Starting phenix.real_space_refine
on Wed Jul  1 22:36:05 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7yr0_34041/07_2026/7yr0_34041.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr0_34041/07_2026/7yr0_34041.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yr0_34041/07_2026/7yr0_34041.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr0_34041/07_2026/7yr0_34041.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr0_34041/07_2026/7yr0_34041.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr0_34041/07_2026/7yr0_34041.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7yr0_34041/07_2026/7yr0_34041.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7yr0_34041/07_2026/7yr0_34041.cif"
  }
  resolution = 3.98
  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=  -0.001 sd=   0.044
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      15      5.16       5
     C    2149      2.51       5
     N     571      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3383
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1560
          Classifications: {'peptide': 196}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 183}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "C"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 959
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
    Chain: "B"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 815
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 0.78, per 1000 atoms: 0.23
  Number of scatterers: 3383
  At special positions: 0
  Unit cell: (73.83, 85.6, 81.32, 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      15     16.00
     O     648      8.00
     N     571      7.00
     C    2149      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  89 " 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
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    BETA1-6
      " NAG D   1 " - " FUC D   4 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG D   1 " - " ASN A 343 "
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 108.8 milliseconds
  

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 8 sheets defined
      6.3% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.995A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   PHE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 337 through 342'
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 3.799A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'C' and resid 61 through 65
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.310A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
      removed outlier: 3.597A  pdb=" N   TYR A 453 " --> pdb=" O   GLN A 493 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 51
      removed outlier: 3.890A  pdb=" N   GLY C  33 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ASN C 116 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 51
      removed outlier: 3.890A  pdb=" N   GLY C  33 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11
      removed outlier: 3.697A  pdb=" N   LEU B  11 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 22
      removed outlier: 3.763A  pdb=" N   ASP B  71 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 47
      removed outlier: 4.117A  pdb=" N   THR B  97 " --> pdb=" O   GLN B  91 " (cutoff:3.500A)

    82 hydrogen bonds defined for protein.
    189 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: 0.42

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1073
        1.35 -     1.46: 942
        1.46 -     1.58: 1439
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 3472
  Sorted by residual:
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.547 -0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C2  NAG D   2 "
       pdb=" N2  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.58e+00
  bond pdb=" CA  GLY A 381 "
       pdb=" C   GLY A 381 "
    ideal  model  delta    sigma   weight residual
    1.512  1.523 -0.011 8.70e-03 1.32e+04 1.56e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.38e+00
  bond pdb=" C5  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.36e+00
  ... (remaining 3467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 4462
        1.26 -     2.51: 185
        2.51 -     3.77: 51
        3.77 -     5.02: 17
        5.02 -     6.28: 5
  Bond angle restraints: 4720
  Sorted by residual:
  angle pdb=" N   ILE A 402 "
        pdb=" CA  ILE A 402 "
        pdb=" C   ILE A 402 "
      ideal   model   delta    sigma   weight residual
     108.53  111.81   -3.28 1.22e+00 6.72e-01 7.23e+00
  angle pdb=" C   GLU C  82 "
        pdb=" CA  GLU C  82 "
        pdb=" CB  GLU C  82 "
      ideal   model   delta    sigma   weight residual
     110.42  115.40   -4.98 1.99e+00 2.53e-01 6.25e+00
  angle pdb=" C   GLU B  80 "
        pdb=" CA  GLU B  80 "
        pdb=" CB  GLU B  80 "
      ideal   model   delta    sigma   weight residual
     109.26  112.83   -3.57 1.47e+00 4.63e-01 5.91e+00
  angle pdb=" C   MET C  48 "
        pdb=" N   GLY C  49 "
        pdb=" CA  GLY C  49 "
      ideal   model   delta    sigma   weight residual
     121.46  119.21    2.25 9.50e-01 1.11e+00 5.63e+00
  angle pdb=" N   GLY C  49 "
        pdb=" CA  GLY C  49 "
        pdb=" C   GLY C  49 "
      ideal   model   delta    sigma   weight residual
     110.90  114.36   -3.46 1.53e+00 4.27e-01 5.12e+00
  ... (remaining 4715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 1787
       17.67 -    35.35: 177
       35.35 -    53.02: 28
       53.02 -    70.69: 2
       70.69 -    88.36: 4
  Dihedral angle restraints: 1998
    sinusoidal: 773
      harmonic: 1225
  Sorted by residual:
  dihedral pdb=" CA  SER B   7 "
           pdb=" C   SER B   7 "
           pdb=" N   PRO B   8 "
           pdb=" CA  PRO B   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.07   25.93     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.67   38.33     1      1.00e+01 1.00e-02 2.07e+01
  dihedral pdb=" CA  TYR C  80 "
           pdb=" C   TYR C  80 "
           pdb=" N   MET C  81 "
           pdb=" CA  MET C  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.93   22.07     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 1995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 448
       0.066 -    0.133: 61
       0.133 -    0.199: 4
       0.199 -    0.265: 0
       0.265 -    0.331: 2
  Chirality restraints: 515
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" C2  NAG D   2 "
            pdb=" C1  NAG D   2 "
            pdb=" C3  NAG D   2 "
            pdb=" N2  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.31   -0.19 2.00e-01 2.50e+01 8.59e-01
  ... (remaining 512 not shown)

