Starting phenix.real_space_refine
on Wed Sep 17 03:20:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fgt_50424/09_2025/9fgt_50424.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fgt_50424/09_2025/9fgt_50424.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fgt_50424/09_2025/9fgt_50424.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fgt_50424/09_2025/9fgt_50424.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fgt_50424/09_2025/9fgt_50424.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fgt_50424/09_2025/9fgt_50424.cif"
  }
  resolution = 3.8
  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=  -0.006 sd=   0.052
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      10      5.16       5
     C    1863      2.51       5
     N     496      2.21       5
     O     552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2921
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1280
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 8, 'TRANS': 148}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 1627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1627
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 9, 'TRANS': 206}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.00, per 1000 atoms: 0.34
  Number of scatterers: 2921
  At special positions: 0
  Unit cell: (78.232, 65.786, 79.121, 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      10     16.00
     O     552      8.00
     N     496      7.00
     C    1863      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 156 " - pdb=" SG  CYS E 222 " distance=2.03

  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 C1301 " - " ASN C 343 "
  Time building additional restraints: 0.20
  Conformation dependent library (CDL) restraints added in 111.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  676

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 9 sheets defined
      8.0% alpha, 29.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
      removed outlier: 3.523A  pdb=" N   ASN C 343 " --> pdb=" O   ASP C 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 411
      removed outlier: 4.211A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLN C 409 " --> pdb=" O   GLU C 406 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 417 through 422
      removed outlier: 3.589A  pdb=" N   TYR C 421 " --> pdb=" O   ASN C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 438 through 443
    Processing helix  chain 'C' and resid 479 through 483
      removed outlier: 3.884A  pdb=" N   GLY C 482 " --> pdb=" O   PRO C 479 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 376 through 379
      removed outlier: 3.586A  pdb=" N   THR C 376 " --> pdb=" O   ALA C 435 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA C 435 " --> pdb=" O   THR C 376 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 396 through 397
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'C' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.761A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER E  25 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU E  18 " --> pdb=" O   MET E  82 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR E  77 " --> pdb=" O   ASP E  72 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.921A  pdb=" N   ALA E  96 " --> pdb=" O   SER E  35 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   TYR E  33 " --> pdb=" O   ASP E  98 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 138 through 139
    Processing sheet with id=AA8, first strand: chain 'E' and resid 179 through 182
      removed outlier: 6.668A  pdb=" N   TRP E 169 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR E 221 " --> pdb=" O   TYR E 170 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLN E 172 " --> pdb=" O   VAL E 219 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR E 231 " --> pdb=" O   GLN E 224 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 179 through 182
      removed outlier: 6.668A  pdb=" N   TRP E 169 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR E 221 " --> pdb=" O   TYR E 170 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLN E 172 " --> pdb=" O   VAL E 219 " (cutoff:3.500A)

    77 hydrogen bonds defined for protein.
    183 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: 0.36

