Starting phenix.real_space_refine
on Thu Jul 24 02:19:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e9p_31035/07_2025/7e9p_31035.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e9p_31035/07_2025/7e9p_31035.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e9p_31035/07_2025/7e9p_31035.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e9p_31035/07_2025/7e9p_31035.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e9p_31035/07_2025/7e9p_31035.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e9p_31035/07_2025/7e9p_31035.cif"
  }
  resolution = 3.69
  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=  -0.004 sd=   0.036
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      22      5.16       5
     C    3095      2.51       5
     N     823      2.21       5
     O     958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 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: 4898
  Number of models: 1
  Model: ""
    Number of chains: 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: "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: "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: "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: 4.20, per 1000 atoms: 0.86
  Number of scatterers: 4898
  At special positions: 0
  Unit cell: (70.08, 102.93, 98.55, 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      22     16.00
     O     958      8.00
     N     823      7.00
     C    3095      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    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=2.04
    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
    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

  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 "
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1170

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 11 sheets defined
      8.3% alpha, 30.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
      removed outlier: 3.512A  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: 3.589A  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: 3.901A  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: 3.607A  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 'L' and resid 126 through 130
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 4.114A  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 sheet with id=AA1, 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=AA2, first strand: chain 'B' and resid 452 through 453
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.562A  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: 6.518A  pdb=" N   TRP L  40 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 119 through 123
      removed outlier: 5.920A  pdb=" N   TYR L 178 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
    Processing sheet with id=AA7, 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)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.666A  pdb=" N   THR H 124 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TYR H  94 " --> pdb=" O   THR H 124 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL H 126 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
      removed outlier: 5.757A  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=AB1, 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=AB2, first strand: chain 'H' and resid 167 through 171

    162 hydrogen bonds defined for protein.
    387 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: 1.61

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 802
        1.31 -     1.44: 1423
        1.44 -     1.57: 2765
        1.57 -     1.70: 0
        1.70 -     1.83: 28
  Bond restraints: 5018
  Sorted by residual:
  bond pdb=" C7  NAG B1301 "
       pdb=" N2  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.346  1.454 -0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.502 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" N   GLU B 484 "
       pdb=" CA  GLU B 484 "
    ideal  model  delta    sigma   weight residual
    1.459  1.505 -0.046 1.27e-02 6.20e+03 1.33e+01
  bond pdb=" N   LEU H 206 "
       pdb=" CA  LEU H 206 "
    ideal  model  delta    sigma   weight residual
    1.458  1.503 -0.045 1.27e-02 6.20e+03 1.26e+01
  bond pdb=" N   VAL B 483 "
       pdb=" CA  VAL B 483 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.11e-02 8.12e+03 1.17e+01
  ... (remaining 5013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 6604
        1.89 -     3.78: 189
        3.78 -     5.68: 27
        5.68 -     7.57: 6
        7.57 -     9.46: 3
  Bond angle restraints: 6829
  Sorted by residual:
  angle pdb=" N   PHE B 486 "
        pdb=" CA  PHE B 486 "
        pdb=" C   PHE B 486 "
      ideal   model   delta    sigma   weight residual
     112.97  105.34    7.63 1.06e+00 8.90e-01 5.18e+01
  angle pdb=" CA  VAL B 483 "
        pdb=" C   VAL B 483 "
        pdb=" O   VAL B 483 "
      ideal   model   delta    sigma   weight residual
     121.63  114.88    6.75 9.90e-01 1.02e+00 4.66e+01
  angle pdb=" C   GLU B 484 "
        pdb=" CA  GLU B 484 "
        pdb=" CB  GLU B 484 "
      ideal   model   delta    sigma   weight residual
