Starting phenix.real_space_refine
on Thu Jul 24 22:42:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x96_33068/07_2025/7x96_33068_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x96_33068/07_2025/7x96_33068.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x96_33068/07_2025/7x96_33068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x96_33068/07_2025/7x96_33068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x96_33068/07_2025/7x96_33068_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x96_33068/07_2025/7x96_33068_trim.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     C    2159      2.51       5
     N     556      2.21       5
     O     670      1.98       5
     H    3184      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6586
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "G"
      Number of atoms: 3065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 3065
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 11, 'TRANS': 186}
    Chain: "H"
      Number of atoms: 1826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 1826
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 1624
          Classifications: {'peptide': 109}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 4.21, per 1000 atoms: 0.64
  Number of scatterers: 6586
  At special positions: 0
  Unit cell: (72.123, 86.216, 92.848, 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)
     S      17     16.00
     O     670      8.00
     N     556      7.00
     C    2159      6.00
     H    3184      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS G 336 " - pdb=" SG  CYS G 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 391 " - pdb=" SG  CYS G 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 480 " - pdb=" SG  CYS G 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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
    ALPHA1-3
      " BMA A   3 " - " MAN A   4 "
    ALPHA1-6
      " BMA A   3 " - " MAN A   5 "
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
    BETA1-6
      " NAG A   1 " - " FUC A   6 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A   1 " - " ASN G 343 "
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 683.0 milliseconds
  

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  782

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 12 sheets defined
      14.3% alpha, 34.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'G' and resid 337 through 343
    Processing helix  chain 'G' and resid 364 through 371
      removed outlier: 4.481A  pdb=" N   LEU G 368 " --> pdb=" O   ASP G 364 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 386 through 389
    Processing helix  chain 'G' and resid 403 through 408
      removed outlier: 3.922A  pdb=" N   GLU G 406 " --> pdb=" O   ARG G 403 " (cutoff:3.500A)
      removed outlier: 4.262A  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 'G' and resid 502 through 506
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.524A  pdb=" N   SER H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.581A  pdb=" N   GLN H  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 87 through 90
    Processing helix  chain 'L' and resid 79 through 83
    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 354 through 358
    Processing sheet with id=AA3, first strand: chain 'G' and resid 361 through 362
      removed outlier: 6.720A  pdb=" N   CYS G 361 " --> pdb=" O   CYS G 525 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 379 through 380
    Processing sheet with id=AA5, first strand: chain 'G' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.518A  pdb=" N   VAL H 116 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA H  92 " --> pdb=" O   VAL H 116 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ILE H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   TRP H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 23
    Processing sheet with id=AA8, first strand: chain 'H' and resid 17 through 23
    Processing sheet with id=AA9, first strand: chain 'H' and resid 100 through 102
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.677A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.563A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 105 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.216A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.563A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 105 " (cutoff:3.500A)

    114 hydrogen bonds defined for protein.
    264 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: 2.40

  Time building geometry restraints manager: 2.09 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3183
