Starting phenix.real_space_refine
on Tue Feb  3 15:56:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uel_64085/02_2026/9uel_64085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uel_64085/02_2026/9uel_64085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uel_64085/02_2026/9uel_64085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uel_64085/02_2026/9uel_64085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uel_64085/02_2026/9uel_64085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uel_64085/02_2026/9uel_64085.cif"
  }
  resolution = 3.37
  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=   0.002 sd=   0.033
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      19      5.16       5
     C    2863      2.51       5
     N     724      2.21       5
     O     879      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4485
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 576, 4387
          Classifications: {'peptide': 576}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 30, 'TRANS': 545}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 200
          Unresolved non-hydrogen angles: 247
          Unresolved non-hydrogen dihedrals: 178
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 3, 'GLN:plan1': 5, 'TYR:plan': 5, 'ASP:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 128
    Chain: "A"
      Number of atoms: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 98
          Unusual residues: {'NAG': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
  Time building chain proxies: 0.76, per 1000 atoms: 0.17
  Number of scatterers: 4485
  At special positions: 0
  Unit cell: (79.8, 116.28, 113.24, 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      19     16.00
     O     879      8.00
     N     724      7.00
     C    2863      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 289 " - pdb=" SG  CYS A 299 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 377 " - pdb=" SG  CYS A 430 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 522 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 478 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 535 " - pdb=" SG  CYS A 587 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 614 " - pdb=" SG  CYS A 646 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 659 " - pdb=" SG  CYS A 668 " 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 A1401 " - " ASN A 613 "
      " NAG A1402 " - " ASN A 232 "
      " NAG A1403 " - " ASN A 280 "
      " NAG A1404 " - " ASN A 329 "
      " NAG A1405 " - " ASN A 352 "
      " NAG A1406 " - " ASN A  30 "
      " NAG A1407 " - " ASN A  60 "
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 225.6 milliseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1082

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 11 sheets defined
      4.3% alpha, 15.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 3.516A  pdb=" N   LYS A 298 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   CYS A 299 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 341
      removed outlier: 3.536A  pdb=" N   PHE A 340 " --> pdb=" O   PHE A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 623
      removed outlier: 3.880A  pdb=" N   HIS A 622 " --> pdb=" O   SER A 618 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A 623 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54
      removed outlier: 3.659A  pdb=" N   GLN A 269 " --> pdb=" O   PHE A  54 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A 287 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   ASP A 285 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84
    Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 117
      removed outlier: 3.573A  pdb=" N   LYS A 128 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 191
      removed outlier: 3.896A  pdb=" N   GLU A 190 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LYS A 205 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 196
      removed outlier: 3.542A  pdb=" N   LEU A 227 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 309 through 312
      removed outlier: 4.328A  pdb=" N   GLY A 591 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR A 609 " --> pdb=" O   CYS A 646 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   CYS A 646 " --> pdb=" O   TYR A 609 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 355
      removed outlier: 3.880A  pdb=" N   SER A 511 " --> pdb=" O   TYR A 394 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 371 through 372
      removed outlier: 4.805A  pdb=" N   SER A 371 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ARG A 506 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 535 through 538
      removed outlier: 3.614A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   PHE A 538 " --> pdb=" O   GLY A 545 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLY A 545 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 657
      removed outlier: 3.728A  pdb=" N   GLU A 651 " --> pdb=" O   ILE A 689 " (cutoff:3.500A)
      removed outlier: 5.191A  pdb=" N   THR A 693 " --> pdb=" O   VAL A 653 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   ASN A 655 " --> pdb=" O   THR A 693 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL A 667 " --> pdb=" O   ILE A 663 " (cutoff:3.500A)

    59 hydrogen bonds defined for protein.
