Starting phenix.real_space_refine
on Sat Apr  4 20:45:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w14_65523/04_2026/9w14_65523.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w14_65523/04_2026/9w14_65523.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w14_65523/04_2026/9w14_65523.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w14_65523/04_2026/9w14_65523.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w14_65523/04_2026/9w14_65523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w14_65523/04_2026/9w14_65523.map"
  }
  resolution = 2.33
  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=  -0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2024      2.51       5
     N     522      2.21       5
     O     601      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3161
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "G"
      Number of atoms: 1405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1405
          Classifications: {'peptide': 186}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 9, 'TRANS': 176}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 49
    Chain: "B"
      Number of atoms: 774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 774
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "C"
      Number of atoms: 933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 933
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 0.96, per 1000 atoms: 0.30
  Number of scatterers: 3161
  At special positions: 0
  Unit cell: (65, 81.25, 72.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     601      8.00
     N     522      7.00
     C    2024      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 480 " - pdb=" SG  CYS G 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
    BETA1-6
      " NAG A   1 " - " FUC A   4 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A   1 " - " ASN G 343 "
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 127.7 milliseconds
  

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  754

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 10 sheets defined
      13.6% alpha, 30.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'G' and resid 337 through 343
      removed outlier: 3.982A  pdb=" N   VAL G 341 " --> pdb=" O   PRO G 337 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 364 through 371
      removed outlier: 4.244A  pdb=" N   LEU G 368 " --> pdb=" O   ASP G 364 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 385 through 390
      removed outlier: 4.204A  pdb=" N   ASN G 388 " --> pdb=" O   THR G 385 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU G 390 " --> pdb=" O   LEU G 387 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 403 through 410
      removed outlier: 4.406A  pdb=" N   ARG G 408 " --> pdb=" O   ASP G 405 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 416 through 422
    Processing helix  chain 'G' and resid 438 through 443
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.936A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 65
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.823A  pdb=" N   THR C  91 " --> pdb=" O   ASN C  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'G' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'G' and resid 473 through 474
      removed outlier: 3.561A  pdb=" N   TYR G 489 " --> pdb=" O   TYR G 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7
      removed outlier: 3.668A  pdb=" N   SER B   7 " --> pdb=" O   SER B  22 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER B  22 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   PHE B  71 " --> pdb=" O   CYS B  23 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ASP B  70 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER B  67 " --> pdb=" O   ASP B  70 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12
      removed outlier: 4.085A  pdb=" N   THR B  97 " --> pdb=" O   GLN B  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 49
    Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.520A  pdb=" N   GLU C  10 " --> pdb=" O   THR C 116 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   LEU C  34 " --> pdb=" O   TRP C  50 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   TRP C  50 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   TRP C  36 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 18 through 20
      removed outlier: 3.630A  pdb=" N   THR C  78 " --> pdb=" O   GLU C  73 " (cutoff:3.500A)

    109 hydrogen bonds defined for protein.
    249 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.53

