Starting phenix.real_space_refine
on Thu Jul 24 22:17:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f46_31444/07_2025/7f46_31444.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f46_31444/07_2025/7f46_31444.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f46_31444/07_2025/7f46_31444.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f46_31444/07_2025/7f46_31444.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f46_31444/07_2025/7f46_31444.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f46_31444/07_2025/7f46_31444.cif"
  }
  resolution = 4.79
  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=   0.001 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    4187      2.51       5
     N    1091      2.21       5
     O    1261      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6564
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1652
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 10, 'TRANS': 192}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1543
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "H"
      Number of atoms: 1668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1668
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 16
    Chain: "L"
      Number of atoms: 1673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1673
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.70, per 1000 atoms: 0.72
  Number of scatterers: 6564
  At special positions: 0
  Unit cell: (91.98, 82.125, 129.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1261      8.00
     N    1091      7.00
     C    4187      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 157 " - pdb=" SG  CYS H 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 139 " - pdb=" SG  CYS L 199 " 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
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG C1301 " - " ASN C 165 "
  Time building additional restraints: 1.58
  Conformation dependent library (CDL) restraints added in 983.2 milliseconds
  

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1556

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 13 sheets defined
      6.3% alpha, 32.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
      removed outlier: 3.520A  pdb=" N   ASN B 343 " --> pdb=" O   GLY B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.520A  pdb=" N   ALA B 352 " --> pdb=" O   SER B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 371
      removed outlier: 4.529A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TYR B 369 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 5.674A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ASP B 389 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 3.761A  pdb=" N   VAL B 407 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE B 410 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.905A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 173 through 175
      No H-bonds generated for 'chain 'H' and resid 173 through 175'
    Processing helix  chain 'L' and resid 126 through 130
    Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31
      removed outlier: 3.726A  pdb=" N   SER C  60 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
      removed outlier: 8.430A  pdb=" N   ASN C  61 " --> pdb=" O   TYR C 269 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   TYR C 269 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   ALA C 264 " --> pdb=" O   THR C  95 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   THR C  95 " --> pdb=" O   ALA C 264 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   SER C 205 " --> pdb=" O   PRO C 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 55
      removed outlier: 4.174A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85
      removed outlier: 3.723A  pdb=" N   GLY C 103 " --> pdb=" O   LEU C 241 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.603A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 453
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.668A  pdb=" N   THR H 124 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   TYR H  94 " --> pdb=" O   THR H 124 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL H 126 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 137 through 141
      removed outlier: 6.009A  pdb=" N   TYR H 193 " --> pdb=" O   ASP H 161 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 167 through 171
    Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.563A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 108 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ASP L 110 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   TRP L  40 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 119 through 123
      removed outlier: 5.918A  pdb=" N   TYR L 178 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 158 through 159
      removed outlier: 3.771A  pdb=" N   VAL L 155 " --> pdb=" O   ALA L 158 " (cutoff:3.500A)

    221 hydrogen bonds defined for protein.
