Starting phenix.real_space_refine
on Tue Mar  3 15:01:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vrl_21370/03_2026/6vrl_21370.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrl_21370/03_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrl_21370/03_2026/6vrl_21370.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrl_21370/03_2026/6vrl_21370.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vrl_21370/03_2026/6vrl_21370.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrl_21370/03_2026/6vrl_21370.map"
  }
  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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6141
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4311
          Classifications: {'peptide': 541}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 23, 'TRANS': 517}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100}
    Chain: "B"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 924
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 5, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 87
          Unusual residues: {'LMT': 1, 'NAG': 2, 'RFY': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.92, per 1000 atoms: 0.31
  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: 0.79
  Conformation dependent library (CDL) restraints added in 287.9 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: 0.20
  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: 1.00

  Time building geometry restraints manager: 1.01 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: 3299
       17.53 -    35.07: 321
       35.07 -    52.60: 54
       52.60 -    70.14: 14
       70.14 -    87.67: 4
  Dihedral angle restraints: 3692
    sinusoidal: 1478
      harmonic: 2214
  Sorted by residual:
  dihedral pdb=" CA  ARG B 121 "
           pdb=" C   ARG B 121 "
           pdb=" N   PRO B 122 "
           pdb=" CA  PRO B 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  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 3689 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:             5.400
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.840
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
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  : 13.973  87.674   2277
  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
  covalent geometry    : bond        0.00360 ( 6326)
  covalent geometry    : angle       0.63334 ( 8619)
  SS BOND              : bond        0.00176 (    3)
  SS BOND              : angle       0.83461 (    6)
  hydrogen bonds       : bond        0.16879 (  312)
  hydrogen bonds       : angle       6.71669 (  888)
  link_NAG-ASN         : bond        0.00214 (    2)
  link_NAG-ASN         : angle       0.89954 (    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  : 0.242 
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: 0.0754
  time to fit residues: 20.8890
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  : 0.224 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4276 r_free = 0.4276 target = 0.183625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.166930 restraints weight = 11198.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.171005 restraints weight = 6790.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.173929 restraints weight = 4514.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.175979 restraints weight = 3199.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.177058 restraints weight = 2404.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6331  Z= 0.126
  Angle     :  0.627   9.785   8631  Z= 0.314
  Chirality :  0.041   0.247    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  7.295  78.535    961
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  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: -1.80 (0.30), residues: 758
  helix:  0.23 (0.26), residues: 363
  sheet: -2.62 (0.45), residues: 100
  loop : -2.45 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 116 
 TYR   0.020   0.001   TYR B 123 
 PHE   0.017   0.001   PHE A 423 
 TRP   0.015   0.001   TRP A 220 
 HIS   0.005   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6326)
  covalent geometry    : angle       0.62654 ( 8619)
  SS BOND              : bond        0.00438 (    3)
  SS BOND              : angle       1.04549 (    6)
  hydrogen bonds       : bond        0.04247 (  312)
  hydrogen bonds       : angle       5.14014 (  888)
  link_NAG-ASN         : bond        0.00212 (    2)
  link_NAG-ASN         : angle       0.61066 (    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
  183 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 168
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6407 (mm-30)
REVERT: A  151 TRP cc_start: 0.7760 (m100) cc_final: 0.7122 (m100)
REVERT: A  240 HIS cc_start: 0.6958 (p90) cc_final: 0.6665 (m170)
REVERT: A  373 PHE cc_start: 0.8287 (t80) cc_final: 0.7831 (t80)
REVERT: A  417 MET cc_start: 0.6378 (mtm) cc_final: 0.6011 (mtm)
REVERT: A  494 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6584 (mm-30)
