Starting phenix.real_space_refine
on Thu Jul 24 17:17:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x91_33063/07_2025/7x91_33063_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x91_33063/07_2025/7x91_33063.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x91_33063/07_2025/7x91_33063.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x91_33063/07_2025/7x91_33063.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x91_33063/07_2025/7x91_33063_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x91_33063/07_2025/7x91_33063_trim.cif"
  }
  resolution = 4.3
  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      14      5.16       5
     C    2137      2.51       5
     N     560      2.21       5
     O     652      1.98       5
     H    3196      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 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: 6559
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 3094
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 11, 'TRANS': 188}
    Chain: "H"
      Number of atoms: 1834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 1834
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 5, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 1603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 1603
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 8, 'TRANS': 98}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 3.38, per 1000 atoms: 0.52
  Number of scatterers: 6559
  At special positions: 0
  Unit cell: (85.387, 96.164, 81.242, 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      14     16.00
     O     652      8.00
     N     560      7.00
     C    2137      6.00
     H    3196      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " 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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 706.3 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:  788

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 7 sheets defined
      4.7% alpha, 27.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.068A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 5.611A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
      removed outlier: 3.615A  pdb=" N   ALA A 397 " --> pdb=" O   LYS A 356 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.682A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.681A  pdb=" N   VAL H  18 " --> pdb=" O   LEU H  83 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LEU H  83 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASP H  73 " --> pdb=" O   THR H  78 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 59 through 60
      removed outlier: 4.148A  pdb=" N   ASN H  59 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   TRP H  50 " --> pdb=" O   ASN H  59 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG H  44 " --> pdb=" O   ALA H  40 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   TRP H  50 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 5.031A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 106 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ILE L  48 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)

    87 hydrogen bonds defined for protein.
    207 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: 2.00

  Time building geometry restraints manager: 2.10 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: 3193
        1.03 -     1.23: 8
        1.23 -     1.42: 1510
        1.42 -     1.62: 1920
        1.62 -     1.81: 15
  Bond restraints: 6646
  Sorted by residual:
  bond pdb=" N   GLU H   1 "
       pdb=" CA  GLU H   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  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 2.97e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" N   GLU H   1 "
       pdb=" H   GLU H   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.23e+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 2.19e+00
  ... (remaining 6641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 11620
        1.52 -     3.04: 267
        3.04 -     4.56: 30
        4.56 -     6.08: 0
        6.08 -     7.60: 1
  Bond angle restraints: 11918
  Sorted by residual:
  angle pdb=" N   PRO L  95 "
        pdb=" CA  PRO L  95 "
        pdb=" C   PRO L  95 "
      ideal   model   delta    sigma   weight residual
     110.70  113.67   -2.97 1.22e+00 6.72e-01 5.91e+00
  angle pdb=" CA  PRO L  95 "
        pdb=" C   PRO L  95 "
        pdb=" N   PRO L  96 "
      ideal   model   delta    sigma   weight residual
     117.93  120.78   -2.85 1.20e+00 6.94e-01 5.64e+00
  angle pdb=" N   GLY H   8 "
        pdb=" CA  GLY H   8 "
        pdb=" C   GLY H   8 "
      ideal   model   delta    sigma   weight residual
     112.34  116.84   -4.50 2.04e+00 2.40e-01 4.88e+00
  angle pdb=" N   GLY A 381 "
        pdb=" CA  GLY A 381 "
        pdb=" C   GLY A 381 "
      ideal   model   delta    sigma   weight residual
     115.08  112.69    2.39 1.19e+00 7.06e-01 4.05e+00
  angle pdb=" CA  CYS L  88 "
        pdb=" CB  CYS L  88 "
        pdb=" SG  CYS L  88 "
      ideal   model   delta    sigma   weight residual
     114.40  118.93   -4.53 2.30e+00 1.89e-01 3.89e+00
  ... (remaining 11913 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 2898
       17.76 -    35.53: 265
       35.53 -    53.29: 55
       53.29 -    71.06: 22
       71.06 -    88.82: 6
  Dihedral angle restraints: 3246
    sinusoidal: 1739
      harmonic: 1507
  Sorted by residual:
  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  150.68  -57.68     1      1.00e+01 1.00e-02 4.47e+01
  dihedral pdb=" CA  SER H  75 "
           pdb=" C   SER H  75 "
           pdb=" N   THR H  76 "
           pdb=" CA  THR H  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.03   23.97     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  ALA L  92 "
           pdb=" C   ALA L  92 "
           pdb=" N   ASN L  93 "
           pdb=" CA  ASN L  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.16   15.84     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 3243 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 299
       0.032 -    0.064: 139
       0.064 -    0.096: 43
       0.096 -    0.128: 26
       0.128 -    0.160: 7
  Chirality restraints: 514
  Sorted by residual:
  chirality pdb=" CA  ILE L  39 "
            pdb=" N   ILE L  39 "
            pdb=" C   ILE L  39 "
            pdb=" CB  ILE L  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ILE L  21 "
            pdb=" N   ILE L  21 "
            pdb=" C   ILE L  21 "
            pdb=" CB  ILE L  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ILE H  70 "
            pdb=" N   ILE H  70 "
            pdb=" C   ILE H  70 "
            pdb=" CB  ILE H  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  ... (remaining 511 not shown)