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 988
        1.34 -     1.46: 879
        1.46 -     1.58: 1361
        1.58 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 3244
  Sorted by residual:
  bond pdb=" C1  BMA A   3 "
       pdb=" C2  BMA A   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.555 -0.036 2.00e-02 2.50e+03 3.22e+00
  bond pdb=" C1  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.19e+00
  bond pdb=" C5  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.38e+00
  bond pdb=" C5  NAG A   1 "
       pdb=" O5  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.16e+00
  bond pdb=" C3  NAG A   2 "
       pdb=" O3  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.403  1.424 -0.021 2.00e-02 2.50e+03 1.06e+00
  ... (remaining 3239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 4274
        1.39 -     2.78: 115
        2.78 -     4.16: 22
        4.16 -     5.55: 8
        5.55 -     6.94: 4
  Bond angle restraints: 4423
  Sorted by residual:
  angle pdb=" C   SER B  30 "
        pdb=" CA  SER B  30 "
        pdb=" CB  SER B  30 "
      ideal   model   delta    sigma   weight residual
     116.54  109.98    6.56 1.15e+00 7.56e-01 3.25e+01
  angle pdb=" CA  SER B  30 "
        pdb=" C   SER B  30 "
        pdb=" N   ASN B  31 "
      ideal   model   delta    sigma   weight residual
     119.52  116.85    2.67 7.90e-01 1.60e+00 1.14e+01
  angle pdb=" N   SER B  30 "
        pdb=" CA  SER B  30 "
        pdb=" C   SER B  30 "
      ideal   model   delta    sigma   weight residual
     108.31  112.39   -4.08 1.52e+00 4.33e-01 7.19e+00
  angle pdb=" N   ASN C 101 "
        pdb=" CA  ASN C 101 "
        pdb=" C   ASN C 101 "
      ideal   model   delta    sigma   weight residual
     113.28  109.66    3.62 1.57e+00 4.06e-01 5.33e+00
  angle pdb=" C   GLY C 100 "
        pdb=" N   ASN C 101 "
        pdb=" CA  ASN C 101 "
      ideal   model   delta    sigma   weight residual
     126.45  130.20   -3.75 1.77e+00 3.19e-01 4.49e+00
  ... (remaining 4418 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.79: 1826
       21.79 -    43.58: 72
       43.58 -    65.37: 13
       65.37 -    87.16: 7
       87.16 -   108.95: 4
  Dihedral angle restraints: 1922
    sinusoidal: 735
      harmonic: 1187
  Sorted by residual:
  dihedral pdb=" CA  ASN C 101 "
           pdb=" C   ASN C 101 "
           pdb=" N   TRP C 102 "
           pdb=" CA  TRP C 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.89   21.11     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  TRP C 104 "
           pdb=" C   TRP C 104 "
           pdb=" N   TYR C 105 "
           pdb=" CA  TYR C 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.36   19.64     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" O4  BMA A   3 "
           pdb=" C4  BMA A   3 "
           pdb=" C5  BMA A   3 "
           pdb=" O5  BMA A   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  179.76  108.95     1      3.00e+01 1.11e-03 1.41e+01
  ... (remaining 1919 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 405
       0.057 -    0.113: 75
       0.113 -    0.169: 11
       0.169 -    0.226: 0
       0.226 -    0.282: 2
  Chirality restraints: 493
  Sorted by residual:
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN G 343 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" C5  BMA A   3 "
            pdb=" C4  BMA A   3 "
            pdb=" C6  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" C4  NAG A   2 "
            pdb=" C3  NAG A   2 "
            pdb=" C5  NAG A   2 "
            pdb=" O4  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.37   -0.16 2.00e-01 2.50e+01 6.37e-01
  ... (remaining 490 not shown)