REVERT: A  553 ILE cc_start: 0.9021 (pt) cc_final: 0.8813 (pt)
REVERT: C  101 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6859 (tp30)
REVERT: B   42 LYS cc_start: 0.6266 (mttt) cc_final: 0.5842 (tptt)
REVERT: B   53 MET cc_start: 0.9014 (tpp) cc_final: 0.8730 (tpt)
  outliers start: 15
  outliers final: 8
  residues processed: 171
  average time/residue: 0.0676
  time to fit residues: 15.8339
Evaluate side-chains
  151 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 143
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 34 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0470
   chunk 25 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 416 ASN
** C  57 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 = 0.4292 r_free = 0.4292 target = 0.185430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.168291 restraints weight = 11188.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.172405 restraints weight = 6886.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.175190 restraints weight = 4566.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.177095 restraints weight = 3335.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.178314 restraints weight = 2551.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6331  Z= 0.119
  Angle     :  0.621  11.659   8631  Z= 0.307
  Chirality :  0.041   0.215    966
  Planarity :  0.004   0.071   1048
  Dihedral  :  7.096  76.623    961
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.85 %
    Favored  : 78.15 %
  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: -1.17 (0.31), residues: 758
  helix:  0.78 (0.27), residues: 353
  sheet: -2.43 (0.46), residues: 100
  loop : -2.04 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  81 
 TYR   0.019   0.001   TYR B 123 
 PHE   0.020   0.001   PHE A 423 
 TRP   0.014   0.001   TRP A 220 
 HIS   0.004   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6326)
  covalent geometry    : angle       0.62100 ( 8619)
  SS BOND              : bond        0.00124 (    3)
  SS BOND              : angle       0.86356 (    6)
  hydrogen bonds       : bond        0.03708 (  312)
  hydrogen bonds       : angle       4.80998 (  888)
  link_NAG-ASN         : bond        0.00212 (    2)
  link_NAG-ASN         : angle       0.68732 (    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
  160 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 147
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6627 (mm-30)
REVERT: A  151 TRP cc_start: 0.7768 (m100) cc_final: 0.7130 (m100)
REVERT: A  373 PHE cc_start: 0.8316 (t80) cc_final: 0.7796 (t80)
REVERT: A  417 MET cc_start: 0.6435 (mtm) cc_final: 0.5676 (mtm)
REVERT: A  494 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6418 (mm-30)
REVERT: A  553 ILE cc_start: 0.9063 (pt) cc_final: 0.8830 (pt)
REVERT: B   42 LYS cc_start: 0.6196 (mttt) cc_final: 0.5794 (tptt)
REVERT: B  126 ASP cc_start: 0.8029 (m-30) cc_final: 0.7291 (p0)
  outliers start: 13
  outliers final: 9
  residues processed: 152
  average time/residue: 0.0633
  time to fit residues: 13.4888
Evaluate side-chains
  145 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
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  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:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 2 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 37 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4231 r_free = 0.4231 target = 0.179499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.162440 restraints weight = 11302.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.166395 restraints weight = 6891.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.169386 restraints weight = 4679.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.171591 restraints weight = 3381.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.172982 restraints weight = 2447.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6331  Z= 0.157
  Angle     :  0.657  11.920   8631  Z= 0.328
  Chirality :  0.042   0.203    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  7.288  78.339    961
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 21.54 %
    Favored  : 74.92 %
  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: -1.18 (0.30), residues: 758
  helix:  0.69 (0.27), residues: 356
  sheet: -2.45 (0.46), residues: 100
  loop : -1.96 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  81 
 TYR   0.029   0.002   TYR A 134 
 PHE   0.023   0.001   PHE A 521 
 TRP   0.020   0.001   TRP A 103 
 HIS   0.006   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6326)
  covalent geometry    : angle       0.65674 ( 8619)
  SS BOND              : bond        0.00276 (    3)
  SS BOND              : angle       1.14737 (    6)
  hydrogen bonds       : bond        0.03904 (  312)
  hydrogen bonds       : angle       4.85935 (  888)
  link_NAG-ASN         : bond        0.00137 (    2)
  link_NAG-ASN         : angle       0.80457 (    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
  163 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6755 (mm-30)