  Planarity restraints: 1010
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  36 "   -0.020 2.00e-02 2.50e+03   1.30e-02 6.71e+00
        pdb=" CG  TRP H  36 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  36 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  36 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  36 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  36 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  36 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD1 TRP H  36 "   -0.008 2.00e-02 2.50e+03
        pdb=" HE1 TRP H  36 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE3 TRP H  36 "    0.004 2.00e-02 2.50e+03
        pdb=" HZ2 TRP H  36 "    0.005 2.00e-02 2.50e+03
        pdb=" HZ3 TRP H  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" HH2 TRP H  36 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP H  73 "    0.007 2.00e-02 2.50e+03   1.48e-02 2.20e+00
        pdb=" CG  ASP H  73 "   -0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASP H  73 "    0.009 2.00e-02 2.50e+03
        pdb=" OD2 ASP H  73 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE L  39 "   -0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO L  40 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO L  40 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO L  40 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1007 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 357
        2.17 -     2.78: 12569
        2.78 -     3.38: 17088
        3.38 -     3.99: 22024
        3.99 -     4.60: 33342
  Nonbonded interactions: 85380
  Sorted by model distance:
  nonbonded pdb=" O   VAL H  52 "
            pdb="HH21 ARG H  72 "
     model   vdw
     1.559 2.450
  nonbonded pdb="HH21 ARG H  67 "
            pdb=" O   SER H  85 "
     model   vdw
     1.632 2.450
  nonbonded pdb=" OD1 ASP L 106 "
            pdb=" H   ILE L 107 "
     model   vdw
     1.693 2.450
  nonbonded pdb=" OE1 GLU A 340 "
            pdb=" H   GLU A 340 "
     model   vdw
     1.707 2.450
  nonbonded pdb=" OG  SER A 349 "
            pdb=" H   LEU A 452 "
     model   vdw
     1.708 2.450
  ... (remaining 85375 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.190
  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:             0.120
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.680
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
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   3457  Z= 0.143
  Angle     :  0.628   7.597   4715  Z= 0.335
  Chirality :  0.046   0.160    514
  Planarity :  0.003   0.030    609
  Dihedral  : 14.403  88.821   1261
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.69 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.69 (0.38), residues: 421
  helix: -3.86 (0.64), residues: 24
  sheet: -0.91 (0.48), residues: 117
  loop : -2.10 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP H  36 
 HIS   0.004   0.003   HIS A 519 
 PHE   0.011   0.001   PHE L  99 
 TYR   0.011   0.001   TYR A 453 
 ARG   0.001   0.000   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00045 (    1)
  link_NAG-ASN         : angle       1.85756 (    3)
  link_BETA1-4         : bond        0.00213 (    1)
  link_BETA1-4         : angle       0.97940 (    3)
  hydrogen bonds       : bond        0.13760 (   87)
  hydrogen bonds       : angle       6.91154 (  207)
  SS BOND              : bond        0.00287 (    5)
  SS BOND              : angle       0.90919 (   10)
  covalent geometry    : bond        0.00306 ( 3450)
  covalent geometry    : angle       0.62557 ( 4699)