        1.03 -     1.23: 20
        1.23 -     1.43: 1514
        1.43 -     1.62: 1934
        1.62 -     1.82: 21
  Bond restraints: 6672
  Sorted by residual:
  bond pdb=" N   ASP L   1 "
       pdb=" CA  ASP L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  bond pdb=" N   GLU H   1 "
       pdb=" CA  GLU H   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.90e+00
  bond pdb=" C1  MAN A   4 "
       pdb=" C2  MAN A   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.557 -0.031 2.00e-02 2.50e+03 2.41e+00
  bond pdb=" C1  MAN A   5 "
       pdb=" C2  MAN A   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.556 -0.030 2.00e-02 2.50e+03 2.28e+00
  bond pdb=" N   ASP L   1 "
       pdb=" H   ASP L   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.24e+00
  ... (remaining 6667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 11726
        1.51 -     3.03: 178
        3.03 -     4.54: 26
        4.54 -     6.06: 7
        6.06 -     7.57: 4
  Bond angle restraints: 11941
  Sorted by residual:
  angle pdb=" CA  ARG L  97 "
        pdb=" CB  ARG L  97 "
        pdb=" CG  ARG L  97 "
      ideal   model   delta    sigma   weight residual
     114.10  121.67   -7.57 2.00e+00 2.50e-01 1.43e+01
  angle pdb=" N   VAL H 102 "
        pdb=" CA  VAL H 102 "
        pdb=" C   VAL H 102 "
      ideal   model   delta    sigma   weight residual
     110.21  106.93    3.28 1.13e+00 7.83e-01 8.43e+00
  angle pdb=" C   PRO L  96 "
        pdb=" N   ARG L  97 "
        pdb=" CA  ARG L  97 "
      ideal   model   delta    sigma   weight residual
     122.30  125.62   -3.32 1.35e+00 5.49e-01 6.04e+00
  angle pdb=" CB  ARG L  97 "
        pdb=" CG  ARG L  97 "
        pdb=" CD  ARG L  97 "
      ideal   model   delta    sigma   weight residual
     111.30  116.67   -5.37 2.30e+00 1.89e-01 5.45e+00
  angle pdb=" C3  MAN A   4 "
        pdb=" C2  MAN A   4 "
        pdb=" O2  MAN A   4 "
      ideal   model   delta    sigma   weight residual
     111.77  105.58    6.19 3.00e+00 1.11e-01 4.25e+00
  ... (remaining 11936 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.62: 3063
       21.62 -    43.23: 166
       43.23 -    64.85: 57
       64.85 -    86.47: 13
       86.47 -   108.08: 5
  Dihedral angle restraints: 3304
    sinusoidal: 1796
      harmonic: 1508
  Sorted by residual:
  dihedral pdb=" CB  CYS G 480 "
           pdb=" SG  CYS G 480 "
           pdb=" SG  CYS G 488 "
           pdb=" CB  CYS G 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.36  -88.64     1      1.00e+01 1.00e-02 9.37e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.29  -53.29     1      1.00e+01 1.00e-02 3.86e+01
  dihedral pdb=" CA  PHE L  94 "
           pdb=" C   PHE L  94 "
           pdb=" N   PRO L  95 "
           pdb=" CA  PRO L  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.30   18.70     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 3301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 454
       0.054 -    0.107: 55
       0.107 -    0.161: 25
       0.161 -    0.214: 0
       0.214 -    0.268: 1
  Chirality restraints: 535
  Sorted by residual:
  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   -2.54    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" C2  BMA A   3 "
            pdb=" C1  BMA A   3 "
            pdb=" C3  BMA A   3 "
            pdb=" O2  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.61   -0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE G 402 "
            pdb=" N   ILE G 402 "
            pdb=" C   ILE G 402 "
            pdb=" CB  ILE G 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  ... (remaining 532 not shown)

  Planarity restraints: 1007
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L  97 "    0.199 9.50e-02 1.11e+02   6.65e-02 4.79e+00
        pdb=" NE  ARG L  97 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG L  97 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG L  97 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG L  97 "    0.002 2.00e-02 2.50e+03
        pdb="HH11 ARG L  97 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG L  97 "    0.002 2.00e-02 2.50e+03
        pdb="HH21 ARG L  97 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG L  97 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA G 520 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO G 521 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO G 521 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO G 521 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L  95 "    0.018 5.00e-02 4.00e+02   2.75e-02 1.21e+00