REVERT: A  386 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7456 (ttp)
REVERT: A  494 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6618 (mm-30)
REVERT: A  553 ILE cc_start: 0.9089 (pt) cc_final: 0.8840 (pt)
REVERT: C  101 GLU cc_start: 0.7099 (tp30) cc_final: 0.6735 (tp30)
REVERT: B   42 LYS cc_start: 0.6130 (mttt) cc_final: 0.5825 (tptt)
REVERT: B   58 GLN cc_start: 0.5398 (OUTLIER) cc_final: 0.4672 (tt0)
  outliers start: 23
  outliers final: 17
  residues processed: 149
  average time/residue: 0.0595
  time to fit residues: 12.6268
Evaluate side-chains
  154 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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  206 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  274 VAL
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  430 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 A residue  611 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0980
   chunk 52 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   chunk 69 optimal weight:    7.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 520 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.188892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.171169 restraints weight = 10819.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.175334 restraints weight = 6681.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.178239 restraints weight = 4477.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.180468 restraints weight = 3196.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.180468 restraints weight = 2382.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.3118

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= 0.115
  Angle     :  0.615  10.276   8631  Z= 0.308
  Chirality :  0.041   0.208    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  7.176  78.247    961
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.77 %
    Favored  : 73.85 %
  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: -0.94 (0.31), residues: 758
  helix:  0.83 (0.27), residues: 356
  sheet: -2.18 (0.47), residues: 96
  loop : -1.84 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  81 
 TYR   0.022   0.001   TYR A 134 
 PHE   0.017   0.001   PHE A 521 
 TRP   0.031   0.001   TRP B  55 
 HIS   0.003   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6326)
  covalent geometry    : angle       0.61516 ( 8619)
  SS BOND              : bond        0.00206 (    3)
  SS BOND              : angle       0.77064 (    6)
  hydrogen bonds       : bond        0.03541 (  312)
  hydrogen bonds       : angle       4.67965 (  888)
  link_NAG-ASN         : bond        0.00172 (    2)
  link_NAG-ASN         : angle       0.80665 (    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
  160 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6782 (mm-30)
REVERT: A  151 TRP cc_start: 0.7912 (m100) cc_final: 0.7363 (m100)
REVERT: A  386 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7397 (ttp)
REVERT: A  417 MET cc_start: 0.6496 (mtm) cc_final: 0.5925 (mtm)
REVERT: A  528 MET cc_start: 0.6555 (mtp) cc_final: 0.6243 (mtp)
REVERT: A  553 ILE cc_start: 0.9103 (pt) cc_final: 0.8852 (pt)
REVERT: C  101 GLU cc_start: 0.7260 (tp30) cc_final: 0.6946 (tp30)
REVERT: B   42 LYS cc_start: 0.5985 (mttt) cc_final: 0.5739 (tptt)
REVERT: B   64 LEU cc_start: 0.8670 (mm) cc_final: 0.8372 (mm)
REVERT: B  100 MET cc_start: 0.3486 (ppp) cc_final: 0.3273 (ppp)
  outliers start: 22
  outliers final: 15
  residues processed: 149
  average time/residue: 0.0547
  time to fit residues: 11.4426
Evaluate side-chains
  144 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  430 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 B residue   77 THR
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:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 69 optimal weight:    0.2980
   chunk 51 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0570
   overall best weight:    0.6100

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

Flipped N/Q/H residues before XYZ refinement:
C 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.189892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.172568 restraints weight = 10726.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.176586 restraints weight = 6678.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.179576 restraints weight = 4517.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.180474 restraints weight = 3247.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.182474 restraints weight = 2696.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6851
moved from start:          0.3325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6331  Z= 0.113
  Angle     :  0.625  13.064   8631  Z= 0.309
  Chirality :  0.041   0.253    966
  Planarity :  0.004   0.071   1048
  Dihedral  :  6.799  73.453    961
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 24.31 %
    Favored  : 72.92 %
  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: -0.80 (0.31), residues: 758
  helix:  0.92 (0.27), residues: 356