*********************** 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
  96 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.507 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7342 (mm-30)
REVERT: H   80 TYR cc_start: 0.8271 (m-80) cc_final: 0.7786 (m-10)
REVERT: L   32 ASN cc_start: 0.7872 (m-40) cc_final: 0.7627 (m-40)
REVERT: L   53 ASN cc_start: 0.8995 (t0) cc_final: 0.8747 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.5069
  time to fit residues: 55.1544
Evaluate side-chains
  66 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 21 optimal weight:   30.0000
   chunk 32 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 38 optimal weight:   40.0000
   chunk 11 optimal weight:    3.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 474 GLN
A 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.042184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.032174 restraints weight = 71618.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.034082 restraints weight = 30585.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.035407 restraints weight = 16990.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   3457  Z= 0.253
  Angle     :  0.664   7.293   4715  Z= 0.347
  Chirality :  0.043   0.140    514
  Planarity :  0.005   0.056    609
  Dihedral  :  6.363  56.135    511
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.64 %
    Favored  : 88.36 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  4.09 %
    Favored  : 95.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.78 (0.38), residues: 421
  helix: -3.26 (0.86), residues: 24
  sheet: -1.17 (0.43), residues: 133
  loop : -2.16 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  36 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.026   0.002   PHE A 377 
 TYR   0.016   0.002   TYR A 449 
 ARG   0.007   0.001   ARG H  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00770 (    1)
  link_NAG-ASN         : angle       2.39417 (    3)
  link_BETA1-4         : bond        0.00597 (    1)
  link_BETA1-4         : angle       1.68792 (    3)
  hydrogen bonds       : bond        0.04210 (   87)
  hydrogen bonds       : angle       6.75312 (  207)
  SS BOND              : bond        0.00399 (    5)
  SS BOND              : angle       1.80338 (   10)
  covalent geometry    : bond        0.00511 ( 3450)
  covalent geometry    : angle       0.65541 ( 4699)

*********************** 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
  67 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.555 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8998 (ttt90) cc_final: 0.8699 (mmm-85)
REVERT: A  442 ASP cc_start: 0.8978 (m-30) cc_final: 0.8502 (m-30)
REVERT: A  484 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8229 (mm-30)
REVERT: H   59 ASN cc_start: 0.9113 (m-40) cc_final: 0.8708 (m110)
REVERT: H   63 LYS cc_start: 0.9720 (mptt) cc_final: 0.9276 (mptt)
REVERT: H   80 TYR cc_start: 0.9422 (m-80) cc_final: 0.9220 (m-10)
REVERT: L   32 ASN cc_start: 0.9049 (m-40) cc_final: 0.8782 (m-40)
  outliers start: 2
  outliers final: 1
  residues processed: 66
  average time/residue: 0.5129
  time to fit residues: 38.6060
Evaluate side-chains
  51 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 37 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** L  89 GLN ** 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 = 0.3040 r_free = 0.3040 target = 0.042543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.032434 restraints weight = 70261.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.034363 restraints weight = 29425.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.035656 restraints weight = 16208.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3457  Z= 0.137
  Angle     :  0.579   6.797   4715  Z= 0.299
  Chirality :  0.044   0.140    514
  Planarity :  0.005   0.051    609
  Dihedral  :  6.044  54.417    511
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.40 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.63 (0.38), residues: 421
  helix: -3.39 (0.82), residues: 24
  sheet: -1.06 (0.45), residues: 127
  loop : -2.02 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP H  36 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.010   0.001   PHE L  71 
 TYR   0.019   0.001   TYR A 449 
 ARG   0.005   0.001   ARG A 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00166 (    1)
  link_NAG-ASN         : angle       1.70405 (    3)
  link_BETA1-4         : bond        0.00096 (    1)
  link_BETA1-4         : angle       1.12541 (    3)
  hydrogen bonds       : bond        0.03739 (   87)
  hydrogen bonds       : angle       6.70915 (  207)
  SS BOND              : bond        0.00465 (    5)
  SS BOND              : angle       1.71992 (   10)
  covalent geometry    : bond        0.00304 ( 3450)
  covalent geometry    : angle       0.57271 ( 4699)