    546 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2075
        1.34 -     1.46: 1637
        1.46 -     1.58: 2986
        1.58 -     1.71: 0
        1.71 -     1.83: 31
  Bond restraints: 6729
  Sorted by residual:
  bond pdb=" N   LEU H 206 "
       pdb=" CA  LEU H 206 "
    ideal  model  delta    sigma   weight residual
    1.458  1.503 -0.046 1.27e-02 6.20e+03 1.29e+01
  bond pdb=" N   VAL B 524 "
       pdb=" CA  VAL B 524 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.18e-02 7.18e+03 9.96e+00
  bond pdb=" N   LYS H  76 "
       pdb=" CA  LYS H  76 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.16e-02 7.43e+03 9.70e+00
  bond pdb=" N   VAL H 103 "
       pdb=" CA  VAL H 103 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.19e-02 7.06e+03 8.96e+00
  bond pdb=" N   VAL B 483 "
       pdb=" CA  VAL B 483 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.036 1.21e-02 6.83e+03 8.86e+00
  ... (remaining 6724 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 8293
        1.33 -     2.66: 678
        2.66 -     3.99: 146
        3.99 -     5.31: 30
        5.31 -     6.64: 9
  Bond angle restraints: 9156
  Sorted by residual:
  angle pdb=" N   SER H 204 "
        pdb=" CA  SER H 204 "
        pdb=" C   SER H 204 "
      ideal   model   delta    sigma   weight residual
     112.38  107.89    4.49 1.22e+00 6.72e-01 1.35e+01
  angle pdb=" CA  CYS C 166 "
        pdb=" C   CYS C 166 "
        pdb=" O   CYS C 166 "
      ideal   model   delta    sigma   weight residual
     121.40  117.34    4.06 1.13e+00 7.83e-01 1.29e+01
  angle pdb=" CA  SER B 477 "
        pdb=" C   SER B 477 "
        pdb=" O   SER B 477 "
      ideal   model   delta    sigma   weight residual
     122.13  118.24    3.89 1.13e+00 7.83e-01 1.18e+01
  angle pdb=" N   LYS C 187 "
        pdb=" CA  LYS C 187 "
        pdb=" C   LYS C 187 "
      ideal   model   delta    sigma   weight residual
     113.89  108.54    5.35 1.58e+00 4.01e-01 1.14e+01
  angle pdb=" N   SER L  57 "
        pdb=" CA  SER L  57 "
        pdb=" C   SER L  57 "
      ideal   model   delta    sigma   weight residual
     114.56  110.32    4.24 1.27e+00 6.20e-01 1.12e+01
  ... (remaining 9151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 3578
       17.08 -    34.15: 347
       34.15 -    51.23: 54
       51.23 -    68.31: 10
       68.31 -    85.38: 3
  Dihedral angle restraints: 3992
    sinusoidal: 1559
      harmonic: 2433
  Sorted by residual:
  dihedral pdb=" CB  CYS H 157 "
           pdb=" SG  CYS H 157 "
           pdb=" SG  CYS H 213 "
           pdb=" CB  CYS H 213 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.24  -48.24     1      1.00e+01 1.00e-02 3.21e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.52   44.48     1      1.00e+01 1.00e-02 2.75e+01
  dihedral pdb=" CA  CYS B 361 "
           pdb=" C   CYS B 361 "
           pdb=" N   VAL B 362 "
           pdb=" CA  VAL B 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.16   22.84     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 3989 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 677
       0.045 -    0.089: 243
       0.089 -    0.134: 77
       0.134 -    0.178: 18
       0.178 -    0.222: 4
  Chirality restraints: 1019
  Sorted by residual:
  chirality pdb=" C1  NAG B1301 "
            pdb=" ND2 ASN B 343 "
            pdb=" C2  NAG B1301 "
            pdb=" O5  NAG B1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  ALA C 222 "
            pdb=" N   ALA C 222 "
            pdb=" C   ALA C 222 "
            pdb=" CB  ALA C 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.68   -0.20 2.00e-01 2.50e+01 9.74e-01
  chirality pdb=" CA  LEU H 206 "
            pdb=" N   LEU H 206 "
            pdb=" C   LEU H 206 "
            pdb=" CB  LEU H 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.45e-01
  ... (remaining 1016 not shown)

  Planarity restraints: 1180
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B1301 "   -0.287 2.00e-02 2.50e+03   2.46e-01 7.56e+02
        pdb=" C7  NAG B1301 "    0.064 2.00e-02 2.50e+03
        pdb=" C8  NAG B1301 "    0.017 2.00e-02 2.50e+03
        pdb=" N2  NAG B1301 "    0.414 2.00e-02 2.50e+03
        pdb=" O7  NAG B1301 "   -0.208 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C1301 "    0.257 2.00e-02 2.50e+03   2.14e-01 5.71e+02
        pdb=" C7  NAG C1301 "   -0.070 2.00e-02 2.50e+03
        pdb=" C8  NAG C1301 "    0.176 2.00e-02 2.50e+03
        pdb=" N2  NAG C1301 "   -0.355 2.00e-02 2.50e+03
        pdb=" O7  NAG C1301 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 224 "   -0.065 5.00e-02 4.00e+02   1.00e-01 1.60e+01
        pdb=" N   PRO C 225 "    0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO C 225 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO C 225 "   -0.054 5.00e-02 4.00e+02
  ... (remaining 1177 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 908
        2.75 -     3.29: 6132