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 925
        1.34 -     1.46: 657
        1.46 -     1.57: 1399
        1.57 -     1.69: 0
        1.69 -     1.81: 12
  Bond restraints: 2993
  Sorted by residual:
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.487 -0.081 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" C5  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.446 -0.033 2.00e-02 2.50e+03 2.64e+00
  bond pdb=" CA  VAL C 395 "
       pdb=" C   VAL C 395 "
    ideal  model  delta    sigma   weight residual
    1.525  1.502  0.023 2.10e-02 2.27e+03 1.21e+00
  bond pdb=" C   SER E 100 "
       pdb=" O   SER E 100 "
    ideal  model  delta    sigma   weight residual
    1.235  1.222  0.013 1.26e-02 6.30e+03 1.12e+00
  bond pdb=" CB  TRP E  47 "
       pdb=" CG  TRP E  47 "
    ideal  model  delta    sigma   weight residual
    1.498  1.466  0.032 3.10e-02 1.04e+03 1.04e+00
  ... (remaining 2988 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 3878
        1.51 -     3.03: 150
        3.03 -     4.54: 21
        4.54 -     6.05: 8
        6.05 -     7.56: 1
  Bond angle restraints: 4058
  Sorted by residual:
  angle pdb=" C   ASN C 343 "
        pdb=" CA  ASN C 343 "
        pdb=" CB  ASN C 343 "
      ideal   model   delta    sigma   weight residual
     109.80  115.12   -5.32 1.70e+00 3.46e-01 9.80e+00
  angle pdb=" C   PRO C 479 "
        pdb=" N   CYS C 480 "
        pdb=" CA  CYS C 480 "
      ideal   model   delta    sigma   weight residual
     121.54  127.00   -5.46 1.91e+00 2.74e-01 8.18e+00
  angle pdb=" C   LEU E  99 "
        pdb=" N   SER E 100 "
        pdb=" CA  SER E 100 "
      ideal   model   delta    sigma   weight residual
     121.54  126.93   -5.39 1.91e+00 2.74e-01 7.98e+00
  angle pdb=" C1  NAG C1301 "
        pdb=" O5  NAG C1301 "
        pdb=" C5  NAG C1301 "
      ideal   model   delta    sigma   weight residual
     113.21  120.77   -7.56 3.00e+00 1.11e-01 6.36e+00
  angle pdb=" CA  ASP C 428 "
        pdb=" CB  ASP C 428 "
        pdb=" CG  ASP C 428 "
      ideal   model   delta    sigma   weight residual
     112.60  114.61   -2.01 1.00e+00 1.00e+00 4.05e+00
  ... (remaining 4053 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.35: 1640
       22.35 -    44.69: 96
       44.69 -    67.04: 21
       67.04 -    89.39: 0
       89.39 -   111.73: 3
  Dihedral angle restraints: 1760
    sinusoidal: 691
      harmonic: 1069
  Sorted by residual:
  dihedral pdb=" CB  CYS E 156 "
           pdb=" SG  CYS E 156 "
           pdb=" SG  CYS E 222 "
           pdb=" CB  CYS E 222 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.53  -52.53     1      1.00e+01 1.00e-02 3.76e+01
  dihedral pdb=" C1  NAG C1301 "
           pdb=" C5  NAG C1301 "
           pdb=" O5  NAG C1301 "
           pdb=" C4  NAG C1301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   47.62 -111.73     1      3.00e+01 1.11e-03 1.46e+01
  dihedral pdb=" C1  NAG C1301 "
           pdb=" C5  NAG C1301 "
           pdb=" O5  NAG C1301 "
           pdb=" C6  NAG C1301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -78.54 -110.30     1      3.00e+01 1.11e-03 1.44e+01
  ... (remaining 1757 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 319
       0.047 -    0.094: 84
       0.094 -    0.141: 29
       0.141 -    0.188: 1
       0.188 -    0.236: 2
  Chirality restraints: 435
  Sorted by residual:
  chirality pdb=" C1  NAG C1301 "
            pdb=" ND2 ASN C 343 "
            pdb=" C2  NAG C1301 "
            pdb=" O5  NAG C1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  ILE C 468 "
            pdb=" CA  ILE C 468 "
            pdb=" CG1 ILE C 468 "
            pdb=" CG2 ILE C 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.77e-01
  chirality pdb=" CG  LEU E 167 "
            pdb=" CB  LEU E 167 "
            pdb=" CD1 LEU E 167 "
            pdb=" CD2 LEU E 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.46e-01
  ... (remaining 432 not shown)

  Planarity restraints: 522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN E  13 "   -0.033 5.00e-02 4.00e+02   5.00e-02 4.01e+00
        pdb=" N   PRO E  14 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO E  14 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E  14 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 225 "   -0.012 2.00e-02 2.50e+03   1.31e-02 3.44e+00
        pdb=" CG  TYR E 225 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 225 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 225 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 225 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 225 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 225 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR E 225 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 453 "    0.016 2.00e-02 2.50e+03   1.13e-02 2.54e+00
        pdb=" CG  TYR C 453 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 453 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 453 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 453 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 453 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 453 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 453 "    0.002 2.00e-02 2.50e+03
  ... (remaining 519 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 44
        2.66 -     3.22: 2668
        3.22 -     3.78: 3965
        3.78 -     4.34: 5381
        4.34 -     4.90: 9059
  Nonbonded interactions: 21117
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 421 "
            pdb=" O   PRO E  53 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" O   GLY E 142 "
            pdb=" OG1 THR E 236 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OG1 THR C 376 "
            pdb=" O   ALA C 435 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OH  TYR C 473 "
            pdb=" O   ALA E  31 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" NH1 ARG E 188 "
            pdb=" O   PHE E 196 "
     model   vdw
     2.315 3.120
  ... (remaining 21112 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:             4.100
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.470
  Find NCS groups from input model:        0.010
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
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   0.081   2998  Z= 0.238
  Angle     :  0.709   7.564   4069  Z= 0.371
  Chirality :  0.049   0.236    435
  Planarity :  0.005   0.050    521
  Dihedral  : 14.859 111.732   1072
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.56 (0.43), residues: 361
  helix: -3.41 (1.05), residues: 13
  sheet: -0.18 (0.51), residues: 117
  loop : -1.41 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 493 
 TYR   0.029   0.002   TYR E 225 
 PHE   0.017   0.002   PHE E 205 
 TRP   0.009   0.002   TRP E 169 
 HIS   0.002   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 2993)
  covalent geometry    : angle       0.70291 ( 4058)
  SS BOND              : bond        0.00257 (    4)
  SS BOND              : angle       1.08017 (    8)
  hydrogen bonds       : bond        0.30511 (   70)
  hydrogen bonds       : angle      10.49492 (  183)
  link_NAG-ASN         : bond        0.01418 (    1)
  link_NAG-ASN         : angle       3.23295 (    3)