  Planarity restraints: 606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B   7 "   -0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO B   8 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B   8 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B   8 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP C  47 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.35e+00
        pdb=" C   TRP C  47 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   TRP C  47 "    0.008 2.00e-02 2.50e+03
        pdb=" N   MET C  48 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  47 "    0.009 2.00e-02 2.50e+03   7.14e-03 1.27e+00
        pdb=" CG  TRP C  47 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  47 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  47 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  47 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  47 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  47 "    0.001 2.00e-02 2.50e+03
  ... (remaining 603 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 130
        2.71 -     3.26: 3238
        3.26 -     3.81: 5061
        3.81 -     4.35: 6100
        4.35 -     4.90: 10380
  Nonbonded interactions: 24909
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  69 "
            pdb=" OE2 GLU C  82 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   VAL B   3 "
            pdb=" OG  SER B  26 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OG  SER C  35 "
            pdb=" OD2 ASP C  99 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" NH1 ARG C  87 "
            pdb=" OD1 ASP C  89 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   ALA A 419 "
            pdb=" NZ  LYS A 424 "
     model   vdw
     2.259 3.120
  ... (remaining 24904 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:             2.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     3.800
  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:0.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3481  Z= 0.154
  Angle     :  0.708   8.519   4742  Z= 0.353
  Chirality :  0.049   0.331    515
  Planarity :  0.004   0.034    605
  Dihedral  : 13.750  88.364   1209
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  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 are not related in a simple way.
  whole: -1.76 (0.43), residues: 421
  helix: -0.21 (3.10), residues: 6
  sheet:  0.50 (0.59), residues: 92
  loop : -1.86 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  78 
 TYR   0.012   0.001   TYR B  50 
 PHE   0.017   0.001   PHE C  29 
 TRP   0.020   0.001   TRP C  47 
 HIS   0.002   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.15 ( 3472)
  covalent geometry    : angle       0.68081 /  0.35 ( 4720)
  SS BOND              : bond        0.00316 /  0.16 (    5)
  SS BOND              : angle       0.74826 /  0.42 (   10)
  hydrogen bonds       : bond        0.13084 /  8.54 (   71)
  hydrogen bonds       : angle       5.73812 /  3.93 (  189)
  link_BETA1-4         : bond        0.00448 /  0.23 (    2)
  link_BETA1-4         : angle       2.64261 /  1.50 (    6)
  link_BETA1-6         : bond        0.00327 /  0.17 (    1)
  link_BETA1-6         : angle       1.33975 /  0.76 (    3)
  link_NAG-ASN         : bond        0.02652 /  1.40 (    1)
  link_NAG-ASN         : angle       6.73296 /  3.00 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.119 
Fit side-chains
REVERT: C   80 TYR cc_start: 0.8048 (m-80) cc_final: 0.7822 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0491
  time to fit residues: 4.5225
Evaluate side-chains
  57 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0670
   chunk 30 optimal weight:    0.2980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7320