  Planarity restraints: 563
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS G 336 "   -0.023 5.00e-02 4.00e+02   3.53e-02 2.00e+00
        pdb=" N   PRO G 337 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO G 337 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO G 337 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN G 343 "   -0.011 2.00e-02 2.50e+03   1.22e-02 1.86e+00
        pdb=" CG  ASN G 343 "    0.004 2.00e-02 2.50e+03
        pdb=" OD1 ASN G 343 "    0.003 2.00e-02 2.50e+03
        pdb=" ND2 ASN G 343 "    0.019 2.00e-02 2.50e+03
        pdb=" C1  NAG A   1 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE G 490 "   -0.020 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO G 491 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO G 491 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO G 491 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 560 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 505
        2.77 -     3.30: 2775
        3.30 -     3.83: 5048
        3.83 -     4.37: 6179
        4.37 -     4.90: 10523
  Nonbonded interactions: 25030
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  43 "
            pdb=" O   GLY C 110 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" NH2 ARG C  98 "
            pdb=" OD2 ASP C 107 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" O   LEU B  21 "
            pdb=" OG1 THR B  72 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" NH2 ARG B  61 "
            pdb=" OE2 GLU B  81 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" N   GLN G 498 "
            pdb=" OD1 ASN G 501 "
     model   vdw
     2.398 3.120
  ... (remaining 25025 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 individual isotropic
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:             28.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.440
  Find NCS groups from input model:        0.010
  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:7.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5112
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      :  0.003   0.036   3252  Z= 0.169
  Angle     :  0.641   7.556   4443  Z= 0.329
  Chirality :  0.048   0.282    493
  Planarity :  0.004   0.035    562
  Dihedral  : 14.685 108.947   1156
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.13 (0.42), residues: 404
  helix: -1.84 (0.97), residues: 21
  sheet:  0.51 (0.45), residues: 150
  loop : -0.25 (0.40), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  45 
 TYR   0.011   0.001   TYR C 105 
 PHE   0.010   0.001   PHE B  71 
 TRP   0.009   0.002   TRP C 104 
 HIS   0.001   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3244)
  covalent geometry    : angle       0.60533 ( 4423)
  SS BOND              : bond        0.00321 (    4)
  SS BOND              : angle       0.49255 (    8)
  hydrogen bonds       : bond        0.23412 (  103)
  hydrogen bonds       : angle       9.40835 (  249)
  link_BETA1-4         : bond        0.00328 (    2)
  link_BETA1-4         : angle       4.22933 (    6)
  link_BETA1-6         : bond        0.00235 (    1)
  link_BETA1-6         : angle       1.77583 (    3)
  link_NAG-ASN         : bond        0.01720 (    1)
  link_NAG-ASN         : angle       5.40792 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.5542
  time to fit residues: 33.6336
Evaluate side-chains
  12 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    0.0030
   chunk 26 optimal weight:   20.0000
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 19 optimal weight:   20.0000
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 37 optimal weight:    8.9990
   overall best weight:    3.6796

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

Flipped N/Q/H residues before XYZ refinement:
G 394 ASN
B  37 GLN
** B  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  53 GLN
C   6 GLN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.069492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.058369 restraints weight = 20343.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.4092 rms_B_bonded: 3.59
r_work: 0.3993 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   3252  Z= 0.203
  Angle     :  0.754   6.987   4443  Z= 0.370
  Chirality :  0.049   0.183    493
  Planarity :  0.005   0.037    562
  Dihedral  :  9.054  61.269    525
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  9.62 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.05 (0.43), residues: 404
  helix: -2.24 (1.18), residues: 15
  sheet:  0.47 (0.43), residues: 159
  loop : -0.16 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 408 
 TYR   0.022   0.002   TYR C 105 
 PHE   0.014   0.002   PHE B  87 
 TRP   0.009   0.002   TRP C  50 
 HIS   0.002   0.002   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 3244)
  covalent geometry    : angle       0.72670 ( 4423)
  SS BOND              : bond        0.00128 (    4)
  SS BOND              : angle       1.06599 (    8)
  hydrogen bonds       : bond        0.04184 (  103)
  hydrogen bonds       : angle       7.15343 (  249)
  link_BETA1-4         : bond        0.00399 (    2)
  link_BETA1-4         : angle       4.24266 (    6)
  link_BETA1-6         : bond        0.00057 (    1)
  link_BETA1-6         : angle       1.49699 (    3)
  link_NAG-ASN         : bond        0.01282 (    1)
  link_NAG-ASN         : angle       4.76229 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: G  470 THR cc_start: 0.7078 (OUTLIER) cc_final: 0.6752 (p)
REVERT: B   85 MET cc_start: 0.4638 (mmm) cc_final: 0.4293 (mmm)
  outliers start: 7
  outliers final: 2
  residues processed: 30
  average time/residue: 0.7128
  time to fit residues: 21.9201
Evaluate side-chains
  13 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 10
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  375 SER
Chi-restraints excluded: chain G residue  470 THR
Chi-restraints excluded: chain B residue    5 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 2 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  38 GLN
B  76 ASN
** C  35 ASN ** 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 = 0.4510 r_free = 0.4510 target = 0.068985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.058021 restraints weight = 20845.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.4078 rms_B_bonded: 3.55
r_work: 0.3976 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3252  Z= 0.169
  Angle     :  0.672   7.123   4443  Z= 0.331
  Chirality :  0.046   0.169    493
  Planarity :  0.004   0.037    562
  Dihedral  :  7.008  42.362    525
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.74 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.22 (0.42), residues: 404
  helix: -2.51 (1.03), residues: 21
  sheet:  0.35 (0.42), residues: 162
  loop : -0.20 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG G 355 
 TYR   0.029   0.002   TYR B  86 
 PHE   0.008   0.002   PHE C  29 
 TRP   0.009   0.002   TRP B  94 
 HIS   0.002   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3244)
  covalent geometry    : angle       0.64552 ( 4423)
  SS BOND              : bond        0.00163 (    4)
  SS BOND              : angle       0.73634 (    8)
  hydrogen bonds       : bond        0.03632 (  103)
  hydrogen bonds       : angle       6.67322 (  249)
  link_BETA1-4         : bond        0.00363 (    2)
  link_BETA1-4         : angle       3.95458 (    6)
  link_BETA1-6         : bond        0.00156 (    1)
  link_BETA1-6         : angle       1.35454 (    3)
  link_NAG-ASN         : bond        0.01048 (    1)
  link_NAG-ASN         : angle       4.49099 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 13
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 18
  average time/residue: 0.7222
  time to fit residues: 13.3974
Evaluate side-chains
  13 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 9
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  375 SER
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   72 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 7 optimal weight:    0.3980
   chunk 9 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 26 optimal weight:   20.0000
   chunk 16 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    4.4788