     110.78  101.60    9.18 1.60e+00 3.91e-01 3.29e+01
  angle pdb=" N   GLU B 484 "
        pdb=" CA  GLU B 484 "
        pdb=" C   GLU B 484 "
      ideal   model   delta    sigma   weight residual
     108.20  117.66   -9.46 1.71e+00 3.42e-01 3.06e+01
  angle pdb=" CB  GLN B 474 "
        pdb=" CG  GLN B 474 "
        pdb=" CD  GLN B 474 "
      ideal   model   delta    sigma   weight residual
     112.60  105.42    7.18 1.70e+00 3.46e-01 1.78e+01
  ... (remaining 6824 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.00: 2774
       23.00 -    46.00: 184
       46.00 -    69.00: 23
       69.00 -    92.00: 3
       92.00 -   115.00: 8
  Dihedral angle restraints: 2992
    sinusoidal: 1154
      harmonic: 1838
  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  141.21  -48.21     1      1.00e+01 1.00e-02 3.20e+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   48.54   44.46     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  157.14   22.86     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 2989 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 583
       0.052 -    0.105: 144
       0.105 -    0.157: 23
       0.157 -    0.210: 4
       0.210 -    0.262: 1
  Chirality restraints: 755
  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   -2.14   -0.26 2.00e-01 2.50e+01 1.72e+00
  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 9.43e-01
  chirality pdb=" CA  PHE B 486 "
            pdb=" N   PHE B 486 "
            pdb=" C   PHE B 486 "
            pdb=" CB  PHE B 486 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.76e-01
  ... (remaining 752 not shown)

  Planarity restraints: 886
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 473 "    0.014 2.00e-02 2.50e+03   1.41e-02 3.96e+00
        pdb=" CG  TYR B 473 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 473 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 473 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 473 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 473 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 473 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 473 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 453 "    0.015 2.00e-02 2.50e+03   1.15e-02 2.65e+00
        pdb=" CG  TYR B 453 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 453 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 453 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 453 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 453 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 453 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 453 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 473 "   -0.008 2.00e-02 2.50e+03   1.61e-02 2.60e+00
        pdb=" C   TYR B 473 "    0.028 2.00e-02 2.50e+03
        pdb=" O   TYR B 473 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLN B 474 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 883 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 690
        2.75 -     3.29: 4535
        3.29 -     3.83: 7332
        3.83 -     4.36: 8186
        4.36 -     4.90: 15089
  Nonbonded interactions: 35832
  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
     2.221 3.040
  nonbonded pdb=" O   SER H  52 "
            pdb=" NH1 ARG H  72 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OG  SER B 443 "
            pdb=" O   PHE B 497 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   ARG L 147 "
            pdb=" NH1 ARG L 147 "
     model   vdw
     2.304 3.120
  ... (remaining 35827 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:             59.950
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     18.830
  Find NCS groups from input model:        0.070
  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:3.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   82.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
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      :  0.005   0.108   5026  Z= 0.279
  Angle     :  0.795   9.461   6846  Z= 0.458
  Chirality :  0.048   0.262    755
  Planarity :  0.004   0.038    885
  Dihedral  : 16.126 115.002   1801
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -2.51 (0.31), residues: 629
  helix: -3.97 (0.66), residues: 25
  sheet: -0.64 (0.33), residues: 240
  loop : -2.30 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 436 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.020   0.001   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        0.01099 (    1)
  link_NAG-ASN         : angle       6.35897 (    3)
  hydrogen bonds       : bond        0.13273 (  162)
  hydrogen bonds       : angle       6.75560 (  387)
  SS BOND              : bond        0.00633 (    7)
  SS BOND              : angle       1.08115 (   14)
  covalent geometry    : bond        0.00516 ( 5018)
  covalent geometry    : angle       0.78342 ( 6829)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 ILE cc_start: 0.8922 (mp) cc_final: 0.8705 (mt)
REVERT: H   30 ASP cc_start: 0.7983 (p0) cc_final: 0.7570 (p0)
REVERT: H   31 ASP cc_start: 0.8192 (m-30) cc_final: 0.7574 (m-30)