*********************** 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
  66 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.626 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 ASP cc_start: 0.8851 (m-30) cc_final: 0.8419 (m-30)
REVERT: A  484 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8186 (mm-30)
REVERT: H   59 ASN cc_start: 0.9032 (m-40) cc_final: 0.8646 (m110)
REVERT: H   63 LYS cc_start: 0.9556 (mptt) cc_final: 0.9296 (mptt)
REVERT: H   80 TYR cc_start: 0.9427 (m-80) cc_final: 0.9173 (m-10)
REVERT: L   32 ASN cc_start: 0.9040 (m-40) cc_final: 0.8765 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.5405
  time to fit residues: 40.3854
Evaluate side-chains
  54 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 19 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 29 optimal weight:   20.0000
   chunk 36 optimal weight:   30.0000
   chunk 38 optimal weight:   40.0000
   chunk 27 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
H 105 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.041055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.030911 restraints weight = 72508.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.032805 restraints weight = 31479.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.034089 restraints weight = 17597.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3457  Z= 0.235
  Angle     :  0.625   6.964   4715  Z= 0.327
  Chirality :  0.043   0.133    514
  Planarity :  0.005   0.057    609
  Dihedral  :  6.155  53.856    511
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.83 %
    Favored  : 87.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.64 (0.39), residues: 421
  helix: -2.52 (1.12), residues: 18
  sheet: -0.91 (0.47), residues: 126
  loop : -2.23 (0.35), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 436 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.015   0.002   PHE A 377 
 TYR   0.026   0.002   TYR A 449 
 ARG   0.007   0.001   ARG H  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00802 (    1)
  link_NAG-ASN         : angle       2.14809 (    3)
  link_BETA1-4         : bond        0.00186 (    1)
  link_BETA1-4         : angle       1.54948 (    3)
  hydrogen bonds       : bond        0.03601 (   87)
  hydrogen bonds       : angle       6.54469 (  207)
  SS BOND              : bond        0.00348 (    5)
  SS BOND              : angle       0.90775 (   10)
  covalent geometry    : bond        0.00482 ( 3450)
  covalent geometry    : angle       0.62156 ( 4699)

*********************** 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
  59 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.556 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 ASP cc_start: 0.8822 (m-30) cc_final: 0.8341 (m-30)
REVERT: A  484 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8170 (mm-30)
REVERT: H   59 ASN cc_start: 0.9069 (m-40) cc_final: 0.8679 (m110)
REVERT: H   63 LYS cc_start: 0.9589 (mptt) cc_final: 0.9336 (mptt)
REVERT: H   80 TYR cc_start: 0.9431 (m-80) cc_final: 0.9206 (m-10)
REVERT: L   32 ASN cc_start: 0.9176 (m-40) cc_final: 0.8877 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.5070
  time to fit residues: 34.4727
Evaluate side-chains
  45 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 38 optimal weight:   30.0000
   chunk 11 optimal weight:    7.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 493 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 = 0.3002 r_free = 0.3002 target = 0.040973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.030633 restraints weight = 68981.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.032532 restraints weight = 30240.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.033841 restraints weight = 17128.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3457  Z= 0.176
  Angle     :  0.579   6.686   4715  Z= 0.299
  Chirality :  0.043   0.140    514
  Planarity :  0.004   0.033    609
  Dihedral  :  6.011  54.110    511
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.83 %
    Favored  : 87.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.50 (0.39), residues: 421
  helix: -2.45 (1.18), residues: 18
  sheet: -0.75 (0.48), residues: 126
  loop : -2.17 (0.35), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 436 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.013   0.001   PHE A 400 
 TYR   0.017   0.001   TYR A 449 
 ARG   0.005   0.001   ARG H  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00313 (    1)
  link_NAG-ASN         : angle       1.69242 (    3)
  link_BETA1-4         : bond        0.00051 (    1)
  link_BETA1-4         : angle       1.24883 (    3)
  hydrogen bonds       : bond        0.03417 (   87)
  hydrogen bonds       : angle       6.41974 (  207)
  SS BOND              : bond        0.00335 (    5)
  SS BOND              : angle       0.95002 (   10)
  covalent geometry    : bond        0.00368 ( 3450)
  covalent geometry    : angle       0.57560 ( 4699)

