Starting phenix.real_space_refine
on Tue Mar  3 13:16:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e9p_31035/03_2026/7e9p_31035.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e9p_31035/03_2026/7e9p_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e9p_31035/03_2026/7e9p_31035.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e9p_31035/03_2026/7e9p_31035.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e9p_31035/03_2026/7e9p_31035.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e9p_31035/03_2026/7e9p_31035.map"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.004 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.05, per 1000 atoms: 0.21
  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: 0.37
  Conformation dependent library (CDL) restraints added in 374.0 milliseconds
  

  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: 0.10
  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: 0.54

  Time building geometry restraints manager: 0.54 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:             2.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.640
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.170
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.005   0.001   ARG B 408 
 TYR   0.034   0.002   TYR B 473 
 PHE   0.020   0.001   PHE H 139 
 TRP   0.015   0.001   TRP B 436 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 5018)
  covalent geometry    : angle       0.78342 ( 6829)
  SS BOND              : bond        0.00633 (    7)
  SS BOND              : angle       1.08115 (   14)
  hydrogen bonds       : bond        0.13273 (  162)
  hydrogen bonds       : angle       6.75560 (  387)
  link_NAG-ASN         : bond        0.01099 (    1)
  link_NAG-ASN         : angle       6.35897 (    3)

*********************** 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  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 ILE cc_start: 0.8922 (mp) cc_final: 0.8706 (mt)
REVERT: H   30 ASP cc_start: 0.7983 (p0) cc_final: 0.7572 (p0)
REVERT: H   31 ASP cc_start: 0.8192 (m-30) cc_final: 0.7576 (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: 0.0656
  time to fit residues: 6.0502
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  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    0.4980
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.098849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.084688 restraints weight = 11426.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.086876 restraints weight = 5983.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.088318 restraints weight = 3695.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.089277 restraints weight = 2544.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.089910 restraints weight = 1907.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1257

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= 0.135
  Angle     :  0.652  10.358   6846  Z= 0.325
  Chirality :  0.046   0.264    755
  Planarity :  0.004   0.038    885
  Dihedral  :  7.308  52.323    713
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  9.98 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.32), residues: 629
  helix: -4.02 (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
 ARG   0.003   0.000   ARG L  59 
 TYR   0.020   0.001   TYR B 453 
 PHE   0.013   0.001   PHE H 139 
 TRP   0.013   0.001   TRP B 436 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5018)
  covalent geometry    : angle       0.64271 ( 6829)
  SS BOND              : bond        0.00482 (    7)
  SS BOND              : angle       1.13014 (   14)
  hydrogen bonds       : bond        0.03376 (  162)
  hydrogen bonds       : angle       5.95864 (  387)
  link_NAG-ASN         : bond        0.00902 (    1)
  link_NAG-ASN         : angle       4.96720 (    3)

*********************** 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
  69 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   30 ASP cc_start: 0.8240 (p0) cc_final: 0.7960 (p0)
REVERT: H   31 ASP cc_start: 0.8206 (m-30) cc_final: 0.7744 (m-30)
REVERT: H  161 ASP cc_start: 0.8248 (m-30) cc_final: 0.7983 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 69
  average time/residue: 0.0678
  time to fit residues: 6.2277
Evaluate side-chains
  56 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  483 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.106169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.091491 restraints weight = 11392.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.093706 restraints weight = 5730.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.095130 restraints weight = 3493.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.096081 restraints weight = 2414.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.096602 restraints weight = 1833.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5026  Z= 0.206
  Angle     :  0.684   9.261   6846  Z= 0.348
  Chirality :  0.048   0.323    755
  Planarity :  0.004   0.038    885
  Dihedral  :  5.484  33.811    713
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.12 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.32), residues: 629
  helix: -4.10 (0.57), residues: 31
  sheet: -0.34 (0.34), residues: 242
  loop : -2.14 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  59 
 TYR   0.028   0.002   TYR B 473 
 PHE   0.012   0.002   PHE H 139 
 TRP   0.013   0.001   TRP B 436 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 5018)
  covalent geometry    : angle       0.67753 ( 6829)
  SS BOND              : bond        0.00880 (    7)
  SS BOND              : angle       1.09076 (   14)
  hydrogen bonds       : bond        0.03878 (  162)
  hydrogen bonds       : angle       6.10242 (  387)
  link_NAG-ASN         : bond        0.00439 (    1)
  link_NAG-ASN         : angle       4.23078 (    3)