REVERT: H  161 ASP cc_start: 0.8187 (m-30) cc_final: 0.7939 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2267
  time to fit residues: 20.8512
Evaluate side-chains
  61 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    0.4980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 450 ASN
H 221 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.098991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.084859 restraints weight = 11322.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.087050 restraints weight = 5952.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.088483 restraints weight = 3674.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5026  Z= 0.131
  Angle     :  0.649  10.477   6846  Z= 0.323
  Chirality :  0.046   0.265    755
  Planarity :  0.004   0.038    885
  Dihedral  :  7.411  53.364    713
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  9.61 %
    Favored  : 90.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -2.22 (0.32), residues: 629
  helix: -4.00 (0.66), residues: 25
  sheet: -0.44 (0.33), residues: 244
  loop : -2.11 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 436 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.013   0.001   PHE H 139 
 TYR   0.020   0.001   TYR B 453 
 ARG   0.003   0.000   ARG L  59 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00968 (    1)
  link_NAG-ASN         : angle       4.94995 (    3)
  hydrogen bonds       : bond        0.03379 (  162)
  hydrogen bonds       : angle       5.96037 (  387)
  SS BOND              : bond        0.00526 (    7)
  SS BOND              : angle       1.07446 (   14)
  covalent geometry    : bond        0.00304 ( 5018)
  covalent geometry    : angle       0.63917 ( 6829)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  148 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7137 (tm-30)
REVERT: H   30 ASP cc_start: 0.8247 (p0) cc_final: 0.7974 (p0)
REVERT: H   31 ASP cc_start: 0.8233 (m-30) cc_final: 0.7774 (m-30)
REVERT: H  161 ASP cc_start: 0.8256 (m-30) cc_final: 0.7991 (m-30)
REVERT: H  221 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.7152 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 68
  average time/residue: 0.2817
  time to fit residues: 26.5743
Evaluate side-chains
  56 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 1.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain H residue  221 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 0 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
H 221 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.097027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.082934 restraints weight = 11433.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.085079 restraints weight = 6019.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.086496 restraints weight = 3735.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5026  Z= 0.166
  Angle     :  0.639   7.260   6846  Z= 0.323
  Chirality :  0.046   0.296    755
  Planarity :  0.004   0.035    885
  Dihedral  :  5.465  32.125    713
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.38 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -2.12 (0.32), residues: 629
  helix: -3.68 (0.66), residues: 31
  sheet: -0.28 (0.34), residues: 242
  loop : -2.08 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.010   0.001   PHE B 456 
 TYR   0.027   0.002   TYR B 473 
 ARG   0.003   0.000   ARG L  59 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00597 (    1)
  link_NAG-ASN         : angle       4.07711 (    3)
  hydrogen bonds       : bond        0.03514 (  162)
  hydrogen bonds       : angle       5.90529 (  387)
  SS BOND              : bond        0.00530 (    7)
  SS BOND              : angle       1.00823 (   14)
  covalent geometry    : bond        0.00385 ( 5018)
  covalent geometry    : angle       0.63232 ( 6829)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
REVERT: H   30 ASP cc_start: 0.8237 (p0) cc_final: 0.7962 (p0)
REVERT: H   31 ASP cc_start: 0.8265 (m-30) cc_final: 0.7825 (m-30)
REVERT: H  161 ASP cc_start: 0.8153 (m-30) cc_final: 0.7901 (m-30)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 0.2024
  time to fit residues: 18.6061
Evaluate side-chains
  58 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
L 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.094733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.080778 restraints weight = 11787.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.082932 restraints weight = 6059.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.084313 restraints weight = 3695.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5026  Z= 0.232
  Angle     :  0.717  11.255   6846  Z= 0.363
  Chirality :  0.048   0.312    755
  Planarity :  0.004   0.039    885
  Dihedral  :  5.410  31.950    713
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.71 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -2.20 (0.32), residues: 629
  helix: -3.93 (0.59), residues: 31
  sheet: -0.29 (0.34), residues: 242
  loop : -2.15 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.015   0.002   PHE L 144 
 TYR   0.025   0.002   TYR B 453 