        pdb=" N   PRO L  96 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO L  96 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO L  96 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1004 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 288
        2.17 -     2.78: 12644
        2.78 -     3.38: 17363
        3.38 -     3.99: 23147
        3.99 -     4.60: 35239
  Nonbonded interactions: 88681
  Sorted by model distance:
  nonbonded pdb=" O   TRP G 353 "
            pdb="HH12 ARG G 466 "
     model   vdw
     1.562 2.450
  nonbonded pdb=" HG  SER L  12 "
            pdb=" O   ASP L 107 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" H   LEU G 455 "
            pdb=" O   PRO G 491 "
     model   vdw
     1.641 2.450
  nonbonded pdb=" OE1 GLU L  81 "
            pdb=" H   GLU L  81 "
     model   vdw
     1.643 2.450
  nonbonded pdb=" OE1 GLU H  89 "
            pdb=" H   GLU H  89 "
     model   vdw
     1.649 2.450
  ... (remaining 88676 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:             0.370
  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:             0.130
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.530
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
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   0.033   3500  Z= 0.158
  Angle     :  0.615   7.571   4777  Z= 0.301
  Chirality :  0.045   0.268    535
  Planarity :  0.005   0.086    603
  Dihedral  : 15.740 108.084   1322
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.42), residues: 421
  helix: -1.99 (1.15), residues: 19
  sheet: -0.82 (0.42), residues: 167
  loop : -0.77 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  99 
 PHE   0.005   0.001   PHE G 400 
 TYR   0.011   0.001   TYR H  80 
 ARG   0.005   0.001   ARG L  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00102 (    1)
  link_NAG-ASN         : angle       1.75245 (    3)
  link_ALPHA1-6        : bond        0.00442 (    1)
  link_ALPHA1-6        : angle       1.51718 (    3)
  link_BETA1-4         : bond        0.00288 (    2)
  link_BETA1-4         : angle       1.16527 (    6)
  link_ALPHA1-3        : bond        0.00427 (    1)
  link_ALPHA1-3        : angle       1.55077 (    3)
  hydrogen bonds       : bond        0.19473 (   99)
  hydrogen bonds       : angle       7.60033 (  264)
  link_BETA1-6         : bond        0.00415 (    1)
  link_BETA1-6         : angle       1.55489 (    3)
  SS BOND              : bond        0.00201 (    6)
  SS BOND              : angle       0.82262 (   12)
  covalent geometry    : bond        0.00329 ( 3488)
  covalent geometry    : angle       0.60890 ( 4747)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  493 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8639 (tp-100)
REVERT: H   62 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8353 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.3805
  time to fit residues: 32.5646
Evaluate side-chains
  64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 23 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  93 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 = 0.3004 r_free = 0.3004 target = 0.058591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.048243 restraints weight = 34464.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.2725 rms_B_bonded: 4.29
r_work: 0.2609 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3500  Z= 0.215
  Angle     :  0.572   5.715   4777  Z= 0.297
  Chirality :  0.042   0.174    535
  Planarity :  0.004   0.032    603
  Dihedral  : 10.293  75.302    582
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  8.47 %
    Favored  : 90.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.41), residues: 421
  helix: -2.05 (1.13), residues: 20
  sheet: -0.77 (0.43), residues: 152
  loop : -0.97 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  99 
 PHE   0.009   0.001   PHE H  64 
 TYR   0.011   0.001   TYR L  49 
 ARG   0.003   0.000   ARG L  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00008 (    1)
  link_NAG-ASN         : angle       2.38236 (    3)
  link_ALPHA1-6        : bond        0.00943 (    1)
  link_ALPHA1-6        : angle       1.89597 (    3)
  link_BETA1-4         : bond        0.00361 (    2)
  link_BETA1-4         : angle       1.67494 (    6)
  link_ALPHA1-3        : bond        0.00708 (    1)
  link_ALPHA1-3        : angle       3.96142 (    3)
  hydrogen bonds       : bond        0.03798 (   99)
  hydrogen bonds       : angle       6.06294 (  264)
  link_BETA1-6         : bond        0.00139 (    1)
  link_BETA1-6         : angle       1.64534 (    3)
  SS BOND              : bond        0.00232 (    6)
  SS BOND              : angle       0.86654 (   12)
  covalent geometry    : bond        0.00471 ( 3488)