*********************** 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
  60 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.563 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 ASP cc_start: 0.8794 (m-30) cc_final: 0.8582 (m-30)
REVERT: A  484 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: H   59 ASN cc_start: 0.9045 (m-40) cc_final: 0.8688 (m-40)
REVERT: H   63 LYS cc_start: 0.9589 (mptt) cc_final: 0.9328 (mptt)
REVERT: H   80 TYR cc_start: 0.9420 (m-80) cc_final: 0.9202 (m-10)
REVERT: L   32 ASN cc_start: 0.9206 (m-40) cc_final: 0.8936 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.4929
  time to fit residues: 33.9994
Evaluate side-chains
  44 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 38 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    3.5786

-------------------------------------------------------------------------------
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 = 0.3010 r_free = 0.3010 target = 0.041183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.031133 restraints weight = 71225.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.033024 restraints weight = 30568.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.034317 restraints weight = 17030.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3457  Z= 0.141
  Angle     :  0.565   6.500   4715  Z= 0.289
  Chirality :  0.043   0.141    514
  Planarity :  0.005   0.073    609
  Dihedral  :  5.847  54.048    511
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.16 %
    Favored  : 88.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.37 (0.39), residues: 421
  helix: -2.42 (1.15), residues: 18
  sheet: -0.77 (0.48), residues: 126
  loop : -2.01 (0.35), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  36 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.009   0.001   PHE A 377 
 TYR   0.020   0.001   TYR H 103 
 ARG   0.007   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00225 (    1)
  link_NAG-ASN         : angle       1.52333 (    3)
  link_BETA1-4         : bond        0.00005 (    1)
  link_BETA1-4         : angle       1.16489 (    3)
  hydrogen bonds       : bond        0.03163 (   87)
  hydrogen bonds       : angle       6.44669 (  207)
  SS BOND              : bond        0.00354 (    5)
  SS BOND              : angle       1.15330 (   10)
  covalent geometry    : bond        0.00309 ( 3450)
  covalent geometry    : angle       0.56114 ( 4699)

*********************** 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
  59 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.579 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 ASP cc_start: 0.8793 (m-30) cc_final: 0.8305 (m-30)
REVERT: A  484 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8139 (mm-30)
REVERT: H   59 ASN cc_start: 0.9053 (m-40) cc_final: 0.8767 (m-40)
REVERT: H   80 TYR cc_start: 0.9406 (m-80) cc_final: 0.9186 (m-10)
REVERT: L   32 ASN cc_start: 0.9219 (m-40) cc_final: 0.8956 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.4958
  time to fit residues: 33.5955
Evaluate side-chains
  48 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 29 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
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 = 0.2978 r_free = 0.2978 target = 0.040097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.030053 restraints weight = 71092.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.031866 restraints weight = 31166.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.033114 restraints weight = 17543.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3457  Z= 0.222
  Angle     :  0.604   6.674   4715  Z= 0.314
  Chirality :  0.043   0.129    514
  Planarity :  0.005   0.035    609
  Dihedral  :  6.007  53.377    511
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.54 %
    Favored  : 86.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.39 (0.40), residues: 421
  helix: -2.36 (1.15), residues: 19
  sheet: -0.71 (0.47), residues: 130
  loop : -2.09 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.011   0.002   PHE A 429 
 TYR   0.011   0.002   TYR A 380 
 ARG   0.005   0.001   ARG H  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00651 (    1)
  link_NAG-ASN         : angle       1.77158 (    3)
  link_BETA1-4         : bond        0.00201 (    1)
  link_BETA1-4         : angle       1.31982 (    3)
  hydrogen bonds       : bond        0.03373 (   87)
  hydrogen bonds       : angle       6.50762 (  207)
  SS BOND              : bond        0.00394 (    5)
  SS BOND              : angle       1.26704 (   10)
  covalent geometry    : bond        0.00455 ( 3450)
  covalent geometry    : angle       0.59941 ( 4699)