 ARG   0.004   0.001   ARG H  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    1)
  link_NAG-ASN         : angle       3.82686 (    3)
  hydrogen bonds       : bond        0.04082 (  162)
  hydrogen bonds       : angle       6.08102 (  387)
  SS BOND              : bond        0.00687 (    7)
  SS BOND              : angle       1.02310 (   14)
  covalent geometry    : bond        0.00540 ( 5018)
  covalent geometry    : angle       0.71223 ( 6829)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  417 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7772 (tptp)
REVERT: B  470 THR cc_start: 0.8952 (p) cc_final: 0.8709 (p)
REVERT: H   30 ASP cc_start: 0.8215 (p0) cc_final: 0.7916 (p0)
REVERT: H  161 ASP cc_start: 0.8140 (m-30) cc_final: 0.7896 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 70
  average time/residue: 0.1683
  time to fit residues: 15.6196
Evaluate side-chains
  62 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  159 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0570
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.6698

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.103753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.089637 restraints weight = 11455.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.091929 restraints weight = 5710.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.093411 restraints weight = 3433.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5026  Z= 0.119
  Angle     :  0.614   9.697   6846  Z= 0.308
  Chirality :  0.044   0.242    755
  Planarity :  0.004   0.033    885
  Dihedral  :  4.681  26.272    713
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 18.11 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -1.94 (0.32), residues: 629
  helix: -3.50 (0.78), residues: 25
  sheet: -0.17 (0.34), residues: 241
  loop : -1.99 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 436 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.009   0.001   PHE B 456 
 TYR   0.016   0.001   TYR B 473 
 ARG   0.003   0.000   ARG H  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00426 (    1)
  link_NAG-ASN         : angle       2.80884 (    3)
  hydrogen bonds       : bond        0.03087 (  162)
  hydrogen bonds       : angle       5.63023 (  387)
  SS BOND              : bond        0.00508 (    7)
  SS BOND              : angle       0.79287 (   14)
  covalent geometry    : bond        0.00276 ( 5018)
  covalent geometry    : angle       0.61041 ( 6829)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: L  148 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7198 (tm-30)
REVERT: L  150 LYS cc_start: 0.7777 (tmtt) cc_final: 0.7220 (tptp)
REVERT: H   30 ASP cc_start: 0.8107 (p0) cc_final: 0.7847 (p0)
REVERT: H  161 ASP cc_start: 0.8160 (m-30) cc_final: 0.7940 (m-30)
  outliers start: 8
  outliers final: 6
  residues processed: 68
  average time/residue: 0.1510
  time to fit residues: 14.1049
Evaluate side-chains
  62 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  159 VAL
Chi-restraints excluded: chain H residue  215 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 38 optimal weight:    0.0870
   chunk 46 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0670
   chunk 20 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  33 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.105570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.091084 restraints weight = 11340.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.093421 restraints weight = 5663.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.094919 restraints weight = 3424.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5026  Z= 0.108
  Angle     :  0.643  10.939   6846  Z= 0.324
  Chirality :  0.045   0.271    755
  Planarity :  0.004   0.035    885
  Dihedral  :  4.472  24.612    713
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 18.30 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -1.76 (0.32), residues: 629
  helix: -3.46 (0.81), residues: 25
  sheet: -0.04 (0.34), residues: 238
  loop : -1.86 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.012   0.001   PHE B 486 
 TYR   0.013   0.001   TYR B 473 
 ARG   0.002   0.000   ARG H  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00437 (    1)
  link_NAG-ASN         : angle       2.36743 (    3)
  hydrogen bonds       : bond        0.02889 (  162)
  hydrogen bonds       : angle       5.46378 (  387)
  SS BOND              : bond        0.00578 (    7)
  SS BOND              : angle       3.38949 (   14)
  covalent geometry    : bond        0.00246 ( 5018)
  covalent geometry    : angle       0.62358 ( 6829)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
REVERT: L  150 LYS cc_start: 0.7722 (tmtt) cc_final: 0.7230 (tptt)
REVERT: H   30 ASP cc_start: 0.8097 (p0) cc_final: 0.7876 (p0)
REVERT: H  161 ASP cc_start: 0.8146 (m-30) cc_final: 0.7938 (m-30)
  outliers start: 9
  outliers final: 6
  residues processed: 71
  average time/residue: 0.2298
  time to fit residues: 20.8755
Evaluate side-chains
  63 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  159 VAL
Chi-restraints excluded: chain H residue  215 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.4988