        3.29 -     3.83: 9898
        3.83 -     4.36: 11286
        4.36 -     4.90: 20294
  Nonbonded interactions: 48518
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG  SER B 349 "
            pdb=" O   LEU B 452 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   PHE C 106 "
            pdb=" OG  SER C 116 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG  SER B 443 "
            pdb=" O   PHE B 497 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ARG L 147 "
            pdb=" NH1 ARG L 147 "
     model   vdw
     2.304 3.120
  ... (remaining 48513 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:             1.460
  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:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.770
  Find NCS groups from input model:        0.120
  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:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6012
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      :  0.006   0.054   6739  Z= 0.349
  Angle     :  0.846   7.883   9178  Z= 0.508
  Chirality :  0.053   0.222   1019
  Planarity :  0.011   0.246   1178
  Dihedral  : 13.319  85.382   2412
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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: -2.90 (0.27), residues: 822
  helix: -3.98 (0.66), residues: 25
  sheet: -0.97 (0.27), residues: 327
  loop : -2.62 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 436 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.020   0.002   PHE H 139 
 TYR   0.034   0.002   TYR B 473 
 ARG   0.005   0.001   ARG B 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00684 (    2)
  link_NAG-ASN         : angle       3.72883 (    6)
  hydrogen bonds       : bond        0.12061 (  221)
  hydrogen bonds       : angle       6.76126 (  546)
  SS BOND              : bond        0.00545 (    8)
  SS BOND              : angle       1.10280 (   16)
  covalent geometry    : bond        0.00584 ( 6729)
  covalent geometry    : angle       0.84030 ( 9156)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.688 
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: C   53 ASP cc_start: 0.8147 (m-30) cc_final: 0.7851 (m-30)
REVERT: H   83 MET cc_start: 0.5586 (mtm) cc_final: 0.4143 (mtm)
REVERT: H  102 MET cc_start: 0.0415 (ppp) cc_final: -0.0067 (mpp)
REVERT: H  117 MET cc_start: 0.6580 (mtt) cc_final: 0.5373 (mmp)
REVERT: H  198 VAL cc_start: 0.1912 (p) cc_final: 0.1363 (t)
REVERT: L   41 TYR cc_start: 0.6811 (m-80) cc_final: 0.6403 (m-80)
REVERT: L   91 TYR cc_start: 0.6202 (m-10) cc_final: 0.5704 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1691
  time to fit residues: 17.8718
Evaluate side-chains
  40 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 62 optimal weight:    0.2980
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    0.1980
   chunk 33 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 47 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
C 218 GLN
H  82 HIS
L  50 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.146241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.088774 restraints weight = 44651.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.088605 restraints weight = 35811.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.088605 restraints weight = 27976.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6230
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6739  Z= 0.139
  Angle     :  0.615   5.821   9178  Z= 0.323
  Chirality :  0.045   0.139   1019
  Planarity :  0.005   0.061   1178
  Dihedral  :  4.973  21.557    950
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.24 %
    Favored  : 94.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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 (0.28), residues: 822
  helix: -3.54 (0.95), residues: 19
  sheet: -0.55 (0.28), residues: 327
  loop : -2.34 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP H  53 
 HIS   0.009   0.002   HIS H  82 
 PHE   0.012   0.002   PHE L 214 
 TYR   0.017   0.001   TYR H 193 
 ARG   0.005   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00289 (    2)
  link_NAG-ASN         : angle       2.14303 (    6)
  hydrogen bonds       : bond        0.03345 (  221)
  hydrogen bonds       : angle       5.78483 (  546)
  SS BOND              : bond        0.00432 (    8)
  SS BOND              : angle       1.28487 (   16)
  covalent geometry    : bond        0.00306 ( 6729)
  covalent geometry    : angle       0.61115 ( 9156)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  229 LEU cc_start: 0.9149 (tp) cc_final: 0.8934 (tp)
REVERT: H  102 MET cc_start: 0.0295 (ppp) cc_final: 0.0019 (mpp)
REVERT: H  198 VAL cc_start: 0.2688 (p) cc_final: 0.2414 (t)
REVERT: L   94 MET cc_start: 0.7667 (ttt) cc_final: 0.7240 (tmm)
  outliers start: 1
  outliers final: 1
  residues processed: 62
  average time/residue: 0.1418