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.124804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.098121 restraints weight = 8083.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.100733 restraints weight = 5290.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.102622 restraints weight = 4061.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.103883 restraints weight = 3410.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.104800 restraints weight = 3022.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3481  Z= 0.139
  Angle     :  0.678   9.570   4742  Z= 0.327
  Chirality :  0.046   0.267    515
  Planarity :  0.004   0.036    605
  Dihedral  :  4.671  26.070    474
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.52 %
    Favored  : 87.08 %
  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 are not related in a simple way.
  whole: -1.89 (0.41), residues: 421
  helix: -2.09 (1.62), residues: 12
  sheet:  0.28 (0.58), residues: 98
  loop : -1.89 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  38 
 TYR   0.024   0.002   TYR B  50 
 PHE   0.012   0.001   PHE C  29 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.004   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 3472)
  covalent geometry    : angle       0.64603 /  0.32 ( 4720)
  SS BOND              : bond        0.00461 /  0.28 (    5)
  SS BOND              : angle       0.69973 /  0.40 (   10)
  hydrogen bonds       : bond        0.03294 /  2.35 (   71)
  hydrogen bonds       : angle       5.55752 /  3.87 (  189)
  link_BETA1-4         : bond        0.00397 /  0.19 (    2)
  link_BETA1-4         : angle       1.83027 /  1.00 (    6)
  link_BETA1-6         : bond        0.00448 /  0.24 (    1)
  link_BETA1-6         : angle       0.99720 /  0.44 (    3)
  link_NAG-ASN         : bond        0.02207 /  1.16 (    1)
  link_NAG-ASN         : angle       7.72852 /  3.53 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 67
  average time/residue: 0.0574
  time to fit residues: 4.7194
Evaluate side-chains
  59 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0980
   chunk 19 optimal weight:    0.0470
   chunk 5 optimal weight:    0.0050
   chunk 37 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.1692

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.126734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.100290 restraints weight = 7931.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.103049 restraints weight = 5198.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.104998 restraints weight = 3971.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.106328 restraints weight = 3308.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.106848 restraints weight = 2928.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3481  Z= 0.108
  Angle     :  0.663   9.551   4742  Z= 0.312
  Chirality :  0.046   0.281    515
  Planarity :  0.004   0.035    605
  Dihedral  :  4.428  25.907    474
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.89 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.89 %
    Favored  : 83.71 %
  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 are not related in a simple way.
  whole: -1.80 (0.42), residues: 421
  helix: -2.10 (1.66), residues: 12
  sheet:  0.64 (0.59), residues: 92
  loop : -1.90 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 346 
 TYR   0.014   0.001   TYR A 501 
 PHE   0.019   0.001   PHE C  29 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 ( 3472)
  covalent geometry    : angle       0.62916 /  0.30 ( 4720)
  SS BOND              : bond        0.00290 /  0.15 (    5)
  SS BOND              : angle       0.70679 /  0.41 (   10)
  hydrogen bonds       : bond        0.02960 /  2.07 (   71)
  hydrogen bonds       : angle       5.27337 /  3.64 (  189)
  link_BETA1-4         : bond        0.00566 /  0.28 (    2)
  link_BETA1-4         : angle       1.98437 /  1.08 (    6)
  link_BETA1-6         : bond        0.00616 /  0.32 (    1)
  link_BETA1-6         : angle       1.00756 /  0.56 (    3)
  link_NAG-ASN         : bond        0.02633 /  1.39 (    1)
  link_NAG-ASN         : angle       7.85159 /  3.57 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASN cc_start: 0.8058 (m110) cc_final: 0.7691 (p0)
REVERT: C   80 TYR cc_start: 0.7980 (m-80) cc_final: 0.7679 (m-80)
REVERT: C   82 GLU cc_start: 0.5994 (pp20) cc_final: 0.5490 (tm-30)
  outliers start: 5
  outliers final: 4
  residues processed: 67
  average time/residue: 0.0661
  time to fit residues: 5.2910
Evaluate side-chains
  63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.0870
   chunk 36 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0060
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0570
   chunk 31 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.2092