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.101726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.087444 restraints weight = 11424.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.089653 restraints weight = 5736.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.091119 restraints weight = 3485.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5026  Z= 0.200
  Angle     :  0.721  10.666   6846  Z= 0.364
  Chirality :  0.047   0.288    755
  Planarity :  0.004   0.037    885
  Dihedral  :  5.060  30.285    713
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.85 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -1.89 (0.32), residues: 629
  helix: -3.60 (0.76), residues: 25
  sheet: -0.06 (0.34), residues: 240
  loop : -2.00 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.015   0.001   PHE L 144 
 TYR   0.021   0.002   TYR B 453 
 ARG   0.008   0.001   ARG L 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00190 (    1)
  link_NAG-ASN         : angle       2.96935 (    3)
  hydrogen bonds       : bond        0.03762 (  162)
  hydrogen bonds       : angle       5.76739 (  387)
  SS BOND              : bond        0.00639 (    7)
  SS BOND              : angle       3.02820 (   14)
  covalent geometry    : bond        0.00465 ( 5018)
  covalent geometry    : angle       0.70601 ( 6829)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: B  506 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8394 (mp10)
REVERT: L  150 LYS cc_start: 0.7892 (tmtt) cc_final: 0.7366 (tptt)
REVERT: H  161 ASP cc_start: 0.8105 (m-30) cc_final: 0.7885 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 65
  average time/residue: 0.2519
  time to fit residues: 21.8539
Evaluate side-chains
  63 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 1.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  159 VAL
Chi-restraints excluded: chain H residue  186 VAL
Chi-restraints excluded: chain H residue  215 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 36 optimal weight:    0.0170
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0870
   chunk 25 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0970
   chunk 8 optimal weight:    0.0670
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.2332

-------------------------------------------------------------------------------
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 = 0.3668 r_free = 0.3668 target = 0.106878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.092229 restraints weight = 11270.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.094602 restraints weight = 5630.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.096137 restraints weight = 3414.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5026  Z= 0.105
  Angle     :  0.614   7.343   6846  Z= 0.311
  Chirality :  0.043   0.205    755
  Planarity :  0.004   0.035    885
  Dihedral  :  4.304  23.360    713
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.59 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -1.59 (0.33), residues: 629
  helix: -4.08 (0.73), residues: 18
  sheet:  0.13 (0.35), residues: 240
  loop : -1.80 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.015   0.001   PHE B 392 
 TYR   0.011   0.001   TYR B 396 
 ARG   0.006   0.000   ARG L 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00501 (    1)
  link_NAG-ASN         : angle       2.06902 (    3)
  hydrogen bonds       : bond        0.02737 (  162)
  hydrogen bonds       : angle       5.34083 (  387)
  SS BOND              : bond        0.00360 (    7)
  SS BOND              : angle       2.36060 (   14)
  covalent geometry    : bond        0.00237 ( 5018)
  covalent geometry    : angle       0.60357 ( 6829)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 1.692 
Fit side-chains
   revert: symmetry clash
REVERT: B  506 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8375 (mp10)
REVERT: L   86 GLU cc_start: 0.7702 (tp30) cc_final: 0.7457 (tp30)
REVERT: L  150 LYS cc_start: 0.7643 (tmtt) cc_final: 0.7114 (tptt)
REVERT: H  161 ASP cc_start: 0.8123 (m-30) cc_final: 0.7921 (m-30)
  outliers start: 10
  outliers final: 6
  residues processed: 72
  average time/residue: 0.3324
  time to fit residues: 31.2959
Evaluate side-chains
  63 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  127 THR
Chi-restraints excluded: chain H residue  159 VAL
Chi-restraints excluded: chain H residue  215 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.105757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.090814 restraints weight = 11352.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.093213 restraints weight = 5545.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.094737 restraints weight = 3286.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5026  Z= 0.134
  Angle     :  0.656   9.910   6846  Z= 0.333
  Chirality :  0.044   0.241    755
  Planarity :  0.004   0.039    885
  Dihedral  :  4.562  26.206    713
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 19.78 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -1.62 (0.33), residues: 629
  helix: -4.21 (0.65), residues: 18