  time to fit residues: 13.2774
Evaluate side-chains
  40 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 9 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0870
   chunk 18 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 45 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.1162

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  50 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.143744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.088909 restraints weight = 42928.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.088111 restraints weight = 33447.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.088204 restraints weight = 28817.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6270
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6739  Z= 0.133
  Angle     :  0.624   7.579   9178  Z= 0.326
  Chirality :  0.044   0.197   1019
  Planarity :  0.005   0.085   1178
  Dihedral  :  5.038  25.240    950
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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: -2.13 (0.28), residues: 822
  helix: -3.49 (0.87), residues: 26
  sheet: -0.48 (0.29), residues: 330
  loop : -2.06 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  53 
 HIS   0.006   0.001   HIS H 217 
 PHE   0.016   0.002   PHE L 103 
 TYR   0.027   0.002   TYR H  32 
 ARG   0.004   0.001   ARG C 214 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00281 (    2)
  link_NAG-ASN         : angle       1.43888 (    6)
  hydrogen bonds       : bond        0.03263 (  221)
  hydrogen bonds       : angle       5.70573 (  546)
  SS BOND              : bond        0.00734 (    8)
  SS BOND              : angle       1.66990 (   16)
  covalent geometry    : bond        0.00299 ( 6729)
  covalent geometry    : angle       0.61930 ( 9156)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   53 ASP cc_start: 0.8219 (t0) cc_final: 0.7877 (t70)
REVERT: B  390 LEU cc_start: 0.8706 (tp) cc_final: 0.8196 (tt)
REVERT: H  102 MET cc_start: 0.0997 (ppp) cc_final: 0.0608 (mpp)
REVERT: H  198 VAL cc_start: 0.2952 (p) cc_final: 0.2717 (t)
REVERT: L   53 ILE cc_start: 0.2920 (mt) cc_final: 0.1497 (mt)
REVERT: L   77 THR cc_start: 0.4761 (p) cc_final: 0.4546 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.1567
  time to fit residues: 11.4245
Evaluate side-chains
  34 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 58 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0270
   chunk 49 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.5644

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

Flipped N/Q/H residues before XYZ refinement:
** C  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN
L  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.141098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.083692 restraints weight = 40145.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.081755 restraints weight = 31552.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.081756 restraints weight = 26595.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6317
moved from start:          0.5391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6739  Z= 0.172
  Angle     :  0.692   7.434   9178  Z= 0.360
  Chirality :  0.046   0.223   1019
  Planarity :  0.006   0.088   1178
  Dihedral  :  5.401  27.237    950
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.52 %
    Favored  : 94.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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: -2.01 (0.28), residues: 822
  helix: -4.00 (0.65), residues: 25
  sheet: -0.31 (0.28), residues: 325
  loop : -2.01 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  64 
 HIS   0.014   0.002   HIS C  66 
 PHE   0.016   0.002   PHE L 121 
 TYR   0.037   0.002   TYR L 145 
 ARG   0.004   0.000   ARG C 214 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00085 (    2)
  link_NAG-ASN         : angle       1.46558 (    6)
  hydrogen bonds       : bond        0.03813 (  221)
  hydrogen bonds       : angle       6.17595 (  546)
  SS BOND              : bond        0.00675 (    8)
  SS BOND              : angle       2.02220 (   16)
  covalent geometry    : bond        0.00385 ( 6729)
  covalent geometry    : angle       0.68692 ( 9156)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
REVERT: B  390 LEU cc_start: 0.8948 (tp) cc_final: 0.8394 (tt)
REVERT: B  505 TYR cc_start: 0.8928 (m-80) cc_final: 0.8631 (t80)
REVERT: H  102 MET cc_start: 0.1696 (ppp) cc_final: 0.1337 (mpp)
REVERT: H  198 VAL cc_start: 0.3003 (p) cc_final: 0.2788 (t)
REVERT: L   91 TYR cc_start: 0.5416 (m-10) cc_final: 0.5067 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 47
  average time/residue: 0.1382
  time to fit residues: 10.1778
Evaluate side-chains
  35 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** C  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  50 GLN
L 165 GLN
** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.138475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.093959 restraints weight = 44413.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.085201 restraints weight = 46978.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.085577 restraints weight = 35356.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6342
moved from start:          0.6813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079   6739  Z= 0.223
  Angle     :  0.747  10.245   9178  Z= 0.391
  Chirality :  0.047   0.280   1019
  Planarity :  0.006   0.087   1178
  Dihedral  :  6.003  30.633    950
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 18.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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: -2.02 (0.28), residues: 822
  helix: -3.84 (0.82), residues: 19
  sheet: -0.34 (0.29), residues: 326
  loop : -2.04 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C  64 
 HIS   0.020   0.002   HIS C  66 
 PHE   0.017   0.002   PHE C 186 
 TYR   0.033   0.002   TYR L 145 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00129 (    2)
  link_NAG-ASN         : angle       1.93756 (    6)
  hydrogen bonds       : bond        0.04204 (  221)
  hydrogen bonds       : angle       6.62453 (  546)
  SS BOND              : bond        0.01744 (    8)
  SS BOND              : angle       2.29182 (   16)
  covalent geometry    : bond        0.00484 ( 6729)
  covalent geometry    : angle       0.73997 ( 9156)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  390 LEU cc_start: 0.9158 (tp) cc_final: 0.8691 (tt)
REVERT: B  505 TYR cc_start: 0.8899 (m-80) cc_final: 0.8584 (t80)
REVERT: H  102 MET cc_start: 0.2875 (ppp) cc_final: 0.1966 (mpp)
REVERT: H  117 MET cc_start: 0.5910 (mmp) cc_final: 0.5564 (mmp)
REVERT: L   91 TYR cc_start: 0.5052 (m-10) cc_final: 0.4728 (m-10)
REVERT: L   94 MET cc_start: 0.5343 (mpp) cc_final: 0.4850 (mpp)
REVERT: L  178 TYR cc_start: -0.0139 (m-80) cc_final: -0.0420 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1397
  time to fit residues: 9.4399
Evaluate side-chains
  33 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0270
   chunk 40 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 23 optimal weight:    0.4980
   chunk 55 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
C  66 HIS
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 HIS
H 188 GLN
L  50 GLN
L 165 GLN
L 203 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.142772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.111310 restraints weight = 62241.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.108833 restraints weight = 54690.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.108881 restraints weight = 44149.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6308
moved from start:          0.6697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6739  Z= 0.106
  Angle     :  0.586   6.589   9178  Z= 0.305
  Chirality :  0.044   0.169   1019
  Planarity :  0.005   0.089   1178
  Dihedral  :  4.965  21.456    950
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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: -1.82 (0.28), residues: 822
  helix: -3.70 (0.75), residues: 25
  sheet: -0.10 (0.28), residues: 328
  loop : -1.96 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  64 
 HIS   0.014   0.001   HIS C  66 
 PHE   0.014   0.001   PHE L 144 
 TYR   0.014   0.001   TYR C 266 
 ARG   0.004   0.000   ARG B 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00300 (    2)
  link_NAG-ASN         : angle       1.37833 (    6)
  hydrogen bonds       : bond        0.03031 (  221)
  hydrogen bonds       : angle       5.95412 (  546)
  SS BOND              : bond        0.00484 (    8)
  SS BOND              : angle       1.14763 (   16)
  covalent geometry    : bond        0.00235 ( 6729)
  covalent geometry    : angle       0.58328 ( 9156)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.712 
Fit side-chains
REVERT: C   53 ASP cc_start: 0.8165 (t0) cc_final: 0.7841 (t70)
REVERT: B  390 LEU cc_start: 0.9068 (tp) cc_final: 0.8617 (tt)
REVERT: H  102 MET cc_start: 0.2756 (ppp) cc_final: 0.1998 (mpp)
REVERT: L   91 TYR cc_start: 0.5530 (m-10) cc_final: 0.5198 (m-10)
REVERT: L   94 MET cc_start: 0.5062 (mpp) cc_final: 0.3861 (mpp)
REVERT: L  145 TYR cc_start: 0.3268 (t80) cc_final: 0.2654 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1492
  time to fit residues: 8.8578
Evaluate side-chains
  27 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  50 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.137536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.081382 restraints weight = 41045.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.081359 restraints weight = 31312.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.081359 restraints weight = 30453.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6402