*********************** 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
  72 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: B  470 THR cc_start: 0.8650 (p) cc_final: 0.8436 (p)
REVERT: H   30 ASP cc_start: 0.8103 (p0) cc_final: 0.7799 (p0)
REVERT: H  161 ASP cc_start: 0.8069 (m-30) cc_final: 0.7828 (m-30)
REVERT: H  221 ASN cc_start: 0.7105 (p0) cc_final: 0.6765 (p0)
  outliers start: 10
  outliers final: 6
  residues processed: 70
  average time/residue: 0.0685
  time to fit residues: 6.2297
Evaluate side-chains
  61 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
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   70 ILE
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 38 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 52 optimal weight:    0.3980
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.108259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.093609 restraints weight = 11138.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.095935 restraints weight = 5542.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.097401 restraints weight = 3334.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.098283 restraints weight = 2291.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.098990 restraints weight = 1758.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5026  Z= 0.127
  Angle     :  0.619   9.308   6846  Z= 0.312
  Chirality :  0.045   0.252    755
  Planarity :  0.004   0.034    885
  Dihedral  :  4.781  26.523    713
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.45 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.32), residues: 629
  helix: -3.86 (0.68), residues: 25
  sheet: -0.25 (0.34), residues: 239
  loop : -2.03 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  87 
 TYR   0.018   0.001   TYR B 473 
 PHE   0.008   0.001   PHE B 456 
 TRP   0.013   0.001   TRP B 436 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5018)
  covalent geometry    : angle       0.61465 ( 6829)
  SS BOND              : bond        0.00781 (    7)
  SS BOND              : angle       0.81455 (   14)
  hydrogen bonds       : bond        0.03238 (  162)
  hydrogen bonds       : angle       5.71918 (  387)
  link_NAG-ASN         : bond        0.00470 (    1)
  link_NAG-ASN         : angle       3.18856 (    3)

*********************** 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: 11
    poor density    : 61
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: L  150 LYS cc_start: 0.7667 (tmtt) cc_final: 0.7093 (tptp)
REVERT: H   30 ASP cc_start: 0.8058 (p0) cc_final: 0.7796 (p0)
REVERT: H  161 ASP cc_start: 0.8149 (m-30) cc_final: 0.7924 (m-30)
  outliers start: 11
  outliers final: 6
  residues processed: 70
  average time/residue: 0.0677
  time to fit residues: 6.2661
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  : 0.177 
-------------------------------------------------------------------------------
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  415 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain H residue   70 ILE
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 1 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 8 optimal weight:    0.1980
   chunk 41 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0040
   chunk 55 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.9994

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.107878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.093133 restraints weight = 11487.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.095428 restraints weight = 5779.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.096878 restraints weight = 3524.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.097808 restraints weight = 2438.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.098468 restraints weight = 1866.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2028

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= 0.150
  Angle     :  0.684  11.992   6846  Z= 0.345
  Chirality :  0.046   0.268    755
  Planarity :  0.004   0.036    885
  Dihedral  :  4.829  27.832    713
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.38 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.32), residues: 629
  helix: -4.04 (0.63), residues: 25
  sheet: -0.14 (0.34), residues: 239
  loop : -2.02 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  87 
 TYR   0.016   0.001   TYR B 453 
 PHE   0.010   0.001   PHE B 392 
 TRP   0.013   0.001   TRP B 436 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 5018)
  covalent geometry    : angle       0.66536 ( 6829)
  SS BOND              : bond        0.00579 (    7)
  SS BOND              : angle       3.35286 (   14)
  hydrogen bonds       : bond        0.03347 (  162)
  hydrogen bonds       : angle       5.70711 (  387)
  link_NAG-ASN         : bond        0.00323 (    1)
  link_NAG-ASN         : angle       2.86742 (    3)