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

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 = 0.127584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.101212 restraints weight = 7808.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.103940 restraints weight = 5116.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.105862 restraints weight = 3922.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.107195 restraints weight = 3289.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.107911 restraints weight = 2909.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3481  Z= 0.104
  Angle     :  0.646   9.751   4742  Z= 0.305
  Chirality :  0.045   0.274    515
  Planarity :  0.003   0.036    605
  Dihedral  :  4.269  25.736    474
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.60 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.13 %
    Favored  : 80.90 %
  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 are not related in a simple way.
  whole: -1.70 (0.42), residues: 421
  helix: -2.14 (1.68), residues: 12
  sheet:  0.77 (0.60), residues: 92
  loop : -1.84 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  78 
 TYR   0.019   0.001   TYR A 501 
 PHE   0.016   0.001   PHE C  29 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.001   0.000   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00231 /  0.10 ( 3472)
  covalent geometry    : angle       0.61352 /  0.30 ( 4720)
  SS BOND              : bond        0.00258 /  0.13 (    5)
  SS BOND              : angle       0.70725 /  0.42 (   10)
  hydrogen bonds       : bond        0.02822 /  2.00 (   71)
  hydrogen bonds       : angle       5.18429 /  3.57 (  189)
  link_BETA1-4         : bond        0.00625 /  0.31 (    2)
  link_BETA1-4         : angle       2.19539 /  1.21 (    6)
  link_BETA1-6         : bond        0.00780 /  0.41 (    1)
  link_BETA1-6         : angle       0.79168 /  0.42 (    3)
  link_NAG-ASN         : bond        0.02248 /  1.18 (    1)
  link_NAG-ASN         : angle       7.40018 /  3.39 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASN cc_start: 0.8060 (m110) cc_final: 0.7714 (p0)
REVERT: C   80 TYR cc_start: 0.7938 (m-80) cc_final: 0.7707 (m-80)
REVERT: C   82 GLU cc_start: 0.5812 (pp20) cc_final: 0.5288 (tm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 66
  average time/residue: 0.0587
  time to fit residues: 4.6989
Evaluate side-chains
  60 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    0.2980
   chunk 14 optimal weight:    0.2980
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.127429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.103158 restraints weight = 7862.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.105611 restraints weight = 5459.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.107213 restraints weight = 4279.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.108396 restraints weight = 3633.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.108839 restraints weight = 3239.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3481  Z= 0.121
  Angle     :  0.648   9.291   4742  Z= 0.310
  Chirality :  0.046   0.273    515
  Planarity :  0.003   0.033    605
  Dihedral  :  4.325  25.136    474
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.60 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 18.82 %
    Favored  : 78.09 %
  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 are not related in a simple way.
  whole: -1.69 (0.41), residues: 421
  helix: -1.83 (1.32), residues: 20
  sheet:  0.96 (0.61), residues: 90
  loop : -1.89 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  87 
 TYR   0.015   0.001   TYR A 501 
 PHE   0.008   0.001   PHE A 342 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.016   0.003   HIS A 505 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 3472)
  covalent geometry    : angle       0.62225 /  0.30 ( 4720)
  SS BOND              : bond        0.00300 /  0.16 (    5)
  SS BOND              : angle       0.73366 /  0.43 (   10)
  hydrogen bonds       : bond        0.02802 /  2.00 (   71)
  hydrogen bonds       : angle       5.25901 /  3.62 (  189)
  link_BETA1-4         : bond        0.00430 /  0.21 (    2)
  link_BETA1-4         : angle       2.00225 /  1.10 (    6)
  link_BETA1-6         : bond        0.00285 /  0.15 (    1)
  link_BETA1-6         : angle       0.96071 /  0.49 (    3)
  link_NAG-ASN         : bond        0.03162 /  1.66 (    1)
  link_NAG-ASN         : angle       6.56904 /  2.78 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
REVERT: C   80 TYR cc_start: 0.7809 (m-80) cc_final: 0.7569 (m-80)
REVERT: C   82 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.5246 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 64
  average time/residue: 0.0636
  time to fit residues: 4.8885
Evaluate side-chains
  63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.0970
   chunk 14 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6578