  sheet: -2.01 (0.47), residues: 96
  loop : -1.75 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  81 
 TYR   0.021   0.001   TYR A 134 
 PHE   0.017   0.001   PHE A 428 
 TRP   0.034   0.001   TRP A 103 
 HIS   0.004   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6326)
  covalent geometry    : angle       0.62418 ( 8619)
  SS BOND              : bond        0.00174 (    3)
  SS BOND              : angle       0.90946 (    6)
  hydrogen bonds       : bond        0.03451 (  312)
  hydrogen bonds       : angle       4.64680 (  888)
  link_NAG-ASN         : bond        0.00053 (    2)
  link_NAG-ASN         : angle       0.94675 (    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
  159 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6770 (mm-30)
REVERT: A  151 TRP cc_start: 0.7882 (m100) cc_final: 0.7313 (m100)
REVERT: A  180 MET cc_start: 0.7617 (mmm) cc_final: 0.7414 (tpp)
REVERT: A  475 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7946 (m-80)
REVERT: A  553 ILE cc_start: 0.9105 (pt) cc_final: 0.8851 (pt)
REVERT: C   74 ARG cc_start: 0.6819 (ptt-90) cc_final: 0.6544 (ptp90)
REVERT: C  101 GLU cc_start: 0.7298 (tp30) cc_final: 0.7016 (tp30)
REVERT: B   42 LYS cc_start: 0.6072 (mttt) cc_final: 0.5852 (tptt)
REVERT: B  100 MET cc_start: 0.3401 (ppp) cc_final: 0.3200 (ppp)
  outliers start: 18
  outliers final: 14
  residues processed: 149
  average time/residue: 0.0550
  time to fit residues: 11.5939
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  : 0.141 
-------------------------------------------------------------------------------
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  430 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   79 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 58 optimal weight:    0.1980
   chunk 7 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 48 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
C 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.189878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.171695 restraints weight = 10842.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.174743 restraints weight = 6535.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.177503 restraints weight = 4605.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.180354 restraints weight = 3481.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.181406 restraints weight = 2602.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6331  Z= 0.125
  Angle     :  0.634  11.929   8631  Z= 0.314
  Chirality :  0.042   0.335    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  6.649  73.910    961
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 25.08 %
    Favored  : 71.85 %
  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: -0.76 (0.31), residues: 758
  helix:  0.89 (0.27), residues: 356
  sheet: -1.90 (0.47), residues: 96
  loop : -1.68 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  81 
 TYR   0.024   0.002   TYR A 134 
 PHE   0.013   0.001   PHE A 428 
 TRP   0.023   0.001   TRP A 103 
 HIS   0.004   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6326)
  covalent geometry    : angle       0.63323 ( 8619)
  SS BOND              : bond        0.00380 (    3)
  SS BOND              : angle       1.02076 (    6)
  hydrogen bonds       : bond        0.03589 (  312)
  hydrogen bonds       : angle       4.65051 (  888)
  link_NAG-ASN         : bond        0.00061 (    2)
  link_NAG-ASN         : angle       0.90161 (    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
  160 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6820 (mm-30)
REVERT: A  386 MET cc_start: 0.8510 (tpp) cc_final: 0.8189 (mtp)
REVERT: A  417 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.5841 (mtm)
REVERT: A  494 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6455 (mm-30)
REVERT: A  553 ILE cc_start: 0.9135 (pt) cc_final: 0.8884 (pt)
REVERT: C   31 MET cc_start: 0.6351 (ppp) cc_final: 0.6025 (tmm)
REVERT: C   74 ARG cc_start: 0.6854 (ptt-90) cc_final: 0.6553 (ptp90)
REVERT: C  101 GLU cc_start: 0.7303 (tp30) cc_final: 0.7055 (tp30)
REVERT: B   42 LYS cc_start: 0.6167 (mttt) cc_final: 0.5905 (tptt)
REVERT: B   58 GLN cc_start: 0.5019 (OUTLIER) cc_final: 0.4252 (tp40)
  outliers start: 20
  outliers final: 17
  residues processed: 151
  average time/residue: 0.0620
  time to fit residues: 13.2387
Evaluate side-chains
  155 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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  417 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  447 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 C residue  113 SER
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:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 64 optimal weight:    9.9990
   chunk 27 optimal weight:    0.4980
   chunk 40 optimal weight:    0.0170
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