  covalent geometry    : angle       0.55339 ( 4747)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  414 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8538 (tp-100)
REVERT: H   62 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8617 (tm-30)
REVERT: H   82 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7867 (tm-30)
  outliers start: 4
  outliers final: 4
  residues processed: 63
  average time/residue: 0.3659
  time to fit residues: 27.4816
Evaluate side-chains
  63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    0.1980
   chunk 13 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    2.4388

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

Flipped N/Q/H residues before XYZ refinement:
** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.059330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.048954 restraints weight = 33820.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.2741 rms_B_bonded: 4.27
r_work: 0.2626 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3500  Z= 0.136
  Angle     :  0.536   5.028   4777  Z= 0.273
  Chirality :  0.043   0.202    535
  Planarity :  0.004   0.040    603
  Dihedral  :  6.486  48.338    582
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.92 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.41), residues: 421
  helix: -1.98 (1.12), residues: 20
  sheet: -0.59 (0.44), residues: 152
  loop : -1.05 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  99 
 PHE   0.008   0.001   PHE H  64 
 TYR   0.006   0.001   TYR G 380 
 ARG   0.003   0.000   ARG G 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00228 (    1)
  link_NAG-ASN         : angle       2.01457 (    3)
  link_ALPHA1-6        : bond        0.00785 (    1)
  link_ALPHA1-6        : angle       2.23930 (    3)
  link_BETA1-4         : bond        0.00387 (    2)
  link_BETA1-4         : angle       1.40960 (    6)
  link_ALPHA1-3        : bond        0.00903 (    1)
  link_ALPHA1-3        : angle       2.25670 (    3)
  hydrogen bonds       : bond        0.03149 (   99)
  hydrogen bonds       : angle       5.80463 (  264)
  link_BETA1-6         : bond        0.00167 (    1)
  link_BETA1-6         : angle       1.21068 (    3)
  SS BOND              : bond        0.00180 (    6)
  SS BOND              : angle       0.79910 (   12)
  covalent geometry    : bond        0.00305 ( 3488)
  covalent geometry    : angle       0.52476 ( 4747)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  414 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8539 (tp-100)
REVERT: G  427 ASP cc_start: 0.8837 (m-30) cc_final: 0.8518 (p0)
REVERT: H   62 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8610 (tm-30)
REVERT: H   82 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: L   42 GLN cc_start: 0.8336 (mp10) cc_final: 0.8033 (mp10)
  outliers start: 4
  outliers final: 3
  residues processed: 65
  average time/residue: 0.3931
  time to fit residues: 30.8719
Evaluate side-chains
  63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 36 optimal weight:    7.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.059436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.049116 restraints weight = 33620.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.2744 rms_B_bonded: 4.25
r_work: 0.2629 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3500  Z= 0.120
  Angle     :  0.513   5.098   4777  Z= 0.262
  Chirality :  0.042   0.143    535
  Planarity :  0.004   0.046    603
  Dihedral  :  5.849  46.770    582
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  9.56 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.42), residues: 421
  helix: -1.85 (1.14), residues: 20
  sheet: -0.49 (0.44), residues: 152
  loop : -0.94 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  99 
 PHE   0.007   0.001   PHE H  64 
 TYR   0.026   0.001   TYR L  49 
 ARG   0.005   0.001   ARG L  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00216 (    1)
  link_NAG-ASN         : angle       2.22161 (    3)
  link_ALPHA1-6        : bond        0.00308 (    1)
  link_ALPHA1-6        : angle       1.71246 (    3)
  link_BETA1-4         : bond        0.00258 (    2)
  link_BETA1-4         : angle       1.50954 (    6)
  link_ALPHA1-3        : bond        0.01107 (    1)
  link_ALPHA1-3        : angle       2.43166 (    3)
  hydrogen bonds       : bond        0.02775 (   99)
  hydrogen bonds       : angle       5.59587 (  264)
  link_BETA1-6         : bond        0.00199 (    1)
  link_BETA1-6         : angle       1.25658 (    3)
  SS BOND              : bond        0.00177 (    6)
  SS BOND              : angle       0.74617 (   12)
  covalent geometry    : bond        0.00274 ( 3488)