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

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 = 0.125879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.100010 restraints weight = 7907.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.102518 restraints weight = 5337.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.104317 restraints weight = 4151.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.105519 restraints weight = 3500.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.106208 restraints weight = 3118.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3481  Z= 0.124
  Angle     :  0.660   9.450   4742  Z= 0.316
  Chirality :  0.045   0.256    515
  Planarity :  0.003   0.034    605
  Dihedral  :  4.338  25.527    474
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.91 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.63 (0.42), residues: 421
  helix: -1.83 (1.82), residues: 12
  sheet:  0.79 (0.61), residues: 88
  loop : -1.76 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 509 
 TYR   0.016   0.001   TYR C  27 
 PHE   0.014   0.001   PHE A 374 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 339 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 3472)
  covalent geometry    : angle       0.63328 /  0.31 ( 4720)
  SS BOND              : bond        0.00311 /  0.17 (    5)
  SS BOND              : angle       0.77268 /  0.45 (   10)
  hydrogen bonds       : bond        0.02777 /  2.05 (   71)
  hydrogen bonds       : angle       5.30863 /  3.66 (  189)
  link_BETA1-4         : bond        0.00375 /  0.18 (    2)
  link_BETA1-4         : angle       1.43940 /  0.78 (    6)
  link_BETA1-6         : bond        0.00306 /  0.16 (    1)
  link_BETA1-6         : angle       1.22204 /  0.57 (    3)
  link_NAG-ASN         : bond        0.02531 /  1.33 (    1)
  link_NAG-ASN         : angle       7.04644 /  3.14 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
REVERT: C   80 TYR cc_start: 0.7974 (m-80) cc_final: 0.7745 (m-80)
REVERT: C   82 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5256 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 65
  average time/residue: 0.0651
  time to fit residues: 5.1309
Evaluate side-chains
  60 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0980
   chunk 27 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 18 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    0.6984

