : angle       0.66074 /  0.33 ( 8619)
  SS BOND              : bond        0.00246 /  0.15 (    3)
  SS BOND              : angle       0.85347 /  0.33 (    6)
  hydrogen bonds       : bond        0.03429 /  2.26 (  312)
  hydrogen bonds       : angle       4.68512 /  3.45 (  888)
  link_NAG-ASN         : bond        0.00089 /  0.05 (    2)
  link_NAG-ASN         : angle       0.89467 /  0.52 (    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
  158 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7842 (tpp)
REVERT: A  136 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6705 (mm-30)
REVERT: A  151 TRP cc_start: 0.7882 (m100) cc_final: 0.7266 (m100)
REVERT: A  180 MET cc_start: 0.7898 (mmp) cc_final: 0.7457 (mmm)
REVERT: A  370 MET cc_start: 0.5837 (mtt) cc_final: 0.5543 (mtt)
REVERT: A  417 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.5550 (mtm)
REVERT: A  456 HIS cc_start: 0.5624 (p-80) cc_final: 0.5353 (p-80)
REVERT: A  475 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7943 (m-80)
REVERT: A  494 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6444 (mm-30)
REVERT: A  553 ILE cc_start: 0.9104 (pt) cc_final: 0.8846 (pt)
REVERT: C   74 ARG cc_start: 0.6719 (ptt-90) cc_final: 0.6487 (ptp90)
REVERT: C   95 ILE cc_start: 0.4336 (mm) cc_final: 0.4092 (mm)
REVERT: B   58 GLN cc_start: 0.4813 (OUTLIER) cc_final: 0.4001 (tp40)
  outliers start: 17
  outliers final: 13
  residues processed: 150
  average time/residue: 0.0629
  time to fit residues: 13.3022
Evaluate side-chains
  150 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   79 TYR
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:    9.9990
   chunk 53 optimal weight:    0.0670
   chunk 23 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.5518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 416 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.192420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.175704 restraints weight = 10900.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.179950 restraints weight = 6671.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.182480 restraints weight = 4409.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.184737 restraints weight = 3226.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.185523 restraints weight = 2383.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6331  Z= 0.117
  Angle     :  0.654  10.365   8631  Z= 0.328
  Chirality :  0.041   0.285    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  6.253  72.750    869
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 27.85 %
    Favored  : 69.38 %
  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: -0.58 (0.30), residues: 758
  helix:  0.96 (0.27), residues: 355
  sheet: -1.60 (0.48), residues: 94
  loop : -1.57 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 390 
 TYR   0.021   0.001   TYR B 123 
 PHE   0.026   0.001   PHE A 311 
 TRP   0.044   0.001   TRP B  55 
 HIS   0.004   0.001   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 6326)
  covalent geometry    : angle       0.65418 /  0.33 ( 8619)
  SS BOND              : bond        0.00210 /  0.13 (    3)
  SS BOND              : angle       0.88581 /  0.44 (    6)
  hydrogen bonds       : bond        0.03395 /  2.24 (  312)
  hydrogen bonds       : angle       4.66518 /  3.41 (  888)
  link_NAG-ASN         : bond        0.00142 /  0.09 (    2)
  link_NAG-ASN         : angle       0.80064 /  0.47 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1197.20 seconds
wall clock time: 21 minutes 27.52 seconds (1287.52 seconds total)