  covalent geometry    : angle       0.50125 ( 4747)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  414 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8537 (tp-100)
REVERT: G  427 ASP cc_start: 0.8830 (m-30) cc_final: 0.8504 (p0)
REVERT: H   62 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8623 (tm-30)
REVERT: H   82 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7962 (tm-30)
REVERT: L   27 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8396 (tp40)
REVERT: L   42 GLN cc_start: 0.8380 (mp10) cc_final: 0.8156 (mp10)
  outliers start: 4
  outliers final: 3
  residues processed: 66
  average time/residue: 0.3723
  time to fit residues: 29.2613
Evaluate side-chains
  63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain H residue   89 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.059460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.049114 restraints weight = 33520.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 4.27
r_work: 0.2625 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3500  Z= 0.120
  Angle     :  0.509   5.102   4777  Z= 0.260
  Chirality :  0.042   0.134    535
  Planarity :  0.004   0.050    603
  Dihedral  :  5.663  46.881    582
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.84 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.41), residues: 421
  helix: -1.81 (1.11), residues: 20
  sheet: -0.42 (0.44), residues: 152
  loop : -0.89 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP G 436 
 HIS   0.002   0.001   HIS H  99 
 PHE   0.007   0.001   PHE H  64 
 TYR   0.023   0.001   TYR L  49 
 ARG   0.005   0.000   ARG L  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00154 (    1)
  link_NAG-ASN         : angle       2.24626 (    3)
  link_ALPHA1-6        : bond        0.00360 (    1)
  link_ALPHA1-6        : angle       1.57601 (    3)
  link_BETA1-4         : bond        0.00305 (    2)
  link_BETA1-4         : angle       1.48800 (    6)
  link_ALPHA1-3        : bond        0.00976 (    1)
  link_ALPHA1-3        : angle       2.34759 (    3)
  hydrogen bonds       : bond        0.02756 (   99)
  hydrogen bonds       : angle       5.41966 (  264)
  link_BETA1-6         : bond        0.00224 (    1)
  link_BETA1-6         : angle       1.25844 (    3)
  SS BOND              : bond        0.00165 (    6)
  SS BOND              : angle       0.76518 (   12)
  covalent geometry    : bond        0.00273 ( 3488)
  covalent geometry    : angle       0.49706 ( 4747)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  340 GLU cc_start: 0.9347 (tt0) cc_final: 0.9009 (tm-30)
REVERT: G  427 ASP cc_start: 0.8816 (m-30) cc_final: 0.8513 (p0)
REVERT: H   62 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8646 (tm-30)
REVERT: H   80 TYR cc_start: 0.8565 (m-80) cc_final: 0.8295 (m-80)
REVERT: L   42 GLN cc_start: 0.8395 (mp10) cc_final: 0.8171 (mp10)
REVERT: L  102 GLN cc_start: 0.9531 (mm-40) cc_final: 0.9313 (mm-40)
  outliers start: 5
  outliers final: 5
  residues processed: 64
  average time/residue: 0.3849
  time to fit residues: 29.6761
Evaluate side-chains
  63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue   96 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 6 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    3.1188

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

Flipped N/Q/H residues before XYZ refinement:
** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  93 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 = 0.3009 r_free = 0.3009 target = 0.058850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.048476 restraints weight = 33735.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 4.24
r_work: 0.2603 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3500  Z= 0.167
  Angle     :  0.519   4.868   4777  Z= 0.268
  Chirality :  0.041   0.136    535
  Planarity :  0.004   0.030    603
  Dihedral  :  5.465  46.891    582
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.48 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.42), residues: 421
  helix: -1.76 (1.14), residues: 20
  sheet: -0.56 (0.43), residues: 156
  loop : -0.90 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  99 
 PHE   0.008   0.001   PHE H  64 
 TYR   0.025   0.001   TYR L  49 
 ARG   0.005   0.000   ARG H  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       2.40101 (    3)
  link_ALPHA1-6        : bond        0.00378 (    1)
  link_ALPHA1-6        : angle       1.53999 (    3)
  link_BETA1-4         : bond        0.00288 (    2)
  link_BETA1-4         : angle       1.51619 (    6)
  link_ALPHA1-3        : bond        0.00943 (    1)
  link_ALPHA1-3        : angle       2.45736 (    3)