moved from start:          0.7788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   6739  Z= 0.184
  Angle     :  0.694   8.136   9178  Z= 0.362
  Chirality :  0.046   0.200   1019
  Planarity :  0.006   0.094   1178
  Dihedral  :  5.729  28.917    950
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 17.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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: -1.88 (0.28), residues: 822
  helix: -3.70 (0.73), residues: 25
  sheet: -0.17 (0.28), residues: 330
  loop : -1.98 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS C  66 
 PHE   0.020   0.002   PHE C 186 
 TYR   0.024   0.002   TYR L 145 
 ARG   0.003   0.000   ARG H 104 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00129 (    2)
  link_NAG-ASN         : angle       1.63164 (    6)
  hydrogen bonds       : bond        0.03770 (  221)
  hydrogen bonds       : angle       6.34431 (  546)
  SS BOND              : bond        0.00769 (    8)
  SS BOND              : angle       1.77329 (   16)
  covalent geometry    : bond        0.00421 ( 6729)
  covalent geometry    : angle       0.68933 ( 9156)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.787 
Fit side-chains
REVERT: H  102 MET cc_start: 0.1748 (ppp) cc_final: 0.1165 (mpp)
REVERT: L   91 TYR cc_start: 0.5439 (m-10) cc_final: 0.5150 (m-10)
REVERT: L   94 MET cc_start: 0.4548 (mpp) cc_final: 0.3895 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1684
  time to fit residues: 11.3670
Evaluate side-chains
  30 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 72 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 40 optimal weight:   30.0000
   chunk 11 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 172 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 = 0.4289 r_free = 0.4289 target = 0.127470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.090205 restraints weight = 62127.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.088317 restraints weight = 57436.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.089094 restraints weight = 42062.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6305
moved from start:          0.8287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6739  Z= 0.164
  Angle     :  0.673   9.537   9178  Z= 0.348
  Chirality :  0.046   0.215   1019
  Planarity :  0.006   0.098   1178
  Dihedral  :  5.550  22.817    950
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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: -1.92 (0.28), residues: 822
  helix: -3.64 (0.72), residues: 25
  sheet: -0.27 (0.28), residues: 335
  loop : -1.97 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 171 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.014   0.002   PHE C 186 
 TYR   0.026   0.002   TYR L 145 
 ARG   0.004   0.000   ARG H 104 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00162 (    2)
  link_NAG-ASN         : angle       2.07876 (    6)
  hydrogen bonds       : bond        0.03513 (  221)
  hydrogen bonds       : angle       6.33816 (  546)
  SS BOND              : bond        0.00633 (    8)
  SS BOND              : angle       1.57697 (   16)
  covalent geometry    : bond        0.00373 ( 6729)
  covalent geometry    : angle       0.66796 ( 9156)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.753 
Fit side-chains
REVERT: H  102 MET cc_start: 0.3037 (ppp) cc_final: 0.2223 (mpp)
REVERT: L   91 TYR cc_start: 0.5452 (m-80) cc_final: 0.5110 (m-10)
REVERT: L   94 MET cc_start: 0.5522 (mpp) cc_final: 0.4848 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1340
  time to fit residues: 7.8484
Evaluate side-chains
  32 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0060
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.1200

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 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 = 0.4296 r_free = 0.4296 target = 0.127462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.088252 restraints weight = 62555.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.086237 restraints weight = 60879.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.086001 restraints weight = 47128.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6336
moved from start:          0.8510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6739  Z= 0.128
  Angle     :  0.625   8.083   9178  Z= 0.325
  Chirality :  0.045   0.167   1019
  Planarity :  0.005   0.097   1178
  Dihedral  :  5.219  22.116    950
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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: -1.84 (0.28), residues: 822
  helix: -3.79 (0.69), residues: 31
  sheet: -0.03 (0.29), residues: 327
  loop : -2.01 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 171 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.012   0.001   PHE C 186 
 TYR   0.018   0.001   TYR L 145 