C 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.191646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.174060 restraints weight = 10958.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.178287 restraints weight = 6712.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.181314 restraints weight = 4416.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.182880 restraints weight = 3145.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.184724 restraints weight = 2427.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6331  Z= 0.118
  Angle     :  0.643  12.742   8631  Z= 0.319
  Chirality :  0.042   0.321    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  6.203  74.904    961
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.69 %
    Favored  : 70.62 %
  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: -0.73 (0.31), residues: 758
  helix:  0.89 (0.27), residues: 354
  sheet: -1.74 (0.48), residues: 95
  loop : -1.69 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  81 
 TYR   0.021   0.001   TYR B 123 
 PHE   0.029   0.001   PHE A 311 
 TRP   0.023   0.001   TRP B  55 
 HIS   0.006   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6326)
  covalent geometry    : angle       0.64262 ( 8619)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.95046 (    6)
  hydrogen bonds       : bond        0.03592 (  312)
  hydrogen bonds       : angle       4.62767 (  888)
  link_NAG-ASN         : bond        0.00089 (    2)
  link_NAG-ASN         : angle       0.86450 (    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
  165 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6795 (mm-30)
REVERT: A  151 TRP cc_start: 0.7895 (m100) cc_final: 0.7340 (m100)
REVERT: A  370 MET cc_start: 0.6000 (mtt) cc_final: 0.5633 (mtt)
REVERT: A  386 MET cc_start: 0.8461 (tpp) cc_final: 0.8164 (mtp)
REVERT: A  417 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5965 (mtm)
REVERT: A  475 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7957 (m-80)
REVERT: A  494 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6437 (mm-30)
REVERT: A  553 ILE cc_start: 0.9100 (pt) cc_final: 0.8857 (pt)
REVERT: C   31 MET cc_start: 0.6136 (ppp) cc_final: 0.5835 (tmm)
REVERT: C   74 ARG cc_start: 0.6733 (ptt-90) cc_final: 0.6442 (ptp90)
REVERT: B   58 GLN cc_start: 0.4924 (OUTLIER) cc_final: 0.4192 (tp40)
  outliers start: 24
  outliers final: 17
  residues processed: 157
  average time/residue: 0.0598
  time to fit residues: 13.1798
Evaluate side-chains
  157 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
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  430 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   22 ILE
Chi-restraints excluded: chain C residue  113 SER
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
C 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.191631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.173942 restraints weight = 10450.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.178156 restraints weight = 6293.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.181101 restraints weight = 4162.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.183136 restraints weight = 2945.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.183136 restraints weight = 2268.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.3644

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= 0.140
  Angle     :  0.678  11.139   8631  Z= 0.338
  Chirality :  0.043   0.303    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  6.121  74.393    961
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 26.77 %
    Favored  : 70.15 %
  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: -0.70 (0.31), residues: 758
  helix:  0.88 (0.27), residues: 355
  sheet: -1.76 (0.47), residues: 99
  loop : -1.61 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C  81 
 TYR   0.024   0.002   TYR B 123 
 PHE   0.040   0.002   PHE A 311 
 TRP   0.022   0.001   TRP B  55 
 HIS   0.005   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6326)
  covalent geometry    : angle       0.67745 ( 8619)
  SS BOND              : bond        0.00267 (    3)
  SS BOND              : angle       1.08279 (    6)
  hydrogen bonds       : bond        0.03684 (  312)
  hydrogen bonds       : angle       4.68522 (  888)
  link_NAG-ASN         : bond        0.00070 (    2)
  link_NAG-ASN         : angle       0.87633 (    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
  159 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6856 (mm-30)
REVERT: A  180 MET cc_start: 0.8010 (mmp) cc_final: 0.7495 (mmm)
REVERT: A  417 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.5901 (mtm)
REVERT: A  475 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7986 (m-80)
REVERT: A  494 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6473 (mm-30)
REVERT: A  553 ILE cc_start: 0.9133 (pt) cc_final: 0.8887 (pt)
REVERT: C   74 ARG cc_start: 0.6778 (ptt-90) cc_final: 0.6466 (ptp90)
REVERT: B   58 GLN cc_start: 0.4942 (OUTLIER) cc_final: 0.4159 (tp40)
  outliers start: 20
  outliers final: 16
  residues processed: 151
  average time/residue: 0.0656
  time to fit residues: 13.9062
Evaluate side-chains