  hydrogen bonds       : bond        0.02925 (   99)
  hydrogen bonds       : angle       5.39808 (  264)
  link_BETA1-6         : bond        0.00145 (    1)
  link_BETA1-6         : angle       1.32407 (    3)
  SS BOND              : bond        0.00150 (    6)
  SS BOND              : angle       0.76642 (   12)
  covalent geometry    : bond        0.00371 ( 3488)
  covalent geometry    : angle       0.50622 ( 4747)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  340 GLU cc_start: 0.9355 (tt0) cc_final: 0.9033 (tm-30)
REVERT: G  414 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8486 (tp-100)
REVERT: G  427 ASP cc_start: 0.8817 (m-30) cc_final: 0.8520 (p0)
REVERT: H   62 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8648 (tm-30)
REVERT: L   27 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8413 (tp40)
REVERT: L   42 GLN cc_start: 0.8412 (mp10) cc_final: 0.8189 (mp10)
REVERT: L  102 GLN cc_start: 0.9534 (mm-40) cc_final: 0.9321 (mm-40)
  outliers start: 6
  outliers final: 5
  residues processed: 63
  average time/residue: 0.3707
  time to fit residues: 28.0781
Evaluate side-chains
  63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain L residue   20 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0060
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    3.0004

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

Flipped N/Q/H residues before XYZ refinement:
** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  93 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 = 0.3010 r_free = 0.3010 target = 0.059003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.048552 restraints weight = 33641.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.2723 rms_B_bonded: 4.25
r_work: 0.2606 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3500  Z= 0.157
  Angle     :  0.524   4.989   4777  Z= 0.270
  Chirality :  0.042   0.166    535
  Planarity :  0.004   0.032    603
  Dihedral  :  5.407  47.119    582
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.02 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.41), residues: 421
  helix: -1.73 (1.14), residues: 20
  sheet: -0.43 (0.44), residues: 153
  loop : -1.00 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  99 
 PHE   0.011   0.001   PHE G 464 
 TYR   0.026   0.001   TYR L  49 
 ARG   0.004   0.001   ARG H  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00041 (    1)
  link_NAG-ASN         : angle       2.37123 (    3)
  link_ALPHA1-6        : bond        0.00361 (    1)
  link_ALPHA1-6        : angle       1.51189 (    3)
  link_BETA1-4         : bond        0.00308 (    2)
  link_BETA1-4         : angle       1.50115 (    6)
  link_ALPHA1-3        : bond        0.00808 (    1)
  link_ALPHA1-3        : angle       2.30878 (    3)
  hydrogen bonds       : bond        0.02868 (   99)
  hydrogen bonds       : angle       5.36886 (  264)
  link_BETA1-6         : bond        0.00140 (    1)
  link_BETA1-6         : angle       1.30421 (    3)
  SS BOND              : bond        0.00158 (    6)
  SS BOND              : angle       0.78741 (   12)
  covalent geometry    : bond        0.00353 ( 3488)
  covalent geometry    : angle       0.51182 ( 4747)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  340 GLU cc_start: 0.9357 (tt0) cc_final: 0.9036 (tm-30)
REVERT: G  414 GLN cc_start: 0.8781 (tp-100) cc_final: 0.8461 (tp-100)
REVERT: G  427 ASP cc_start: 0.8830 (m-30) cc_final: 0.8543 (p0)
REVERT: H   62 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8639 (tm-30)
REVERT: L   27 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8411 (tp40)
REVERT: L   42 GLN cc_start: 0.8430 (mp10) cc_final: 0.8204 (mp10)
REVERT: L  102 GLN cc_start: 0.9546 (mm-40) cc_final: 0.9324 (mm-40)
  outliers start: 6
  outliers final: 6
  residues processed: 62
  average time/residue: 0.3755
  time to fit residues: 28.0738
Evaluate side-chains
  64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain L residue   20 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 5 optimal weight:    0.5980
   chunk 34 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 36 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
L  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.059307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.048825 restraints weight = 33691.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.2730 rms_B_bonded: 4.29
r_work: 0.2614 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3500  Z= 0.122
  Angle     :  0.510   5.125   4777  Z= 0.263
  Chirality :  0.042   0.137    535
  Planarity :  0.004   0.036    603
  Dihedral  :  5.228  46.951    582