 ARG   0.004   0.000   ARG H 104 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00237 (    2)
  link_NAG-ASN         : angle       2.04385 (    6)
  hydrogen bonds       : bond        0.03172 (  221)
  hydrogen bonds       : angle       6.10017 (  546)
  SS BOND              : bond        0.00562 (    8)
  SS BOND              : angle       1.25953 (   16)
  covalent geometry    : bond        0.00286 ( 6729)
  covalent geometry    : angle       0.62158 ( 9156)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.696 
Fit side-chains
REVERT: B  390 LEU cc_start: 0.9070 (tp) cc_final: 0.8757 (tt)
REVERT: H  102 MET cc_start: 0.2563 (ppp) cc_final: 0.1982 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1290
  time to fit residues: 7.9588
Evaluate side-chains
  33 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 48 optimal weight:   20.0000
   chunk 81 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 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 = 0.4281 r_free = 0.4281 target = 0.137971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.088431 restraints weight = 47965.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.084743 restraints weight = 49343.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.084344 restraints weight = 40404.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.8670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6739  Z= 0.117
  Angle     :  0.614   7.678   9178  Z= 0.320
  Chirality :  0.044   0.161   1019
  Planarity :  0.005   0.098   1178
  Dihedral  :  5.014  21.730    950
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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: -1.66 (0.28), residues: 822
  helix: -3.27 (0.67), residues: 43
  sheet:  0.13 (0.29), residues: 324
  loop : -1.88 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 171 
 HIS   0.007   0.001   HIS H  35 
 PHE   0.012   0.001   PHE L 144 
 TYR   0.016   0.001   TYR L 145 
 ARG   0.003   0.000   ARG H 104 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00305 (    2)
  link_NAG-ASN         : angle       2.18119 (    6)
  hydrogen bonds       : bond        0.03020 (  221)
  hydrogen bonds       : angle       5.92659 (  546)
  SS BOND              : bond        0.00519 (    8)
  SS BOND              : angle       1.14911 (   16)
  covalent geometry    : bond        0.00264 ( 6729)
  covalent geometry    : angle       0.61035 ( 9156)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.739 
Fit side-chains
REVERT: B  390 LEU cc_start: 0.9084 (tp) cc_final: 0.8670 (tt)
REVERT: H  102 MET cc_start: 0.2167 (ppp) cc_final: 0.1647 (mpp)
REVERT: L   94 MET cc_start: 0.3867 (mpp) cc_final: 0.3657 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1385
  time to fit residues: 9.2144
Evaluate side-chains
  34 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   chunk 41 optimal weight:   30.0000
   chunk 39 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 68 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   chunk 36 optimal weight:    0.3980
   chunk 33 optimal weight:    0.4980
   chunk 15 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    2.5384

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

Flipped N/Q/H residues before XYZ refinement:
C 207 HIS
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.136197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.109530 restraints weight = 62780.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.106178 restraints weight = 63586.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.106836 restraints weight = 47254.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6201
moved from start:          0.9852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   6739  Z= 0.236
  Angle     :  0.787  10.136   9178  Z= 0.407
  Chirality :  0.048   0.257   1019
  Planarity :  0.007   0.103   1178
  Dihedral  :  6.152  25.822    950
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 23.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    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: -1.97 (0.28), residues: 822
  helix: -3.65 (0.64), residues: 37
  sheet: -0.07 (0.30), residues: 328
  loop : -2.13 (0.26), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 436 
 HIS   0.005   0.002   HIS H 181 
 PHE   0.032   0.003   PHE C 186 
 TYR   0.034   0.003   TYR L 145 
 ARG   0.008   0.001   ARG H 104 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00204 (    2)
  link_NAG-ASN         : angle       3.06465 (    6)
  hydrogen bonds       : bond        0.04030 (  221)
  hydrogen bonds       : angle       7.18905 (  546)
  SS BOND              : bond        0.00613 (    8)
  SS BOND              : angle       1.82625 (   16)
  covalent geometry    : bond        0.00522 ( 6729)
  covalent geometry    : angle       0.78059 ( 9156)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3623.60 seconds
wall clock time: 63 minutes 11.06 seconds (3791.06 seconds total)