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

Flipped N/Q/H residues before XYZ refinement:
B  38 GLN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.066516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.055646 restraints weight = 20744.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 3.39
r_work: 0.3927 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.5389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   3252  Z= 0.224
  Angle     :  0.711   6.819   4443  Z= 0.352
  Chirality :  0.047   0.188    493
  Planarity :  0.005   0.033    562
  Dihedral  :  6.123  47.307    525
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 13.14 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.56 (0.41), residues: 404
  helix: -2.97 (1.08), residues: 15
  sheet: -0.02 (0.41), residues: 161
  loop : -0.35 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G 355 
 TYR   0.014   0.002   TYR C  54 
 PHE   0.017   0.002   PHE C  70 
 TRP   0.011   0.002   TRP C 109 
 HIS   0.004   0.003   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 3244)
  covalent geometry    : angle       0.68403 ( 4423)
  SS BOND              : bond        0.00172 (    4)
  SS BOND              : angle       0.93827 (    8)
  hydrogen bonds       : bond        0.03496 (  103)
  hydrogen bonds       : angle       6.78844 (  249)
  link_BETA1-4         : bond        0.00604 (    2)
  link_BETA1-4         : angle       3.92177 (    6)
  link_BETA1-6         : bond        0.00232 (    1)
  link_BETA1-6         : angle       1.67037 (    3)
  link_NAG-ASN         : bond        0.01009 (    1)
  link_NAG-ASN         : angle       4.71252 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 10
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: G  470 THR cc_start: 0.7057 (OUTLIER) cc_final: 0.6610 (p)
REVERT: B   11 LEU cc_start: 0.5898 (pt) cc_final: 0.5403 (tp)
  outliers start: 15
  outliers final: 8
  residues processed: 24
  average time/residue: 0.6693
  time to fit residues: 16.5076
Evaluate side-chains
  17 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 8
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  373 SER
Chi-restraints excluded: chain G residue  375 SER
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain G residue  470 THR
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   80 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.067726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.056664 restraints weight = 20313.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.4052 rms_B_bonded: 3.52
r_work: 0.3946 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.5505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3252  Z= 0.135
  Angle     :  0.631   7.715   4443  Z= 0.308
  Chirality :  0.044   0.145    493
  Planarity :  0.004   0.034    562
  Dihedral  :  6.183  52.328    525
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.03 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.59 (0.41), residues: 404
  helix: -2.47 (1.12), residues: 21
  sheet: -0.09 (0.41), residues: 159
  loop : -0.30 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 408 
 TYR   0.012   0.001   TYR C 105 
 PHE   0.009   0.001   PHE B  87 
 TRP   0.010   0.001   TRP C 104 
 HIS   0.002   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3244)
  covalent geometry    : angle       0.60615 ( 4423)
  SS BOND              : bond        0.00134 (    4)
  SS BOND              : angle       0.67930 (    8)
  hydrogen bonds       : bond        0.03055 (  103)
  hydrogen bonds       : angle       6.56479 (  249)
  link_BETA1-4         : bond        0.00587 (    2)
  link_BETA1-4         : angle       3.56544 (    6)
  link_BETA1-6         : bond        0.00013 (    1)
  link_BETA1-6         : angle       1.51842 (    3)
  link_NAG-ASN         : bond        0.01043 (    1)
  link_NAG-ASN         : angle       4.34329 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 12
  time to evaluate  : 0.129 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.6017 (pt) cc_final: 0.5507 (tp)
  outliers start: 11
  outliers final: 6
  residues processed: 22
  average time/residue: 0.6648
  time to fit residues: 15.0859
Evaluate side-chains
  16 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  373 SER
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   80 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0970
   chunk 36 optimal weight:    6.9990
   chunk 37 optimal weight:   30.0000