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.02 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.42), residues: 421
  helix: -1.67 (1.15), residues: 20
  sheet: -0.39 (0.44), residues: 153
  loop : -0.95 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  47 
 HIS   0.002   0.001   HIS L  90 
 PHE   0.007   0.001   PHE H  64 
 TYR   0.025   0.001   TYR L  49 
 ARG   0.005   0.000   ARG H  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00123 (    1)
  link_NAG-ASN         : angle       2.31909 (    3)
  link_ALPHA1-6        : bond        0.00460 (    1)
  link_ALPHA1-6        : angle       1.50616 (    3)
  link_BETA1-4         : bond        0.00274 (    2)
  link_BETA1-4         : angle       1.51619 (    6)
  link_ALPHA1-3        : bond        0.00718 (    1)
  link_ALPHA1-3        : angle       2.03902 (    3)
  hydrogen bonds       : bond        0.02732 (   99)
  hydrogen bonds       : angle       5.30567 (  264)
  link_BETA1-6         : bond        0.00230 (    1)
  link_BETA1-6         : angle       1.30616 (    3)
  SS BOND              : bond        0.00167 (    6)
  SS BOND              : angle       0.75946 (   12)
  covalent geometry    : bond        0.00280 ( 3488)
  covalent geometry    : angle       0.49903 ( 4747)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  340 GLU cc_start: 0.9365 (tt0) cc_final: 0.9052 (tm-30)
REVERT: G  378 LYS cc_start: 0.9122 (ttmm) cc_final: 0.8620 (ptmm)
REVERT: G  414 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8435 (tp-100)
REVERT: G  427 ASP cc_start: 0.8806 (m-30) cc_final: 0.8517 (p0)
REVERT: H   62 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8630 (tm-30)
REVERT: H   99 HIS cc_start: 0.9288 (OUTLIER) cc_final: 0.8588 (t-90)
REVERT: L   42 GLN cc_start: 0.8438 (mp10) cc_final: 0.8214 (mp10)
REVERT: L  102 GLN cc_start: 0.9547 (mm-40) cc_final: 0.9326 (mm-40)
  outliers start: 7
  outliers final: 6
  residues processed: 62
  average time/residue: 0.3447
  time to fit residues: 25.7190
Evaluate side-chains
  66 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   99 HIS
Chi-restraints excluded: chain L residue   20 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    0.4980
   chunk 16 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 26 optimal weight:   10.0000
   overall best weight:    1.4382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.059667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.049262 restraints weight = 33627.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.2745 rms_B_bonded: 4.28
r_work: 0.2628 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3500  Z= 0.102
  Angle     :  0.499   5.247   4777  Z= 0.258
  Chirality :  0.042   0.136    535
  Planarity :  0.004   0.038    603
  Dihedral  :  5.042  46.571    582
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.57 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.42), residues: 421
  helix: -1.60 (1.17), residues: 20
  sheet: -0.33 (0.44), residues: 153
  loop : -0.88 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.002   0.001   HIS L  90 
 PHE   0.007   0.001   PHE H  64 
 TYR   0.026   0.001   TYR L  49 
 ARG   0.004   0.000   ARG H  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00177 (    1)
  link_NAG-ASN         : angle       2.26287 (    3)
  link_ALPHA1-6        : bond        0.00441 (    1)
  link_ALPHA1-6        : angle       1.46115 (    3)
  link_BETA1-4         : bond        0.00290 (    2)
  link_BETA1-4         : angle       1.46935 (    6)
  link_ALPHA1-3        : bond        0.00817 (    1)
  link_ALPHA1-3        : angle       1.93554 (    3)
  hydrogen bonds       : bond        0.02583 (   99)
  hydrogen bonds       : angle       5.24708 (  264)
  link_BETA1-6         : bond        0.00213 (    1)
  link_BETA1-6         : angle       1.27738 (    3)
  SS BOND              : bond        0.00162 (    6)
  SS BOND              : angle       0.76617 (   12)
  covalent geometry    : bond        0.00238 ( 3488)
  covalent geometry    : angle       0.48865 ( 4747)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  340 GLU cc_start: 0.9347 (tt0) cc_final: 0.9078 (tm-30)
REVERT: G  378 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8642 (ptmm)
REVERT: G  414 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8421 (tp-100)
REVERT: G  427 ASP cc_start: 0.8797 (m-30) cc_final: 0.8512 (p0)
REVERT: H   62 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8623 (tm-30)
REVERT: H   99 HIS cc_start: 0.9293 (OUTLIER) cc_final: 0.8628 (t-90)
REVERT: L   42 GLN cc_start: 0.8414 (mp10) cc_final: 0.8189 (mp10)
REVERT: L  102 GLN cc_start: 0.9551 (mm-40) cc_final: 0.9332 (mm-40)
  outliers start: 6
  outliers final: 5
  residues processed: 65