    147 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: 0.44

  Time building geometry restraints manager: 0.32 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: 1409
        1.34 -     1.47: 1226
        1.47 -     1.59: 1934
        1.59 -     1.72: 0
        1.72 -     1.84: 20
  Bond restraints: 4589
  Sorted by residual:
  bond pdb=" N   ASN A 124 "
       pdb=" CA  ASN A 124 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.29e-02 6.01e+03 7.32e+00
  bond pdb=" N   PHE A 125 "
       pdb=" CA  PHE A 125 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.30e-02 5.92e+03 6.90e+00
  bond pdb=" N   THR A 123 "
       pdb=" CA  THR A 123 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.35e-02 5.49e+03 5.51e+00
  bond pdb=" N   ALA A 122 "
       pdb=" CA  ALA A 122 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.23e-02 6.61e+03 3.55e+00
  bond pdb=" CA  ILE A 408 "
       pdb=" CB  ILE A 408 "
    ideal  model  delta    sigma   weight residual
    1.527  1.546 -0.020 1.31e-02 5.83e+03 2.23e+00
  ... (remaining 4584 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 6012
        1.72 -     3.44: 201
        3.44 -     5.17: 36
        5.17 -     6.89: 9
        6.89 -     8.61: 4
  Bond angle restraints: 6262
  Sorted by residual:
  angle pdb=" C   VAL A  61 "
        pdb=" N   THR A  62 "
        pdb=" CA  THR A  62 "
      ideal   model   delta    sigma   weight residual
     121.54  130.15   -8.61 1.91e+00 2.74e-01 2.03e+01
  angle pdb=" N   THR A 123 "
        pdb=" CA  THR A 123 "
        pdb=" C   THR A 123 "
      ideal   model   delta    sigma   weight residual
     113.01  109.06    3.95 1.20e+00 6.94e-01 1.08e+01
  angle pdb=" N   VAL A 567 "
        pdb=" CA  VAL A 567 "
        pdb=" C   VAL A 567 "
      ideal   model   delta    sigma   weight residual
     112.98  108.96    4.02 1.25e+00 6.40e-01 1.03e+01
  angle pdb=" CA  CYS A 377 "
        pdb=" CB  CYS A 377 "
        pdb=" SG  CYS A 377 "
      ideal   model   delta    sigma   weight residual
     114.40  121.76   -7.36 2.30e+00 1.89e-01 1.02e+01
  angle pdb=" CA  CYS A 522 "
        pdb=" CB  CYS A 522 "
        pdb=" SG  CYS A 522 "
      ideal   model   delta    sigma   weight residual
     114.40  120.75   -6.35 2.30e+00 1.89e-01 7.63e+00
  ... (remaining 6257 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.41: 2528
       18.41 -    36.82: 202
       36.82 -    55.24: 46
       55.24 -    73.65: 6
       73.65 -    92.06: 4
  Dihedral angle restraints: 2786
    sinusoidal: 1109
      harmonic: 1677
  Sorted by residual:
  dihedral pdb=" CB  CYS A 535 "
           pdb=" SG  CYS A 535 "
           pdb=" SG  CYS A 587 "
           pdb=" CB  CYS A 587 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.36  -65.36     1      1.00e+01 1.00e-02 5.60e+01
  dihedral pdb=" CB  CYS A 377 "
           pdb=" SG  CYS A 377 "
           pdb=" SG  CYS A 430 "
           pdb=" CB  CYS A 430 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   30.03   62.97     1      1.00e+01 1.00e-02 5.24e+01
  dihedral pdb=" CA  CYS A 587 "
           pdb=" C   CYS A 587 "
           pdb=" N   SER A 588 "
           pdb=" CA  SER A 588 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.43  -29.57     0      5.00e+00 4.00e-02 3.50e+01
  ... (remaining 2783 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 608
       0.065 -    0.129: 122
       0.129 -    0.194: 5
       0.194 -    0.258: 2
       0.258 -    0.323: 2
  Chirality restraints: 739
  Sorted by residual:
  chirality pdb=" CB  THR A  62 "
            pdb=" CA  THR A  62 "
            pdb=" OG1 THR A  62 "
            pdb=" CG2 THR A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.23    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" C1  NAG A1403 "
            pdb=" ND2 ASN A 280 "
            pdb=" C2  NAG A1403 "
            pdb=" O5  NAG A1403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CB  ILE A 408 "
            pdb=" CA  ILE A 408 "
            pdb=" CG1 ILE A 408 "
            pdb=" CG2 ILE A 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 736 not shown)

  Planarity restraints: 804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 482 "    0.049 5.00e-02 4.00e+02   7.46e-02 8.90e+00
        pdb=" N   PRO A 483 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 483 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 483 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 557 "   -0.044 5.00e-02 4.00e+02   6.70e-02 7.18e+00