  153 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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   22 ILE
Chi-restraints excluded: chain C residue  113 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0370
   chunk 68 optimal weight:    0.5980
   chunk 13 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0060
   chunk 9 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 45 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.5074

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

Flipped N/Q/H residues before XYZ refinement:
C 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.192878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.175372 restraints weight = 10949.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.178686 restraints weight = 6433.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.182190 restraints weight = 4609.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.184319 restraints weight = 3197.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.185320 restraints weight = 2359.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6331  Z= 0.117
  Angle     :  0.666  11.414   8631  Z= 0.328
  Chirality :  0.042   0.283    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  5.895  74.258    961
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 27.23 %
    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: -0.53 (0.31), residues: 758
  helix:  1.02 (0.28), residues: 353
  sheet: -1.61 (0.48), residues: 95
  loop : -1.54 (0.36), residues: 310

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   0.035   0.001   PHE A 311 
 TRP   0.017   0.001   TRP B  55 
 HIS   0.002   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6326)
  covalent geometry    : angle       0.66526 ( 8619)
  SS BOND              : bond        0.00259 (    3)
  SS BOND              : angle       1.15075 (    6)
  hydrogen bonds       : bond        0.03471 (  312)
  hydrogen bonds       : angle       4.66679 (  888)
  link_NAG-ASN         : bond        0.00096 (    2)
  link_NAG-ASN         : angle       0.94028 (    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: 18
    poor density    : 140
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6793 (mm-30)
REVERT: A  151 TRP cc_start: 0.7878 (m100) cc_final: 0.7271 (m100)
REVERT: A  180 MET cc_start: 0.7958 (mmp) cc_final: 0.7402 (mmm)
REVERT: A  417 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.5617 (mtm)
REVERT: A  475 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.8011 (m-80)
REVERT: A  494 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6424 (mm-30)
REVERT: A  553 ILE cc_start: 0.9098 (pt) cc_final: 0.8857 (pt)
REVERT: C   74 ARG cc_start: 0.6614 (ptt-90) cc_final: 0.6331 (ptp90)
REVERT: B   58 GLN cc_start: 0.4834 (OUTLIER) cc_final: 0.4139 (tp40)
  outliers start: 18
  outliers final: 15
  residues processed: 151
  average time/residue: 0.0672
  time to fit residues: 14.2932
Evaluate side-chains
  155 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
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  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   22 ILE
Chi-restraints excluded: chain C residue  113 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 13 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 25 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 416 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.190665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.173592 restraints weight = 10803.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.176365 restraints weight = 6631.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.179817 restraints weight = 4789.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.182168 restraints weight = 3427.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.183072 restraints weight = 2527.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.3787

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= 0.126
  Angle     :  0.671  12.252   8631  Z= 0.333
  Chirality :  0.042   0.276    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  5.857  73.212    961
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 26.92 %
    Favored  : 69.85 %
  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: -0.53 (0.31), residues: 758
  helix:  0.99 (0.27), residues: 354
  sheet: -1.69 (0.47), residues: 95
  loop : -1.47 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  81 
 TYR   0.020   0.001   TYR A 134 
 PHE   0.029   0.001   PHE A 311 
 TRP   0.018   0.001   TRP B  55 
 HIS   0.004   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6326)
  covalent geometry    : angle       0.67064 ( 8619)
  SS BOND              : bond        0.00218 (    3)
  SS BOND              : angle       0.83093 (    6)
  hydrogen bonds       : bond        0.03543 (  312)
  hydrogen bonds       : angle       4.66121 (  888)
  link_NAG-ASN         : bond        0.00126 (    2)
  link_NAG-ASN         : angle       0.82961 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1196.76 seconds
wall clock time: 21 minutes 25.98 seconds (1285.98 seconds total)