*********************** 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
  70 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: L  150 LYS cc_start: 0.7862 (tmtt) cc_final: 0.7387 (tptt)
REVERT: H   30 ASP cc_start: 0.8063 (p0) cc_final: 0.7834 (p0)
REVERT: H  161 ASP cc_start: 0.8030 (m-30) cc_final: 0.7807 (m-30)
REVERT: H  221 ASN cc_start: 0.7109 (p0) cc_final: 0.6761 (p0)
  outliers start: 10
  outliers final: 7
  residues processed: 69
  average time/residue: 0.0705
  time to fit residues: 6.5392
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  : 0.188 
-------------------------------------------------------------------------------
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   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
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 22 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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**
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.106135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.091240 restraints weight = 11615.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.093496 restraints weight = 5824.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.094934 restraints weight = 3547.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.095768 restraints weight = 2461.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.096430 restraints weight = 1919.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2234

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= 0.206
  Angle     :  0.721  12.098   6846  Z= 0.365
  Chirality :  0.048   0.299    755
  Planarity :  0.004   0.037    885
  Dihedral  :  5.217  31.075    713
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.67 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.32), residues: 629
  helix: -4.09 (0.63), residues: 25
  sheet: -0.17 (0.34), residues: 239
  loop : -2.06 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  59 
 TYR   0.021   0.002   TYR B 453 
 PHE   0.016   0.002   PHE L 144 
 TRP   0.012   0.001   TRP B 436 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 5018)
  covalent geometry    : angle       0.70622 ( 6829)
  SS BOND              : bond        0.00601 (    7)
  SS BOND              : angle       2.95761 (   14)
  hydrogen bonds       : bond        0.03774 (  162)
  hydrogen bonds       : angle       5.91020 (  387)
  link_NAG-ASN         : bond        0.00208 (    1)
  link_NAG-ASN         : angle       3.24602 (    3)

*********************** 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
  74 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: B  470 THR cc_start: 0.8654 (p) cc_final: 0.8443 (p)
REVERT: B  506 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8378 (mp10)
REVERT: L  150 LYS cc_start: 0.7961 (tmtt) cc_final: 0.7409 (tptt)
REVERT: H  161 ASP cc_start: 0.8097 (m-30) cc_final: 0.7873 (m-30)
REVERT: H  221 ASN cc_start: 0.7166 (p0) cc_final: 0.6830 (p0)
  outliers start: 16
  outliers final: 9
  residues processed: 71
  average time/residue: 0.0723
  time to fit residues: 6.5675
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  : 0.214 
-------------------------------------------------------------------------------
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  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  215 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 13 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0870
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    0.3980
   chunk 18 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0050
   overall best weight:    0.3572

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

Flipped N/Q/H residues before XYZ refinement:
L  33 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.110395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.095381 restraints weight = 11206.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.097766 restraints weight = 5547.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.099290 restraints weight = 3345.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.100281 restraints weight = 2301.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.100851 restraints weight = 1736.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5026  Z= 0.106
  Angle     :  0.627   9.257   6846  Z= 0.316
  Chirality :  0.044   0.221    755
  Planarity :  0.004   0.036    885
  Dihedral  :  4.516  24.785    713
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.33), residues: 629
  helix: -4.24 (0.67), residues: 18
  sheet: -0.02 (0.34), residues: 242
  loop : -1.92 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  87 
 TYR   0.013   0.001   TYR B 396 
 PHE   0.014   0.001   PHE B 392 
 TRP   0.013   0.001   TRP B 436 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5018)
  covalent geometry    : angle       0.61422 ( 6829)
  SS BOND              : bond        0.00398 (    7)
  SS BOND              : angle       2.61601 (   14)
  hydrogen bonds       : bond        0.02854 (  162)
  hydrogen bonds       : angle       5.45522 (  387)
  link_NAG-ASN         : bond        0.00449 (    1)
  link_NAG-ASN         : angle       2.27470 (    3)