        pdb=" N   PRO A 558 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 558 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 558 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 192 "    0.010 2.00e-02 2.50e+03   1.94e-02 3.75e+00
        pdb=" C   VAL A 192 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   VAL A 192 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PHE A 193 "    0.011 2.00e-02 2.50e+03
  ... (remaining 801 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 874
        2.77 -     3.31: 4041
        3.31 -     3.84: 6426
        3.84 -     4.37: 7144
        4.37 -     4.90: 12874
  Nonbonded interactions: 31359
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 288 "
            pdb=" OG  SER A 295 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   GLU A 658 "
            pdb=" OH  TYR A 692 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   PRO A 382 "
            pdb=" OG1 THR A 383 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" N   GLN A 561 "
            pdb=" OE1 GLN A 561 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" NE  ARG A 455 "
            pdb=" O   SER A 457 "
     model   vdw
     2.315 3.120
  ... (remaining 31354 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             4.680
  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:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.530
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
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      :  0.004   0.050   4603  Z= 0.184
  Angle     :  0.810  11.577   6297  Z= 0.416
  Chirality :  0.052   0.323    739
  Planarity :  0.006   0.075    797
  Dihedral  : 13.833  92.062   1683
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 15.05 %
    Favored  : 84.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  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: -3.94 (0.31), residues: 558
  helix: -3.80 (0.65), residues: 28
  sheet: -2.61 (0.55), residues: 98
  loop : -2.77 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  43 
 TYR   0.015   0.002   TYR A 421 
 PHE   0.024   0.002   PHE A 193 
 TRP   0.011   0.002   TRP A  63 
 HIS   0.001   0.000   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 4589)
  covalent geometry    : angle       0.77375 ( 6262)
  SS BOND              : bond        0.00808 (    7)
  SS BOND              : angle       2.10259 (   14)
  hydrogen bonds       : bond        0.30115 (   59)
  hydrogen bonds       : angle       9.09485 (  147)
  link_NAG-ASN         : bond        0.00747 (    7)
  link_NAG-ASN         : angle       3.89742 (   21)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 LYS cc_start: 0.5530 (mmtt) cc_final: 0.5145 (mmmt)
REVERT: A  505 TYR cc_start: 0.5827 (m-80) cc_final: 0.5400 (m-80)
REVERT: A  555 LYS cc_start: 0.8531 (mptt) cc_final: 0.7736 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0563
  time to fit residues: 7.1486
Evaluate side-chains
  73 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 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 = 0.3668 r_free = 0.3668 target = 0.113399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.098807 restraints weight = 9666.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.50
r_work: 0.3352 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   4603  Z= 0.264
  Angle     :  0.891  13.875   6297  Z= 0.446
  Chirality :  0.054   0.264    739
  Planarity :  0.006   0.065    797
  Dihedral  :  8.805  89.040    758
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 16.13 %
    Favored  : 83.69 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.84 %
    Favored  : 85.84 %
  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: -4.17 (0.30), residues: 558
  helix: -3.12 (0.77), residues: 30
  sheet: -3.18 (0.49), residues: 104
  loop : -2.86 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  43 
 TYR   0.015   0.002   TYR A 203 
 PHE   0.021   0.003   PHE A 193 
 TRP   0.015   0.003   TRP A 351 
 HIS   0.003   0.001   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00630 ( 4589)
  covalent geometry    : angle       0.84553 ( 6262)
  SS BOND              : bond        0.01395 (    7)
  SS BOND              : angle       2.40989 (   14)
  hydrogen bonds       : bond        0.05908 (   59)
  hydrogen bonds       : angle       6.32546 (  147)
  link_NAG-ASN         : bond        0.00680 (    7)
  link_NAG-ASN         : angle       4.60980 (   21)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A  555 LYS cc_start: 0.8633 (mptt) cc_final: 0.7950 (pttt)
REVERT: A  660 ASP cc_start: 0.8203 (m-30) cc_final: 0.7969 (m-30)