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

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

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.115 
Fit side-chains
REVERT: C  458 LYS cc_start: 0.8502 (mttt) cc_final: 0.8291 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0492
  time to fit residues: 3.4939
Evaluate side-chains
  49 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.2980
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
E   6 GLN
** E  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E 172 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.150197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.129861 restraints weight = 5140.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.132797 restraints weight = 3148.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.134922 restraints weight = 2210.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.136205 restraints weight = 1709.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.137202 restraints weight = 1436.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2998  Z= 0.159
  Angle     :  0.695  12.961   4069  Z= 0.344
  Chirality :  0.046   0.138    435
  Planarity :  0.005   0.052    521
  Dihedral  :  8.627  65.086    436
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  9.65 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.48 (0.43), residues: 361
  helix: -3.26 (1.16), residues: 13
  sheet:  0.00 (0.53), residues: 110
  loop : -1.40 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 493 
 TYR   0.016   0.001   TYR E 225 
 PHE   0.010   0.001   PHE E 205 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 2993)
  covalent geometry    : angle       0.69017 ( 4058)
  SS BOND              : bond        0.00300 (    4)
  SS BOND              : angle       0.94871 (    8)
  hydrogen bonds       : bond        0.04787 (   70)
  hydrogen bonds       : angle       7.00302 (  183)
  link_NAG-ASN         : bond        0.01443 (    1)
  link_NAG-ASN         : angle       2.83042 (    3)

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

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

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.098 
Fit side-chains
  outliers start: 7
  outliers final: 7
  residues processed: 59
  average time/residue: 0.0534
  time to fit residues: 3.9738
Evaluate side-chains
  58 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue  140 SER
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  225 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    0.1980
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0010
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0980
   chunk 4 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 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 = 0.3770 r_free = 0.3770 target = 0.150970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.131170 restraints weight = 5153.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.134197 restraints weight = 3099.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.136370 restraints weight = 2138.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.137507 restraints weight = 1630.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.138776 restraints weight = 1374.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2998  Z= 0.128
  Angle     :  0.606   7.344   4069  Z= 0.307
  Chirality :  0.045   0.157    435
  Planarity :  0.004   0.051    521
  Dihedral  :  6.797  58.633    436
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.18 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.49 (0.43), residues: 361
  helix: -3.15 (1.21), residues: 13
  sheet:  0.03 (0.54), residues: 110
  loop : -1.43 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 493 
 TYR   0.018   0.001   TYR E 225 
 PHE   0.010   0.001   PHE E 205 
 TRP   0.007   0.001   TRP E 169 
 HIS   0.001   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 2993)
  covalent geometry    : angle       0.60284 ( 4058)
  SS BOND              : bond        0.00236 (    4)
  SS BOND              : angle       0.79704 (    8)
  hydrogen bonds       : bond        0.04243 (   70)
  hydrogen bonds       : angle       6.39305 (  183)
  link_NAG-ASN         : bond        0.00861 (    1)
  link_NAG-ASN         : angle       2.05282 (    3)

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

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

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.120 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0513
  time to fit residues: 3.9535
Evaluate side-chains
  57 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue  140 SER
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  225 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0870
   chunk 16 optimal weight:    0.0050
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 33 optimal weight:    0.3980
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.2972