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

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 = 0.125698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.099651 restraints weight = 8085.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.102187 restraints weight = 5390.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.104029 restraints weight = 4166.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.105290 restraints weight = 3505.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.105802 restraints weight = 3114.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3481  Z= 0.128
  Angle     :  0.671   9.457   4742  Z= 0.321
  Chirality :  0.045   0.251    515
  Planarity :  0.003   0.032    605
  Dihedral  :  4.364  24.980    474
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.84 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.07 %
    Favored  : 76.12 %
  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 are not related in a simple way.
  whole: -1.58 (0.42), residues: 421
  helix: -1.82 (1.81), residues: 12
  sheet:  0.92 (0.60), residues: 90
  loop : -1.77 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 509 
 TYR   0.018   0.001   TYR C  27 
 PHE   0.008   0.001   PHE A 374 
 TRP   0.008   0.001   TRP C  47 
 HIS   0.002   0.001   HIS A 339 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 3472)
  covalent geometry    : angle       0.64368 /  0.32 ( 4720)
  SS BOND              : bond        0.00322 /  0.18 (    5)
  SS BOND              : angle       0.77575 /  0.46 (   10)
  hydrogen bonds       : bond        0.02764 /  2.06 (   71)
  hydrogen bonds       : angle       5.34059 /  3.69 (  189)
  link_BETA1-4         : bond        0.00341 /  0.16 (    2)
  link_BETA1-4         : angle       1.27878 /  0.69 (    6)
  link_BETA1-6         : bond        0.00267 /  0.14 (    1)
  link_BETA1-6         : angle       1.18902 /  0.57 (    3)
  link_NAG-ASN         : bond        0.02332 /  1.23 (    1)
  link_NAG-ASN         : angle       7.32461 /  3.33 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5679 (OUTLIER) cc_final: 0.5359 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 71
  average time/residue: 0.0764
  time to fit residues: 6.5845
Evaluate side-chains
  65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.125309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.101015 restraints weight = 7874.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.103332 restraints weight = 5423.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.104981 restraints weight = 4249.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.105980 restraints weight = 3592.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.105994 restraints weight = 3214.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3481  Z= 0.147
  Angle     :  0.692   9.393   4742  Z= 0.333
  Chirality :  0.046   0.243    515
  Planarity :  0.003   0.034    605
  Dihedral  :  4.524  25.377    474
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.07 %
    Favored  : 76.12 %
  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 are not related in a simple way.
  whole: -1.57 (0.42), residues: 421
  helix: -1.77 (1.83), residues: 12
  sheet:  0.86 (0.60), residues: 90
  loop : -1.75 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 509 
 TYR   0.017   0.001   TYR C  27 
 PHE   0.008   0.001   PHE A 374 
 TRP   0.020   0.001   TRP C  47 
 HIS   0.022   0.004   HIS A 505 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.14 ( 3472)
  covalent geometry    : angle       0.66801 /  0.33 ( 4720)
  SS BOND              : bond        0.00355 /  0.19 (    5)
  SS BOND              : angle       0.80866 /  0.48 (   10)
  hydrogen bonds       : bond        0.02890 /  2.16 (   71)
  hydrogen bonds       : angle       5.44141 /  3.77 (  189)
  link_BETA1-4         : bond        0.00383 /  0.19 (    2)
  link_BETA1-4         : angle       1.51150 /  0.82 (    6)
  link_BETA1-6         : bond        0.00014 /  0.01 (    1)
  link_BETA1-6         : angle       1.35917 /  0.74 (    3)
  link_NAG-ASN         : bond        0.03204 /  1.69 (    1)
  link_NAG-ASN         : angle       6.87955 /  2.99 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5760 (OUTLIER) cc_final: 0.5379 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 65
  average time/residue: 0.0700
  time to fit residues: 5.5893
Evaluate side-chains
  67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0270
   chunk 33 optimal weight:    0.0000
   chunk 27 optimal weight:    0.0970
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0670
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.1778