   chunk 18 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.3980
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
B  37 GLN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.068150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.057035 restraints weight = 20342.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 3.52
r_work: 0.3954 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.5701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3252  Z= 0.112
  Angle     :  0.602   6.351   4443  Z= 0.297
  Chirality :  0.044   0.139    493
  Planarity :  0.004   0.037    562
  Dihedral  :  5.908  50.100    525
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.71 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.54 (0.42), residues: 404
  helix: -2.43 (1.12), residues: 21
  sheet: -0.08 (0.41), residues: 159
  loop : -0.25 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 408 
 TYR   0.009   0.001   TYR C 105 
 PHE   0.009   0.001   PHE B  87 
 TRP   0.010   0.001   TRP C 102 
 HIS   0.001   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 3244)
  covalent geometry    : angle       0.57743 ( 4423)
  SS BOND              : bond        0.00146 (    4)
  SS BOND              : angle       0.58383 (    8)
  hydrogen bonds       : bond        0.02981 (  103)
  hydrogen bonds       : angle       6.41676 (  249)
  link_BETA1-4         : bond        0.00567 (    2)
  link_BETA1-4         : angle       3.43063 (    6)
  link_BETA1-6         : bond        0.00179 (    1)
  link_BETA1-6         : angle       1.66203 (    3)
  link_NAG-ASN         : bond        0.01033 (    1)
  link_NAG-ASN         : angle       4.13888 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 9
  time to evaluate  : 0.120 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.6056 (pt) cc_final: 0.5583 (tp)
  outliers start: 11
  outliers final: 7
  residues processed: 19
  average time/residue: 0.5220
  time to fit residues: 10.3384
Evaluate side-chains
  16 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 9
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   34 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.067622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.056454 restraints weight = 21008.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 3.54
r_work: 0.3935 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.5969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3252  Z= 0.135
  Angle     :  0.624   6.584   4443  Z= 0.307
  Chirality :  0.044   0.142    493
  Planarity :  0.004   0.033    562
  Dihedral  :  5.836  48.326    525
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.03 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.59 (0.42), residues: 404
  helix: -2.35 (1.14), residues: 21
  sheet: -0.20 (0.40), residues: 160
  loop : -0.21 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 408 
 TYR   0.011   0.001   TYR C 105 
 PHE   0.009   0.001   PHE B  87 
 TRP   0.009   0.002   TRP C 102 
 HIS   0.002   0.002   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3244)
  covalent geometry    : angle       0.60143 ( 4423)
  SS BOND              : bond        0.00116 (    4)
  SS BOND              : angle       0.62028 (    8)
  hydrogen bonds       : bond        0.03090 (  103)
  hydrogen bonds       : angle       6.42328 (  249)
  link_BETA1-4         : bond        0.00558 (    2)
  link_BETA1-4         : angle       3.30877 (    6)
  link_BETA1-6         : bond        0.00107 (    1)
  link_BETA1-6         : angle       1.61680 (    3)
  link_NAG-ASN         : bond        0.01041 (    1)
  link_NAG-ASN         : angle       4.13612 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 9
  time to evaluate  : 0.122 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.6108 (pt) cc_final: 0.5685 (tp)
  outliers start: 11
  outliers final: 8
  residues processed: 18
  average time/residue: 0.4512
  time to fit residues: 8.5091
Evaluate side-chains
  16 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 8
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  373 SER
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   34 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 8 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0060
   chunk 28 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 22 optimal weight:   30.0000
   chunk 20 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 17 optimal weight:    0.3980
   overall best weight:    3.6802