*********************** 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
  74 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: B  506 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8334 (mp10)
REVERT: L  150 LYS cc_start: 0.7741 (tmtt) cc_final: 0.7255 (tptt)
REVERT: L  200 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7221 (mm-30)
REVERT: H   38 ARG cc_start: 0.8603 (ptm160) cc_final: 0.8397 (ttp80)
REVERT: H  161 ASP cc_start: 0.8121 (m-30) cc_final: 0.7920 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 73
  average time/residue: 0.0800
  time to fit residues: 7.6301
Evaluate side-chains
  67 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
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   89 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3700 r_free = 0.3700 target = 0.108349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.093444 restraints weight = 11366.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.095789 restraints weight = 5605.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.097265 restraints weight = 3371.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.098191 restraints weight = 2326.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.098841 restraints weight = 1768.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2400

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= 0.148
  Angle     :  0.655   8.988   6846  Z= 0.335
  Chirality :  0.045   0.255    755
  Planarity :  0.004   0.040    885
  Dihedral  :  4.739  27.444    713
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.33), residues: 629
  helix: -3.91 (0.71), residues: 25
  sheet:  0.06 (0.35), residues: 239
  loop : -1.85 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L 216 
 TYR   0.014   0.001   TYR B 453 
 PHE   0.011   0.001   PHE L 144 
 TRP   0.012   0.001   TRP B 436 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5018)
  covalent geometry    : angle       0.64356 ( 6829)
  SS BOND              : bond        0.00480 (    7)
  SS BOND              : angle       2.52956 (   14)
  hydrogen bonds       : bond        0.03331 (  162)
  hydrogen bonds       : angle       5.52675 (  387)
  link_NAG-ASN         : bond        0.00288 (    1)
  link_NAG-ASN         : angle       2.47365 (    3)

*********************** 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
  70 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: B  506 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8367 (mp10)
REVERT: L  150 LYS cc_start: 0.7845 (tmtt) cc_final: 0.7286 (tptt)
REVERT: H  161 ASP cc_start: 0.8100 (m-30) cc_final: 0.7872 (m-30)
REVERT: H  221 ASN cc_start: 0.7022 (p0) cc_final: 0.6686 (p0)
  outliers start: 10
  outliers final: 8
  residues processed: 68
  average time/residue: 0.0696
  time to fit residues: 6.3110
Evaluate side-chains
  64 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
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  506 GLN
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   89 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.109432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.094437 restraints weight = 11256.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.096788 restraints weight = 5586.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.098285 restraints weight = 3367.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.099224 restraints weight = 2319.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.099872 restraints weight = 1763.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5026  Z= 0.136
  Angle     :  0.654   9.888   6846  Z= 0.331
  Chirality :  0.045   0.246    755
  Planarity :  0.004   0.037    885
  Dihedral  :  4.669  27.002    713
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.33), residues: 629
  helix: -4.25 (0.65), residues: 18
  sheet:  0.11 (0.34), residues: 243
  loop : -1.88 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L 216 
 TYR   0.013   0.001   TYR B 453 
 PHE   0.010   0.001   PHE B 392 
 TRP   0.013   0.001   TRP B 436 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5018)
  covalent geometry    : angle       0.64428 ( 6829)
  SS BOND              : bond        0.00426 (    7)
  SS BOND              : angle       2.39158 (   14)
  hydrogen bonds       : bond        0.03166 (  162)
  hydrogen bonds       : angle       5.50439 (  387)
  link_NAG-ASN         : bond        0.00317 (    1)
  link_NAG-ASN         : angle       2.41489 (    3)