  outliers start: 11
  outliers final: 7
  residues processed: 86
  average time/residue: 0.0421
  time to fit residues: 4.9123
Evaluate side-chains
  80 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  378 TYR
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  651 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 51 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 1 optimal weight:    0.3980
   chunk 38 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0020
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 641 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.116371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.101938 restraints weight = 9469.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.47
r_work: 0.3407 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4603  Z= 0.131
  Angle     :  0.730  13.354   6297  Z= 0.362
  Chirality :  0.047   0.197    739
  Planarity :  0.005   0.063    797
  Dihedral  :  8.215  86.554    758
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 13.80 %
    Favored  : 86.02 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.43 %
    Favored  : 82.45 %
  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: -3.94 (0.31), residues: 558
  helix: -3.10 (0.77), residues: 31
  sheet: -2.96 (0.48), residues: 112
  loop : -2.67 (0.26), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 189 
 TYR   0.019   0.001   TYR A 505 
 PHE   0.019   0.002   PHE A 398 
 TRP   0.011   0.001   TRP A 630 
 HIS   0.001   0.000   HIS A 622 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4589)
  covalent geometry    : angle       0.68529 ( 6262)
  SS BOND              : bond        0.00709 (    7)
  SS BOND              : angle       1.70228 (   14)
  hydrogen bonds       : bond        0.04184 (   59)
  hydrogen bonds       : angle       5.90335 (  147)
  link_NAG-ASN         : bond        0.00687 (    7)
  link_NAG-ASN         : angle       4.22159 (   21)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  555 LYS cc_start: 0.8644 (mptt) cc_final: 0.7977 (pttm)
  outliers start: 10
  outliers final: 4
  residues processed: 83
  average time/residue: 0.0476
  time to fit residues: 5.4851
Evaluate side-chains
  76 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 TYR
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  651 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0570
   chunk 19 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0470
   chunk 21 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 0 optimal weight:    0.6980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 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 = 0.3722 r_free = 0.3722 target = 0.116841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.102404 restraints weight = 9490.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.45
r_work: 0.3417 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4603  Z= 0.128
  Angle     :  0.706  13.638   6297  Z= 0.350
  Chirality :  0.046   0.186    739
  Planarity :  0.005   0.060    797
  Dihedral  :  7.960  84.008    758
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 13.44 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.86 %
    Favored  : 80.97 %
  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: -3.89 (0.31), residues: 558
  helix: -3.04 (0.77), residues: 31
  sheet: -2.73 (0.46), residues: 120
  loop : -2.69 (0.26), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 189 
 TYR   0.018   0.001   TYR A 505 
 PHE   0.017   0.002   PHE A 193 
 TRP   0.011   0.001   TRP A 630 
 HIS   0.001   0.000   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4589)
  covalent geometry    : angle       0.65931 ( 6262)
  SS BOND              : bond        0.00753 (    7)
  SS BOND              : angle       1.63395 (   14)
  hydrogen bonds       : bond        0.04007 (   59)
  hydrogen bonds       : angle       5.63762 (  147)
  link_NAG-ASN         : bond        0.00729 (    7)
  link_NAG-ASN         : angle       4.24335 (   21)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 GLN cc_start: 0.8653 (mp10) cc_final: 0.8409 (mp10)
REVERT: A  555 LYS cc_start: 0.8665 (mptt) cc_final: 0.8000 (pttt)
  outliers start: 15
  outliers final: 9
  residues processed: 85
  average time/residue: 0.0550
  time to fit residues: 6.4515
Evaluate side-chains
  79 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  378 TYR
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  651 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    0.0570