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 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 = 0.3786 r_free = 0.3786 target = 0.152247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.132600 restraints weight = 5153.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135677 restraints weight = 3052.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137922 restraints weight = 2093.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.139425 restraints weight = 1572.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.140432 restraints weight = 1283.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2998  Z= 0.112
  Angle     :  0.576   7.179   4069  Z= 0.291
  Chirality :  0.044   0.138    435
  Planarity :  0.004   0.051    521
  Dihedral  :  6.340  59.300    436
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 13.50 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.48 (0.43), residues: 361
  helix: -2.89 (1.33), residues: 13
  sheet:  0.03 (0.54), residues: 110
  loop : -1.44 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 493 
 TYR   0.018   0.001   TYR E 225 
 PHE   0.026   0.001   PHE C 486 
 TRP   0.006   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 2993)
  covalent geometry    : angle       0.57269 ( 4058)
  SS BOND              : bond        0.00220 (    4)
  SS BOND              : angle       0.66240 (    8)
  hydrogen bonds       : bond        0.03655 (   70)
  hydrogen bonds       : angle       6.04234 (  183)
  link_NAG-ASN         : bond        0.00514 (    1)
  link_NAG-ASN         : angle       2.21909 (    3)

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

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

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.113 
Fit side-chains
REVERT: C  473 TYR cc_start: 0.8188 (t80) cc_final: 0.7958 (t80)
REVERT: E   82 MET cc_start: 0.8319 (mtm) cc_final: 0.8082 (mtt)
REVERT: E   83 ASN cc_start: 0.7899 (m110) cc_final: 0.7530 (m-40)
  outliers start: 11
  outliers final: 9
  residues processed: 61
  average time/residue: 0.0459
  time to fit residues: 3.6844
Evaluate side-chains
  62 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue  140 SER
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  225 TYR
Chi-restraints excluded: chain E residue  236 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    0.0370
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0470
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0370
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.3834

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 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 = 0.3781 r_free = 0.3781 target = 0.151848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.132196 restraints weight = 5068.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.135190 restraints weight = 3055.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.137350 restraints weight = 2113.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.138799 restraints weight = 1615.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.139862 restraints weight = 1331.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2998  Z= 0.122
  Angle     :  0.585   7.073   4069  Z= 0.296
  Chirality :  0.045   0.141    435
  Planarity :  0.004   0.051    521
  Dihedral  :  5.929  55.811    436
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.11 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.47 (0.43), residues: 361
  helix: -2.64 (1.51), residues: 13
  sheet:  0.05 (0.54), residues: 108
  loop : -1.45 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 454 
 TYR   0.018   0.001   TYR E 225 
 PHE   0.025   0.001   PHE C 486 
 TRP   0.006   0.001   TRP C 436 
 HIS   0.001   0.000   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2993)
  covalent geometry    : angle       0.58194 ( 4058)
  SS BOND              : bond        0.00241 (    4)
  SS BOND              : angle       0.57535 (    8)
  hydrogen bonds       : bond        0.03539 (   70)
  hydrogen bonds       : angle       5.89941 (  183)
  link_NAG-ASN         : bond        0.00439 (    1)
  link_NAG-ASN         : angle       2.12005 (    3)

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

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

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.118 
Fit side-chains
REVERT: E   83 ASN cc_start: 0.7933 (m110) cc_final: 0.7541 (m-40)
  outliers start: 10
  outliers final: 8
  residues processed: 56
  average time/residue: 0.0496
  time to fit residues: 3.6241
Evaluate side-chains
  58 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue  140 SER
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  236 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 35 optimal weight:    0.0570
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0970
   chunk 29 optimal weight:    0.0980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 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 = 0.3783 r_free = 0.3783 target = 0.151930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.132417 restraints weight = 5054.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135422 restraints weight = 3044.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.137606 restraints weight = 2104.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.139034 restraints weight = 1597.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.139969 restraints weight = 1314.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2998  Z= 0.119
  Angle     :  0.584   8.110   4069  Z= 0.293
  Chirality :  0.044   0.139    435
  Planarity :  0.004   0.051    521
  Dihedral  :  5.555  54.770    436
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.04 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.53 (0.43), residues: 361
  helix: -2.59 (1.56), residues: 13
  sheet:  0.03 (0.54), residues: 108
  loop : -1.50 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 454 
 TYR   0.014   0.001   TYR E 225 
 PHE   0.028   0.001   PHE C 486 
 TRP   0.007   0.001   TRP E 108 
 HIS   0.001   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 2993)
  covalent geometry    : angle       0.58205 ( 4058)
  SS BOND              : bond        0.00231 (    4)
  SS BOND              : angle       0.64499 (    8)
  hydrogen bonds       : bond        0.03318 (   70)
  hydrogen bonds       : angle       5.77959 (  183)
  link_NAG-ASN         : bond        0.00381 (    1)
  link_NAG-ASN         : angle       1.93223 (    3)