*********************** 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
  54 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.543 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8257 (mm-30)
REVERT: H   59 ASN cc_start: 0.9006 (m-40) cc_final: 0.8633 (m-40)
REVERT: H   63 LYS cc_start: 0.9624 (mptt) cc_final: 0.9365 (mptt)
REVERT: L   32 ASN cc_start: 0.9294 (m-40) cc_final: 0.9048 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.5194
  time to fit residues: 32.0418
Evaluate side-chains
  43 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    3.1386

-------------------------------------------------------------------------------
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 = 0.3005 r_free = 0.3005 target = 0.041016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.030928 restraints weight = 70825.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.032822 restraints weight = 30263.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.034102 restraints weight = 16795.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.4537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3457  Z= 0.128
  Angle     :  0.556   6.326   4715  Z= 0.282
  Chirality :  0.044   0.136    514
  Planarity :  0.004   0.032    609
  Dihedral  :  5.774  54.255    511
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.35 %
    Favored  : 87.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.19 (0.40), residues: 421
  helix: -2.37 (1.12), residues: 19
  sheet: -0.60 (0.47), residues: 130
  loop : -1.91 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  36 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.009   0.001   PHE L  99 
 TYR   0.017   0.001   TYR H 103 
 ARG   0.003   0.000   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00033 (    1)
  link_NAG-ASN         : angle       1.24013 (    3)
  link_BETA1-4         : bond        0.00114 (    1)
  link_BETA1-4         : angle       1.11628 (    3)
  hydrogen bonds       : bond        0.03065 (   87)
  hydrogen bonds       : angle       6.44495 (  207)
  SS BOND              : bond        0.00316 (    5)
  SS BOND              : angle       0.99937 (   10)
  covalent geometry    : bond        0.00286 ( 3450)
  covalent geometry    : angle       0.55340 ( 4699)

*********************** 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
  57 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.521 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8196 (mm-30)
REVERT: H   59 ASN cc_start: 0.9006 (m-40) cc_final: 0.8738 (m-40)
REVERT: H   63 LYS cc_start: 0.9616 (mptt) cc_final: 0.9339 (mmtm)
REVERT: L   32 ASN cc_start: 0.9247 (m-40) cc_final: 0.8980 (m-40)
REVERT: L   98 THR cc_start: 0.9347 (t) cc_final: 0.9115 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.5166
  time to fit residues: 33.6973
Evaluate side-chains
  46 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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 = 0.2990 r_free = 0.2990 target = 0.040415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.030505 restraints weight = 72940.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.032348 restraints weight = 31338.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.033595 restraints weight = 17429.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.4736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3457  Z= 0.200
  Angle     :  0.592   6.471   4715  Z= 0.305
  Chirality :  0.043   0.137    514
  Planarity :  0.005   0.081    609
  Dihedral  :  5.872  53.350    511
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.06 %
    Favored  : 86.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.24 (0.40), residues: 421
  helix: -2.17 (1.20), residues: 19
  sheet: -0.65 (0.48), residues: 130
  loop : -1.96 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.010   0.001   PHE L  99 
 TYR   0.018   0.002   TYR A 449 
 ARG   0.008   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00446 (    1)
  link_NAG-ASN         : angle       1.46320 (    3)
  link_BETA1-4         : bond        0.00147 (    1)
  link_BETA1-4         : angle       1.35200 (    3)
  hydrogen bonds       : bond        0.03164 (   87)
  hydrogen bonds       : angle       6.47488 (  207)
  SS BOND              : bond        0.00301 (    5)
  SS BOND              : angle       0.95760 (   10)
  covalent geometry    : bond        0.00416 ( 3450)
  covalent geometry    : angle       0.58871 ( 4699)