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 52 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0370
   chunk 49 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 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 = 0.3727 r_free = 0.3727 target = 0.117142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.102764 restraints weight = 9468.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.46
r_work: 0.3420 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4603  Z= 0.120
  Angle     :  0.699  13.245   6297  Z= 0.342
  Chirality :  0.048   0.322    739
  Planarity :  0.005   0.060    797
  Dihedral  :  7.702  81.581    758
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 13.80 %
    Favored  : 86.02 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.97 %
    Favored  : 78.86 %
  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: -3.85 (0.31), residues: 558
  helix: -2.99 (0.77), residues: 31
  sheet: -2.48 (0.49), residues: 113
  loop : -2.76 (0.26), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 189 
 TYR   0.015   0.001   TYR A 505 
 PHE   0.024   0.002   PHE A 132 
 TRP   0.010   0.001   TRP A 630 
 HIS   0.001   0.000   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4589)
  covalent geometry    : angle       0.65387 ( 6262)
  SS BOND              : bond        0.00669 (    7)
  SS BOND              : angle       1.48002 (   14)
  hydrogen bonds       : bond        0.03765 (   59)
  hydrogen bonds       : angle       5.45251 (  147)
  link_NAG-ASN         : bond        0.00695 (    7)
  link_NAG-ASN         : angle       4.17084 (   21)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 GLN cc_start: 0.8691 (mp10) cc_final: 0.8432 (mp10)
REVERT: A  555 LYS cc_start: 0.8648 (mptt) cc_final: 0.8015 (pttt)
  outliers start: 15
  outliers final: 10
  residues processed: 86
  average time/residue: 0.0573
  time to fit residues: 6.6762
Evaluate side-chains
  79 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  378 TYR
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  663 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0570
   chunk 18 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.6698

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.115798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.101395 restraints weight = 9634.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.47
r_work: 0.3398 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4603  Z= 0.154
  Angle     :  0.730  13.213   6297  Z= 0.363
  Chirality :  0.048   0.235    739
  Planarity :  0.005   0.059    797
  Dihedral  :  7.696  80.390    758
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 14.52 %
    Favored  : 85.30 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.87 %
    Favored  : 76.74 %
  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: -3.76 (0.31), residues: 558
  helix: -2.96 (0.78), residues: 31
  sheet: -2.44 (0.50), residues: 111
  loop : -2.68 (0.26), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 189 
 TYR   0.018   0.002   TYR A 505 
 PHE   0.027   0.002   PHE A 132 
 TRP   0.009   0.002   TRP A 630 
 HIS   0.002   0.000   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4589)
  covalent geometry    : angle       0.68513 ( 6262)
  SS BOND              : bond        0.00677 (    7)
  SS BOND              : angle       1.79575 (   14)
  hydrogen bonds       : bond        0.04271 (   59)
  hydrogen bonds       : angle       5.50250 (  147)
  link_NAG-ASN         : bond        0.00671 (    7)
  link_NAG-ASN         : angle       4.19385 (   21)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  555 LYS cc_start: 0.8660 (mptt) cc_final: 0.8029 (pttt)
  outliers start: 16
  outliers final: 11
  residues processed: 84
  average time/residue: 0.0538
  time to fit residues: 6.2430
Evaluate side-chains
  80 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  378 TYR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  663 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0970
   chunk 45 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0870
   chunk 23 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 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 = 0.3718 r_free = 0.3718 target = 0.116557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.102170 restraints weight = 9477.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.46
r_work: 0.3411 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4603  Z= 0.135
  Angle     :  0.714  13.157   6297  Z= 0.353