*********************** 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
  68 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: B  506 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8376 (mp10)
REVERT: L  150 LYS cc_start: 0.7799 (tmtt) cc_final: 0.7279 (tptt)
REVERT: H  161 ASP cc_start: 0.8135 (m-30) cc_final: 0.7922 (m-30)
REVERT: H  221 ASN cc_start: 0.7148 (p0) cc_final: 0.6907 (p0)
  outliers start: 11
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0562
  time to fit residues: 5.0394
Evaluate side-chains
  65 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
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  506 GLN
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   89 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9980
   chunk 51 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3722 r_free = 0.3722 target = 0.109616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.094710 restraints weight = 11302.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.097069 restraints weight = 5608.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.098577 restraints weight = 3380.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.099529 restraints weight = 2322.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.100174 restraints weight = 1768.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5026  Z= 0.124
  Angle     :  0.637   8.363   6846  Z= 0.326
  Chirality :  0.044   0.236    755
  Planarity :  0.004   0.037    885
  Dihedral  :  4.529  25.956    713
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 20.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.33), residues: 629
  helix: -3.82 (0.76), residues: 25
  sheet:  0.14 (0.35), residues: 242
  loop : -1.74 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L 216 
 TYR   0.011   0.001   TYR B 453 
 PHE   0.012   0.001   PHE B 392 
 TRP   0.012   0.001   TRP B 436 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5018)
  covalent geometry    : angle       0.62864 ( 6829)
  SS BOND              : bond        0.00384 (    7)
  SS BOND              : angle       2.18043 (   14)
  hydrogen bonds       : bond        0.03007 (  162)
  hydrogen bonds       : angle       5.40568 (  387)
  link_NAG-ASN         : bond        0.00369 (    1)
  link_NAG-ASN         : angle       2.25306 (    3)

********************** 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
  67 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: B  506 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8376 (mp10)
REVERT: L  150 LYS cc_start: 0.7775 (tmtt) cc_final: 0.7251 (tptt)
REVERT: H   38 ARG cc_start: 0.8617 (ptm160) cc_final: 0.8410 (ttp80)
REVERT: H  161 ASP cc_start: 0.8110 (m-30) cc_final: 0.7910 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 65
  average time/residue: 0.0581
  time to fit residues: 5.1165
Evaluate side-chains
  65 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
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   89 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0060
   chunk 30 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.6996

-------------------------------------------------------------------------------
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 = 0.3731 r_free = 0.3731 target = 0.110007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.094930 restraints weight = 11242.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.097294 restraints weight = 5567.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.098798 restraints weight = 3355.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.099758 restraints weight = 2308.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.100306 restraints weight = 1751.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5026  Z= 0.128
  Angle     :  0.636   7.282   6846  Z= 0.327
  Chirality :  0.044   0.238    755
  Planarity :  0.004   0.037    885
  Dihedral  :  4.545  26.211    713
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 20.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.33), residues: 629
  helix: -3.82 (0.76), residues: 25
  sheet:  0.16 (0.35), residues: 242
  loop : -1.71 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L 216 
 TYR   0.011   0.001   TYR B 453 
 PHE   0.011   0.001   PHE B 392 
 TRP   0.012   0.001   TRP B 436 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 5018)
  covalent geometry    : angle       0.62712 ( 6829)
  SS BOND              : bond        0.00400 (    7)
  SS BOND              : angle       2.17438 (   14)
  hydrogen bonds       : bond        0.03044 (  162)
  hydrogen bonds       : angle       5.39237 (  387)
  link_NAG-ASN         : bond        0.00357 (    1)
  link_NAG-ASN         : angle       2.24360 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 939.99 seconds
wall clock time: 16 minutes 49.29 seconds (1009.29 seconds total)