*********************** 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
  53 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.606 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8205 (mm-30)
REVERT: H   59 ASN cc_start: 0.8977 (m-40) cc_final: 0.8610 (m-40)
REVERT: H   63 LYS cc_start: 0.9628 (mptt) cc_final: 0.9340 (mmtm)
REVERT: L   32 ASN cc_start: 0.9285 (m-40) cc_final: 0.9042 (m-40)
REVERT: L   98 THR cc_start: 0.9368 (t) cc_final: 0.9140 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.5412
  time to fit residues: 33.0574
Evaluate side-chains
  44 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.2991 r_free = 0.2991 target = 0.040405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.030408 restraints weight = 73524.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.032259 restraints weight = 31634.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.033502 restraints weight = 17659.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3457  Z= 0.177
  Angle     :  0.574   6.377   4715  Z= 0.295
  Chirality :  0.043   0.131    514
  Planarity :  0.004   0.049    609
  Dihedral  :  5.827  53.788    511
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.11 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.18 (0.40), residues: 421
  helix: -2.16 (1.20), residues: 19
  sheet: -0.49 (0.49), residues: 125
  loop : -1.96 (0.35), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.010   0.001   PHE L  99 
 TYR   0.013   0.001   TYR A 449 
 ARG   0.003   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00220 (    1)
  link_NAG-ASN         : angle       1.25531 (    3)
  link_BETA1-4         : bond        0.00131 (    1)
  link_BETA1-4         : angle       1.22795 (    3)
  hydrogen bonds       : bond        0.03068 (   87)
  hydrogen bonds       : angle       6.49161 (  207)
  SS BOND              : bond        0.00297 (    5)
  SS BOND              : angle       0.98286 (   10)
  covalent geometry    : bond        0.00370 ( 3450)
  covalent geometry    : angle       0.57100 ( 4699)

********************** 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
  52 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.525 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8058 (mm-30)
REVERT: H   59 ASN cc_start: 0.8956 (m-40) cc_final: 0.8688 (m-40)
REVERT: L   32 ASN cc_start: 0.9274 (m-40) cc_final: 0.9023 (m-40)
REVERT: L   98 THR cc_start: 0.9312 (t) cc_final: 0.9078 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.5058
  time to fit residues: 30.1250
Evaluate side-chains
  46 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 28 optimal weight:   20.0000
   chunk 2 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.2992 r_free = 0.2992 target = 0.040376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.030265 restraints weight = 71082.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.032123 restraints weight = 30541.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.033406 restraints weight = 17113.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.4873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3457  Z= 0.147
  Angle     :  0.557   6.310   4715  Z= 0.284
  Chirality :  0.043   0.134    514
  Planarity :  0.004   0.041    609
  Dihedral  :  5.728  53.800    511
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.30 %
    Favored  : 86.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.07 (0.40), residues: 421
  helix: -2.20 (1.16), residues: 19
  sheet: -0.43 (0.49), residues: 125
  loop : -1.87 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.011   0.001   PHE L  99 
 TYR   0.013   0.001   TYR A 449 
 ARG   0.006   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00058 (    1)
  link_NAG-ASN         : angle       1.10373 (    3)
  link_BETA1-4         : bond        0.00067 (    1)
  link_BETA1-4         : angle       1.16319 (    3)
  hydrogen bonds       : bond        0.02933 (   87)
  hydrogen bonds       : angle       6.41614 (  207)
  SS BOND              : bond        0.00280 (    5)
  SS BOND              : angle       0.90918 (   10)
  covalent geometry    : bond        0.00317 ( 3450)
  covalent geometry    : angle       0.55511 ( 4699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2729.15 seconds
wall clock time: 47 minutes 23.75 seconds (2843.75 seconds total)