  Chirality :  0.047   0.219    739
  Planarity :  0.005   0.060    797
  Dihedral  :  7.578  78.643    758
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 13.98 %
    Favored  : 85.84 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.93 %
    Favored  : 75.90 %
  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: -3.72 (0.31), residues: 558
  helix: -2.98 (0.77), residues: 31
  sheet: -2.26 (0.52), residues: 106
  loop : -2.71 (0.26), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 189 
 TYR   0.017   0.002   TYR A 505 
 PHE   0.026   0.002   PHE A 132 
 TRP   0.013   0.002   TRP A  63 
 HIS   0.002   0.000   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4589)
  covalent geometry    : angle       0.66815 ( 6262)
  SS BOND              : bond        0.00702 (    7)
  SS BOND              : angle       1.73086 (   14)
  hydrogen bonds       : bond        0.03863 (   59)
  hydrogen bonds       : angle       5.45695 (  147)
  link_NAG-ASN         : bond        0.00585 (    7)
  link_NAG-ASN         : angle       4.21797 (   21)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  555 LYS cc_start: 0.8637 (mptt) cc_final: 0.8045 (pttt)
REVERT: A  560 GLN cc_start: 0.4374 (tp40) cc_final: 0.4073 (tp40)
  outliers start: 15
  outliers final: 9
  residues processed: 86
  average time/residue: 0.0546
  time to fit residues: 6.4056
Evaluate side-chains
  77 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  378 TYR
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  663 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0170
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 18 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 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 = 0.3713 r_free = 0.3713 target = 0.116355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.101998 restraints weight = 9504.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.46
r_work: 0.3406 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4603  Z= 0.138
  Angle     :  0.739  12.697   6297  Z= 0.365
  Chirality :  0.049   0.289    739
  Planarity :  0.005   0.059    797
  Dihedral  :  7.538  76.616    758
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 14.52 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 22.83 %
    Favored  : 74.21 %
  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: -3.73 (0.32), residues: 558
  helix: -2.99 (0.77), residues: 31
  sheet: -2.43 (0.50), residues: 113
  loop : -2.64 (0.27), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 189 
 TYR   0.015   0.002   TYR A 505 
 PHE   0.023   0.002   PHE A 132 
 TRP   0.012   0.002   TRP A  63 
 HIS   0.001   0.000   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4589)
  covalent geometry    : angle       0.69337 ( 6262)
  SS BOND              : bond        0.00745 (    7)
  SS BOND              : angle       1.81827 (   14)
  hydrogen bonds       : bond        0.03877 (   59)
  hydrogen bonds       : angle       5.42370 (  147)
  link_NAG-ASN         : bond        0.00633 (    7)
  link_NAG-ASN         : angle       4.28949 (   21)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 TRP cc_start: 0.7754 (t60) cc_final: 0.7509 (t60)
REVERT: A  555 LYS cc_start: 0.8648 (mptt) cc_final: 0.8059 (pttt)
  outliers start: 14
  outliers final: 11
  residues processed: 83
  average time/residue: 0.0552
  time to fit residues: 6.2859
Evaluate side-chains
  83 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  378 TYR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  663 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    0.1980
   chunk 26 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.115973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.101641 restraints weight = 9445.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.43
r_work: 0.3401 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4603  Z= 0.145
  Angle     :  0.744  13.439   6297  Z= 0.368
  Chirality :  0.048   0.267    739
  Planarity :  0.005   0.060    797
  Dihedral  :  7.420  75.283    758
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 14.70 %
    Favored  : 84.95 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 22.62 %
    Favored  : 74.84 %
  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: -3.77 (0.31), residues: 558
  helix: -3.01 (0.76), residues: 31
  sheet: -2.48 (0.51), residues: 110
  loop : -2.67 (0.26), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 271 
 TYR   0.016   0.002   TYR A 505 
 PHE   0.024   0.002   PHE A 132 
 TRP   0.011   0.002   TRP A 103 