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.066822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.055720 restraints weight = 20925.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 3.47
r_work: 0.3920 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.6391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3252  Z= 0.183
  Angle     :  0.666   8.500   4443  Z= 0.329
  Chirality :  0.045   0.140    493
  Planarity :  0.004   0.033    562
  Dihedral  :  6.071  49.834    525
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 17.31 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.42), residues: 404
  helix: -2.44 (1.07), residues: 21
  sheet: -0.42 (0.40), residues: 162
  loop : -0.24 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG G 408 
 TYR   0.010   0.001   TYR C 105 
 PHE   0.011   0.002   PHE C  29 
 TRP   0.009   0.002   TRP C 104 
 HIS   0.002   0.002   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 3244)
  covalent geometry    : angle       0.64356 ( 4423)
  SS BOND              : bond        0.00146 (    4)
  SS BOND              : angle       0.80207 (    8)
  hydrogen bonds       : bond        0.03217 (  103)
  hydrogen bonds       : angle       6.53029 (  249)
  link_BETA1-4         : bond        0.00656 (    2)
  link_BETA1-4         : angle       3.38828 (    6)
  link_BETA1-6         : bond        0.00056 (    1)
  link_BETA1-6         : angle       1.75522 (    3)
  link_NAG-ASN         : bond        0.01012 (    1)
  link_NAG-ASN         : angle       4.28984 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 9
  time to evaluate  : 0.169 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.6130 (pt) cc_final: 0.5758 (tp)
  outliers start: 11
  outliers final: 9
  residues processed: 19
  average time/residue: 0.4230
  time to fit residues: 8.4341
Evaluate side-chains
  16 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 7
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  373 SER
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain G residue  500 THR
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   34 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    0.2980
   chunk 14 optimal weight:   30.0000
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0670
   chunk 3 optimal weight:    0.0870
   chunk 15 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.8898

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.068170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.057408 restraints weight = 20605.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 3.37
r_work: 0.3960 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.6363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3252  Z= 0.099
  Angle     :  0.623   9.700   4443  Z= 0.303
  Chirality :  0.044   0.139    493
  Planarity :  0.004   0.033    562
  Dihedral  :  5.697  44.480    525
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.95 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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 (0.42), residues: 404
  helix: -2.20 (1.14), residues: 21
  sheet: -0.19 (0.40), residues: 160
  loop : -0.16 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G 408 
 TYR   0.011   0.001   TYR C 105 
 PHE   0.009   0.001   PHE B  87 
 TRP   0.011   0.001   TRP C 102 
 HIS   0.001   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3244)
  covalent geometry    : angle       0.60247 ( 4423)
  SS BOND              : bond        0.00089 (    4)
  SS BOND              : angle       0.51502 (    8)
  hydrogen bonds       : bond        0.02938 (  103)
  hydrogen bonds       : angle       6.21993 (  249)
  link_BETA1-4         : bond        0.00608 (    2)
  link_BETA1-4         : angle       3.32239 (    6)
  link_BETA1-6         : bond        0.00087 (    1)
  link_BETA1-6         : angle       1.44191 (    3)
  link_NAG-ASN         : bond        0.00992 (    1)
  link_NAG-ASN         : angle       3.91462 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 11
  time to evaluate  : 0.129 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.6155 (pt) cc_final: 0.5810 (tp)
  outliers start: 8
  outliers final: 5
  residues processed: 19
  average time/residue: 0.4990
  time to fit residues: 9.9054
Evaluate side-chains
  15 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 10
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  373 SER
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain C residue   34 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 28 optimal weight:    0.4980
   chunk 14 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 2 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 25 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    3.2184