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

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

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.111 
Fit side-chains
REVERT: E   83 ASN cc_start: 0.7888 (m110) cc_final: 0.7507 (m-40)
  outliers start: 11
  outliers final: 11
  residues processed: 58
  average time/residue: 0.0431
  time to fit residues: 3.2697
Evaluate side-chains
  59 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue  140 SER
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  225 TYR
Chi-restraints excluded: chain E residue  236 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    0.0870
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0770
   overall best weight:    0.5116

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 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 = 0.3759 r_free = 0.3759 target = 0.150259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130392 restraints weight = 5162.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.133497 restraints weight = 3043.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.135700 restraints weight = 2081.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.137067 restraints weight = 1575.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.138218 restraints weight = 1300.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   2998  Z= 0.141
  Angle     :  0.610   8.220   4069  Z= 0.305
  Chirality :  0.045   0.140    435
  Planarity :  0.004   0.051    521
  Dihedral  :  5.570  53.198    436
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.36 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.64 (0.43), residues: 361
  helix: -2.90 (1.40), residues: 13
  sheet:  0.02 (0.55), residues: 108
  loop : -1.60 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 403 
 TYR   0.013   0.001   TYR E 225 
 PHE   0.030   0.001   PHE C 486 
 TRP   0.006   0.001   TRP E 108 
 HIS   0.001   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2993)
  covalent geometry    : angle       0.60764 ( 4058)
  SS BOND              : bond        0.00261 (    4)
  SS BOND              : angle       0.76933 (    8)
  hydrogen bonds       : bond        0.03491 (   70)
  hydrogen bonds       : angle       5.86822 (  183)
  link_NAG-ASN         : bond        0.00342 (    1)
  link_NAG-ASN         : angle       2.07153 (    3)

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

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

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.068 
Fit side-chains
REVERT: E   83 ASN cc_start: 0.7962 (m110) cc_final: 0.7542 (m-40)
  outliers start: 12
  outliers final: 11
  residues processed: 57
  average time/residue: 0.0551
  time to fit residues: 3.8723
Evaluate side-chains
  56 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue  140 SER
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  225 TYR
Chi-restraints excluded: chain E residue  236 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0770
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 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 = 0.3760 r_free = 0.3760 target = 0.150384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130548 restraints weight = 5173.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.133593 restraints weight = 3102.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.135637 restraints weight = 2142.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.137146 restraints weight = 1653.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.138110 restraints weight = 1362.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2998  Z= 0.141
  Angle     :  0.609   8.323   4069  Z= 0.304
  Chirality :  0.044   0.139    435
  Planarity :  0.004   0.051    521
  Dihedral  :  5.522  52.884    436
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.36 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.69 (0.43), residues: 361
  helix: -2.93 (1.43), residues: 13
  sheet: -0.01 (0.55), residues: 108
  loop : -1.64 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  86 
 TYR   0.014   0.001   TYR E 225 
 PHE   0.029   0.001   PHE C 486 
 TRP   0.007   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 2993)
  covalent geometry    : angle       0.60649 ( 4058)
  SS BOND              : bond        0.00243 (    4)
  SS BOND              : angle       0.79773 (    8)
  hydrogen bonds       : bond        0.03509 (   70)
  hydrogen bonds       : angle       5.91481 (  183)
  link_NAG-ASN         : bond        0.00304 (    1)
  link_NAG-ASN         : angle       2.10522 (    3)