 HIS   0.002   0.000   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 4589)
  covalent geometry    : angle       0.69773 ( 6262)
  SS BOND              : bond        0.00743 (    7)
  SS BOND              : angle       1.93176 (   14)
  hydrogen bonds       : bond        0.04001 (   59)
  hydrogen bonds       : angle       5.41995 (  147)
  link_NAG-ASN         : bond        0.00654 (    7)
  link_NAG-ASN         : angle       4.28891 (   21)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  555 LYS cc_start: 0.8616 (mptt) cc_final: 0.8069 (pttt)
  outliers start: 12
  outliers final: 11
  residues processed: 84
  average time/residue: 0.0563
  time to fit residues: 6.4690
Evaluate side-chains
  84 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  378 TYR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  663 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.8384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.114050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.099853 restraints weight = 9475.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.43
r_work: 0.3372 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4603  Z= 0.179
  Angle     :  0.796  13.325   6297  Z= 0.397
  Chirality :  0.050   0.268    739
  Planarity :  0.005   0.061    797
  Dihedral  :  7.597  74.451    758
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 16.13 %
    Favored  : 83.51 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 23.26 %
    Favored  : 74.42 %
  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 are not related in a simple way.
  whole: -3.92 (0.31), residues: 558
  helix: -3.06 (0.75), residues: 31
  sheet: -2.79 (0.48), residues: 115
  loop : -2.70 (0.26), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 271 
 TYR   0.018   0.002   TYR A 505 
 PHE   0.023   0.002   PHE A 132 
 TRP   0.013   0.002   TRP A  63 
 HIS   0.002   0.001   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 4589)
  covalent geometry    : angle       0.74821 ( 6262)
  SS BOND              : bond        0.00799 (    7)
  SS BOND              : angle       2.25158 (   14)
  hydrogen bonds       : bond        0.04567 (   59)
  hydrogen bonds       : angle       5.54024 (  147)
  link_NAG-ASN         : bond        0.00604 (    7)
  link_NAG-ASN         : angle       4.43022 (   21)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  555 LYS cc_start: 0.8662 (mptt) cc_final: 0.8053 (pttt)
  outliers start: 11
  outliers final: 9
  residues processed: 81
  average time/residue: 0.0655
  time to fit residues: 7.0066
Evaluate side-chains
  81 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  378 TYR
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  663 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 30 optimal weight:    0.0040
   chunk 35 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.3980
   chunk 54 optimal weight:    0.8980
   chunk 23 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0040
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.3004

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.117031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.102705 restraints weight = 9528.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.45
r_work: 0.3417 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4603  Z= 0.127
  Angle     :  0.731  13.146   6297  Z= 0.362
  Chirality :  0.048   0.269    739
  Planarity :  0.005   0.059    797
  Dihedral  :  7.254  72.640    758
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 14.52 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 23.68 %
    Favored  : 74.00 %
  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: -3.68 (0.32), residues: 558
  helix: -3.02 (0.75), residues: 31
  sheet: -2.25 (0.53), residues: 106
  loop : -2.66 (0.27), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 631 
 TYR   0.012   0.001   TYR A 505 
 PHE   0.025   0.002   PHE A 132 
 TRP   0.013   0.002   TRP A 630 
 HIS   0.001   0.000   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4589)
  covalent geometry    : angle       0.68725 ( 6262)
  SS BOND              : bond        0.00714 (    7)
  SS BOND              : angle       1.72588 (   14)
  hydrogen bonds       : bond        0.03441 (   59)
  hydrogen bonds       : angle       5.44849 (  147)
  link_NAG-ASN         : bond        0.00685 (    7)
  link_NAG-ASN         : angle       4.15611 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1511.89 seconds
wall clock time: 26 minutes 33.21 seconds (1593.21 seconds total)