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.133171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.109069 restraints weight = 8032.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.111767 restraints weight = 5261.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.113674 restraints weight = 3998.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.114872 restraints weight = 3328.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.115597 restraints weight = 2943.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3481  Z= 0.114
  Angle     :  0.696   9.516   4742  Z= 0.333
  Chirality :  0.045   0.262    515
  Planarity :  0.003   0.032    605
  Dihedral  :  4.396  24.466    474
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.89 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.63 %
    Favored  : 76.12 %
  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 are not related in a simple way.
  whole: -1.69 (0.42), residues: 421
  helix: -1.98 (1.72), residues: 12
  sheet:  0.60 (0.59), residues: 95
  loop : -1.80 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  78 
 TYR   0.017   0.001   TYR C  27 
 PHE   0.010   0.001   PHE A 374 
 TRP   0.019   0.002   TRP C  47 
 HIS   0.002   0.001   HIS A 505 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 3472)
  covalent geometry    : angle       0.66797 /  0.33 ( 4720)
  SS BOND              : bond        0.00283 /  0.14 (    5)
  SS BOND              : angle       0.86230 /  0.50 (   10)
  hydrogen bonds       : bond        0.02687 /  1.96 (   71)
  hydrogen bonds       : angle       5.28478 /  3.63 (  189)
  link_BETA1-4         : bond        0.00436 /  0.21 (    2)
  link_BETA1-4         : angle       1.60719 /  0.85 (    6)
  link_BETA1-6         : bond        0.00317 /  0.17 (    1)
  link_BETA1-6         : angle       1.16341 /  0.60 (    3)
  link_NAG-ASN         : bond        0.02720 /  1.43 (    1)
  link_NAG-ASN         : angle       7.38077 /  3.35 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5430 (OUTLIER) cc_final: 0.5065 (tm-30)
REVERT: B   39 GLN cc_start: 0.8579 (tp40) cc_final: 0.8312 (tp-100)
  outliers start: 8
  outliers final: 5
  residues processed: 68
  average time/residue: 0.0810
  time to fit residues: 6.6272
Evaluate side-chains
  67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0980
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    1.3184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.123763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.099447 restraints weight = 7996.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.101663 restraints weight = 5545.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.103217 restraints weight = 4362.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.103817 restraints weight = 3708.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.104859 restraints weight = 3412.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3481  Z= 0.185
  Angle     :  0.722   9.407   4742  Z= 0.349
  Chirality :  0.046   0.234    515
  Planarity :  0.004   0.033    605
  Dihedral  :  4.642  25.164    474
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.26 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.63 %
    Favored  : 76.12 %
  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 are not related in a simple way.
  whole: -1.63 (0.42), residues: 421
  helix: -1.72 (1.85), residues: 12
  sheet:  0.66 (0.60), residues: 90
  loop : -1.74 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  87 
 TYR   0.016   0.002   TYR C  27 
 PHE   0.010   0.001   PHE A 400 
 TRP   0.012   0.001   TRP C  47 
 HIS   0.004   0.001   HIS A 339 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00431 /  0.18 ( 3472)
  covalent geometry    : angle       0.69923 /  0.34 ( 4720)
  SS BOND              : bond        0.00501 /  0.28 (    5)
  SS BOND              : angle       0.88499 /  0.51 (   10)
  hydrogen bonds       : bond        0.03185 /  2.46 (   71)
  hydrogen bonds       : angle       5.58441 /  3.89 (  189)
  link_BETA1-4         : bond        0.00235 /  0.11 (    2)
  link_BETA1-4         : angle       1.00595 /  0.54 (    6)
  link_BETA1-6         : bond        0.00175 /  0.09 (    1)
  link_BETA1-6         : angle       1.41807 /  0.67 (    3)
  link_NAG-ASN         : bond        0.02860 /  1.51 (    1)
  link_NAG-ASN         : angle       6.95051 /  3.18 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5342 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 63
  average time/residue: 0.0718
  time to fit residues: 5.5411
Evaluate side-chains
  65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0970
   chunk 29 optimal weight:    0.0570
   overall best weight:    0.8100

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.124641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.098461 restraints weight = 8236.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.100966 restraints weight = 5495.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.102757 restraints weight = 4246.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.103978 restraints weight = 3567.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.104641 restraints weight = 3175.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3481  Z= 0.141
  Angle     :  0.728   9.426   4742  Z= 0.348
  Chirality :  0.046   0.244    515
  Planarity :  0.003   0.032    605
  Dihedral  :  4.618  25.082    474
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.08 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.91 %
    Favored  : 75.84 %
  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 are not related in a simple way.
  whole: -1.65 (0.42), residues: 421
  helix: -1.81 (1.79), residues: 12
  sheet:  0.61 (0.60), residues: 90
  loop : -1.73 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  78 
 TYR   0.017   0.001   TYR A 501 
 PHE   0.007   0.001   PHE A 374 
 TRP   0.018   0.001   TRP C  47 
 HIS   0.003   0.001   HIS A 339 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 3472)
  covalent geometry    : angle       0.70395 /  0.34 ( 4720)
  SS BOND              : bond        0.00410 /  0.22 (    5)
  SS BOND              : angle       0.89574 /  0.53 (   10)
  hydrogen bonds       : bond        0.03008 /  2.26 (   71)
  hydrogen bonds       : angle       5.58104 /  3.91 (  189)
  link_BETA1-4         : bond        0.00339 /  0.16 (    2)
  link_BETA1-4         : angle       1.10219 /  0.60 (    6)
  link_BETA1-6         : bond        0.00180 /  0.09 (    1)
  link_BETA1-6         : angle       1.25781 /  0.62 (    3)
  link_NAG-ASN         : bond        0.02716 /  1.43 (    1)
  link_NAG-ASN         : angle       7.23621 /  3.34 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 783.03 seconds
wall clock time: 14 minutes 10.36 seconds (850.36 seconds total)