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

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

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.071 
Fit side-chains
REVERT: E   82 MET cc_start: 0.8640 (mtm) cc_final: 0.8248 (mtt)
REVERT: E   83 ASN cc_start: 0.7980 (m110) cc_final: 0.7557 (m-40)
  outliers start: 12
  outliers final: 11
  residues processed: 54
  average time/residue: 0.0490
  time to fit residues: 3.4851
Evaluate side-chains
  55 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  140 SER
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  225 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 5 optimal weight:    0.3980
   chunk 27 optimal weight:    0.0470
   chunk 32 optimal weight:    0.0870
   chunk 1 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 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 = 0.3781 r_free = 0.3781 target = 0.151832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.131820 restraints weight = 5205.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.134914 restraints weight = 3121.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.137084 restraints weight = 2148.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.138352 restraints weight = 1640.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.139477 restraints weight = 1370.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
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   0.035   2998  Z= 0.124
  Angle     :  0.619   8.310   4069  Z= 0.307
  Chirality :  0.045   0.144    435
  Planarity :  0.004   0.051    521
  Dihedral  :  5.443  53.340    436
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 16.72 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.68 (0.43), residues: 361
  helix: -2.88 (1.44), residues: 13
  sheet: -0.01 (0.54), residues: 108
  loop : -1.64 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 454 
 TYR   0.015   0.001   TYR E 225 
 PHE   0.032   0.001   PHE C 486 
 TRP   0.007   0.001   TRP C 436 
 HIS   0.001   0.000   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 2993)
  covalent geometry    : angle       0.61740 ( 4058)
  SS BOND              : bond        0.00249 (    4)
  SS BOND              : angle       0.67180 (    8)
  hydrogen bonds       : bond        0.03373 (   70)
  hydrogen bonds       : angle       5.97257 (  183)
  link_NAG-ASN         : bond        0.00332 (    1)
  link_NAG-ASN         : angle       1.84263 (    3)

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

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

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.105 
Fit side-chains
REVERT: E   83 ASN cc_start: 0.7766 (m110) cc_final: 0.7436 (m-40)
  outliers start: 12
  outliers final: 11
  residues processed: 54
  average time/residue: 0.0457
  time to fit residues: 3.2274
Evaluate side-chains
  54 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  140 SER
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  225 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 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 = 0.3752 r_free = 0.3752 target = 0.149622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.129831 restraints weight = 5193.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.132849 restraints weight = 3124.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.134939 restraints weight = 2166.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.136403 restraints weight = 1664.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.137273 restraints weight = 1373.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2998  Z= 0.164
  Angle     :  0.640   8.395   4069  Z= 0.320
  Chirality :  0.045   0.139    435
  Planarity :  0.004   0.051    521
  Dihedral  :  5.611  51.031    436
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.36 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.81 (0.43), residues: 361
  helix: -2.96 (1.46), residues: 13
  sheet: -0.22 (0.51), residues: 118
  loop : -1.72 (0.38), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  86 
 TYR   0.014   0.001   TYR E 225 
 PHE   0.026   0.002   PHE C 486 
 TRP   0.007   0.001   TRP E 169 
 HIS   0.001   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 2993)
  covalent geometry    : angle       0.63679 ( 4058)
  SS BOND              : bond        0.00285 (    4)
  SS BOND              : angle       0.84123 (    8)
  hydrogen bonds       : bond        0.03654 (   70)
  hydrogen bonds       : angle       5.87719 (  183)
  link_NAG-ASN         : bond        0.00260 (    1)
  link_NAG-ASN         : angle       2.22836 (    3)

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

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

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  722 Ramachandran restraints generated.
    361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.120 
Fit side-chains
REVERT: E   83 ASN cc_start: 0.7873 (m110) cc_final: 0.7548 (m-40)
  outliers start: 11
  outliers final: 11
  residues processed: 52
  average time/residue: 0.0466
  time to fit residues: 3.2396
Evaluate side-chains
  55 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  140 SER
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  225 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0050
   chunk 4 optimal weight:    0.3980
   chunk 0 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 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 = 0.3761 r_free = 0.3761 target = 0.150306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130603 restraints weight = 5130.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.133608 restraints weight = 3090.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135643 restraints weight = 2144.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137083 restraints weight = 1653.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137937 restraints weight = 1368.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2998  Z= 0.147
  Angle     :  0.623   8.379   4069  Z= 0.311
  Chirality :  0.045   0.140    435
  Planarity :  0.004   0.052    521
  Dihedral  :  5.555  52.195    436
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.36 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.72 (0.43), residues: 361
  helix: -2.96 (1.43), residues: 13
  sheet: -0.08 (0.54), residues: 108
  loop : -1.63 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  86 
 TYR   0.015   0.001   TYR E 225 
 PHE   0.030   0.002   PHE C 486 
 TRP   0.007   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 2993)
  covalent geometry    : angle       0.62074 ( 4058)
  SS BOND              : bond        0.00266 (    4)
  SS BOND              : angle       0.74135 (    8)
  hydrogen bonds       : bond        0.03513 (   70)
  hydrogen bonds       : angle       5.83082 (  183)
  link_NAG-ASN         : bond        0.00263 (    1)
  link_NAG-ASN         : angle       2.02181 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 840.98 seconds
wall clock time: 15 minutes 8.86 seconds (908.86 seconds total)