  sheet:  0.13 (0.34), residues: 243
  loop : -1.84 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.025   0.001   PHE B 486 
 TYR   0.013   0.001   TYR B 453 
 ARG   0.008   0.001   ARG L 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00322 (    1)
  link_NAG-ASN         : angle       2.24899 (    3)
  hydrogen bonds       : bond        0.03242 (  162)
  hydrogen bonds       : angle       5.43306 (  387)
  SS BOND              : bond        0.00520 (    7)
  SS BOND              : angle       2.84110 (   14)
  covalent geometry    : bond        0.00311 ( 5018)
  covalent geometry    : angle       0.64193 ( 6829)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 1.570 
Fit side-chains
   revert: symmetry clash
REVERT: B  506 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8355 (mp10)
REVERT: L   86 GLU cc_start: 0.7807 (tp30) cc_final: 0.7547 (tp30)
REVERT: L  150 LYS cc_start: 0.7790 (tmtt) cc_final: 0.7204 (tptt)
REVERT: H  161 ASP cc_start: 0.8154 (m-30) cc_final: 0.7938 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 65
  average time/residue: 0.4283
  time to fit residues: 37.2088
Evaluate side-chains
  62 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  127 THR
Chi-restraints excluded: chain H residue  159 VAL
Chi-restraints excluded: chain H residue  215 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3629 r_free = 0.3629 target = 0.104472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.089821 restraints weight = 11406.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.092112 restraints weight = 5711.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.093600 restraints weight = 3460.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5026  Z= 0.139
  Angle     :  0.662   9.170   6846  Z= 0.335
  Chirality :  0.045   0.249    755
  Planarity :  0.004   0.037    885
  Dihedral  :  4.666  27.234    713
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 19.78 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -1.62 (0.33), residues: 629
  helix: -3.89 (0.72), residues: 25
  sheet:  0.15 (0.34), residues: 241
  loop : -1.81 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.020   0.001   PHE B 486 
 TYR   0.013   0.001   TYR B 453 
 ARG   0.008   0.001   ARG L 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00306 (    1)
  link_NAG-ASN         : angle       2.44216 (    3)
  hydrogen bonds       : bond        0.03258 (  162)
  hydrogen bonds       : angle       5.47350 (  387)
  SS BOND              : bond        0.00486 (    7)
  SS BOND              : angle       2.71267 (   14)
  covalent geometry    : bond        0.00323 ( 5018)
  covalent geometry    : angle       0.64958 ( 6829)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
REVERT: B  506 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8361 (mp10)
REVERT: L   86 GLU cc_start: 0.7790 (tp30) cc_final: 0.7555 (tp30)
REVERT: L  150 LYS cc_start: 0.7810 (tmtt) cc_final: 0.7221 (tptt)
REVERT: H  161 ASP cc_start: 0.8147 (m-30) cc_final: 0.7940 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 67
  average time/residue: 0.3225
  time to fit residues: 31.7442
Evaluate side-chains
  66 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  127 THR
Chi-restraints excluded: chain H residue  159 VAL
Chi-restraints excluded: chain H residue  186 VAL
Chi-restraints excluded: chain H residue  215 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0050
   chunk 58 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.9398

-------------------------------------------------------------------------------
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 = 0.3626 r_free = 0.3626 target = 0.104322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.089573 restraints weight = 11357.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.091863 restraints weight = 5715.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.093346 restraints weight = 3481.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5026  Z= 0.147
  Angle     :  0.660   8.590   6846  Z= 0.337
  Chirality :  0.045   0.255    755
  Planarity :  0.004   0.041    885
  Dihedral  :  4.719  27.689    713
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.78 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    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: -1.63 (0.33), residues: 629
  helix: -3.91 (0.71), residues: 25
  sheet:  0.15 (0.34), residues: 241
  loop : -1.81 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.030   0.001   PHE B 486 
 TYR   0.014   0.001   TYR B 453 
 ARG   0.008   0.001   ARG L 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00306 (    1)
  link_NAG-ASN         : angle       2.51638 (    3)
  hydrogen bonds       : bond        0.03302 (  162)
  hydrogen bonds       : angle       5.50601 (  387)
  SS BOND              : bond        0.00468 (    7)
  SS BOND              : angle       2.59564 (   14)
  covalent geometry    : bond        0.00341 ( 5018)
  covalent geometry    : angle       0.64840 ( 6829)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2715.59 seconds
wall clock time: 53 minutes 9.11 seconds (3189.11 seconds total)