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.067315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.056185 restraints weight = 20873.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 3.54
r_work: 0.3924 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.6580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3252  Z= 0.172
  Angle     :  0.675  10.490   4443  Z= 0.330
  Chirality :  0.045   0.148    493
  Planarity :  0.004   0.032    562
  Dihedral  :  5.736  42.763    525
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.91 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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 (0.42), residues: 404
  helix: -2.28 (1.06), residues: 27
  sheet: -0.40 (0.40), residues: 162
  loop : -0.11 (0.43), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G 408 
 TYR   0.012   0.001   TYR C 105 
 PHE   0.011   0.002   PHE B  87 
 TRP   0.015   0.002   TRP C 109 
 HIS   0.002   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 3244)
  covalent geometry    : angle       0.65493 ( 4423)
  SS BOND              : bond        0.00104 (    4)
  SS BOND              : angle       0.72269 (    8)
  hydrogen bonds       : bond        0.03141 (  103)
  hydrogen bonds       : angle       6.32671 (  249)
  link_BETA1-4         : bond        0.00623 (    2)
  link_BETA1-4         : angle       3.24512 (    6)
  link_BETA1-6         : bond        0.00166 (    1)
  link_BETA1-6         : angle       1.73102 (    3)
  link_NAG-ASN         : bond        0.01029 (    1)
  link_NAG-ASN         : angle       4.20660 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 9
  time to evaluate  : 0.105 
Fit side-chains
REVERT: B   11 LEU cc_start: 0.6212 (pt) cc_final: 0.5854 (tp)
REVERT: C   85 ASN cc_start: 0.8810 (t0) cc_final: 0.8595 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 15
  average time/residue: 0.2459
  time to fit residues: 4.0540
Evaluate side-chains
  14 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 9
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  373 SER
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain C residue   34 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 37 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 21 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0020
   overall best weight:    2.5996

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

Flipped N/Q/H residues before XYZ refinement:
G 448 ASN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.067442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.056309 restraints weight = 21342.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 3.60
r_work: 0.3929 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.6824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3252  Z= 0.140
  Angle     :  0.655  10.382   4443  Z= 0.318
  Chirality :  0.044   0.151    493
  Planarity :  0.004   0.037    562
  Dihedral  :  5.588  39.509    525
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.59 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.71 (0.42), residues: 404
  helix: -2.24 (1.06), residues: 27
  sheet: -0.40 (0.40), residues: 163
  loop : -0.12 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 408 
 TYR   0.011   0.001   TYR C 105 
 PHE   0.008   0.001   PHE C  29 
 TRP   0.010   0.002   TRP C 104 
 HIS   0.001   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3244)
  covalent geometry    : angle       0.63412 ( 4423)
  SS BOND              : bond        0.00091 (    4)
  SS BOND              : angle       0.56545 (    8)
  hydrogen bonds       : bond        0.03080 (  103)
  hydrogen bonds       : angle       6.28834 (  249)
  link_BETA1-4         : bond        0.00556 (    2)
  link_BETA1-4         : angle       3.32541 (    6)
  link_BETA1-6         : bond        0.00052 (    1)
  link_BETA1-6         : angle       1.49020 (    3)
  link_NAG-ASN         : bond        0.01032 (    1)
  link_NAG-ASN         : angle       4.15731 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2452.61 seconds
wall clock time: 42 minutes 33.57 seconds (2553.57 seconds total)