  average time/residue: 0.3821
  time to fit residues: 29.4589
Evaluate side-chains
  68 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   99 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    2.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.059146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.048666 restraints weight = 33774.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.2728 rms_B_bonded: 4.29
r_work: 0.2612 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3500  Z= 0.147
  Angle     :  0.511   4.993   4777  Z= 0.264
  Chirality :  0.041   0.137    535
  Planarity :  0.004   0.037    603
  Dihedral  :  5.013  46.630    582
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.45 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.84 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.41), residues: 421
  helix: -1.61 (1.16), residues: 20
  sheet: -0.35 (0.44), residues: 153
  loop : -0.92 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  99 
 PHE   0.011   0.001   PHE H  64 
 TYR   0.025   0.001   TYR L  49 
 ARG   0.004   0.000   ARG H  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00072 (    1)
  link_NAG-ASN         : angle       2.41917 (    3)
  link_ALPHA1-6        : bond        0.00401 (    1)
  link_ALPHA1-6        : angle       1.50499 (    3)
  link_BETA1-4         : bond        0.00282 (    2)
  link_BETA1-4         : angle       1.48510 (    6)
  link_ALPHA1-3        : bond        0.00704 (    1)
  link_ALPHA1-3        : angle       2.05236 (    3)
  hydrogen bonds       : bond        0.02716 (   99)
  hydrogen bonds       : angle       5.29203 (  264)
  link_BETA1-6         : bond        0.00150 (    1)
  link_BETA1-6         : angle       1.31437 (    3)
  SS BOND              : bond        0.00155 (    6)
  SS BOND              : angle       0.75012 (   12)
  covalent geometry    : bond        0.00329 ( 3488)
  covalent geometry    : angle       0.49966 ( 4747)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  340 GLU cc_start: 0.9365 (tt0) cc_final: 0.9086 (tm-30)
REVERT: G  378 LYS cc_start: 0.9143 (ttmm) cc_final: 0.8660 (ptmm)
REVERT: G  414 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8438 (tp-100)
REVERT: G  427 ASP cc_start: 0.8797 (m-30) cc_final: 0.8526 (p0)
REVERT: H   62 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8622 (tm-30)
REVERT: H   99 HIS cc_start: 0.9302 (OUTLIER) cc_final: 0.8567 (t-90)
REVERT: L   42 GLN cc_start: 0.8445 (mp10) cc_final: 0.8220 (mp10)
REVERT: L  102 GLN cc_start: 0.9551 (mm-40) cc_final: 0.9334 (mm-40)
  outliers start: 6
  outliers final: 5
  residues processed: 65
  average time/residue: 0.3414
  time to fit residues: 26.8855
Evaluate side-chains
  67 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   99 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.7784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.059712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.049278 restraints weight = 33719.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.2741 rms_B_bonded: 4.30
r_work: 0.2625 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3500  Z= 0.111
  Angle     :  0.514   5.188   4777  Z= 0.266
  Chirality :  0.042   0.146    535
  Planarity :  0.004   0.037    603
  Dihedral  :  4.958  46.828    582
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.84 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.42), residues: 421
  helix: -1.59 (1.16), residues: 20
  sheet: -0.28 (0.44), residues: 153
  loop : -0.87 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.002   0.001   HIS L  90 
 PHE   0.007   0.001   PHE G 464 
 TYR   0.025   0.001   TYR L  49 
 ARG   0.004   0.000   ARG H  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00170 (    1)
  link_NAG-ASN         : angle       2.26804 (    3)
  link_ALPHA1-6        : bond        0.00436 (    1)
  link_ALPHA1-6        : angle       1.46583 (    3)
  link_BETA1-4         : bond        0.00287 (    2)
  link_BETA1-4         : angle       1.46090 (    6)
  link_ALPHA1-3        : bond        0.00740 (    1)
  link_ALPHA1-3        : angle       1.88590 (    3)
  hydrogen bonds       : bond        0.02576 (   99)
  hydrogen bonds       : angle       5.25231 (  264)
  link_BETA1-6         : bond        0.00185 (    1)
  link_BETA1-6         : angle       1.28138 (    3)
  SS BOND              : bond        0.00184 (    6)
  SS BOND              : angle       0.76169 (   12)
  covalent geometry    : bond        0.00258 ( 3488)
  covalent geometry    : angle       0.50376 ( 4747)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3581.72 seconds
wall clock time: 61 minutes 44.06 seconds (3704.06 seconds total)