Starting phenix.real_space_refine
on Wed Sep 17 05:00:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jd3_61379/09_2025/9jd3_61379_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jd3_61379/09_2025/9jd3_61379.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jd3_61379/09_2025/9jd3_61379.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jd3_61379/09_2025/9jd3_61379.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jd3_61379/09_2025/9jd3_61379_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jd3_61379/09_2025/9jd3_61379_neut.cif"
  }
  resolution = 3.2
  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=   0.042
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: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     Cl      1      4.86       5
     C    3057      2.51       5
     N     655      2.21       5
     O     751      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4496
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4311
          Classifications: {'peptide': 545}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 28, 'TRANS': 516}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 185
          Unusual residues: {' CL': 1, 'CLR': 1, 'D10': 2, 'D12': 3, 'HEX': 7, 'LNK': 1, 'NAG': 1, 'OCT': 4}
          Classifications: {'undetermined': 20, 'water': 7}
          Link IDs: {None: 26}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.52, per 1000 atoms: 0.34
  Number of scatterers: 4496
  At special positions: 0
  Unit cell: (88.62, 67.52, 87.565, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      32     16.00
     O     751      8.00
     N     655      7.00
     C    3057      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 171 " 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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 720 " - " ASN A 190 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 188.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  992

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 1 sheets defined
      77.2% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 54
    Processing helix  chain 'A' and resid 60 through 65
      removed outlier: 3.659A  pdb=" N   VAL A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 4.075A  pdb=" N   TYR A  69 " --> pdb=" O   TRP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 79 through 90
    Processing helix  chain 'A' and resid 90 through 106
    Processing helix  chain 'A' and resid 110 through 117
    Processing helix  chain 'A' and resid 121 through 152
      removed outlier: 4.311A  pdb=" N   TYR A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE A 139 " --> pdb=" O   ASN A 135 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   VAL A 140 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ILE A 141 " --> pdb=" O   TYR A 137 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LEU A 142 " --> pdb=" O   TYR A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 180
      removed outlier: 4.441A  pdb=" N   LYS A 178 " --> pdb=" O   ASP A 174 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LYS A 180 " --> pdb=" O   MET A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 202
    Processing helix  chain 'A' and resid 217 through 237
    Processing helix  chain 'A' and resid 245 through 267
      removed outlier: 4.064A  pdb=" N   THR A 249 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 269 through 279
      removed outlier: 3.646A  pdb=" N   GLY A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 287
      removed outlier: 3.768A  pdb=" N   LEU A 285 " --> pdb=" O   ASP A 281 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU A 286 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ASP A 287 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 281 through 287'
    Processing helix  chain 'A' and resid 287 through 303
      removed outlier: 4.274A  pdb=" N   TRP A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE A 299 " --> pdb=" O   GLY A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 315
      removed outlier: 3.646A  pdb=" N   SER A 311 " --> pdb=" O   GLY A 307 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   TYR A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 356
      removed outlier: 4.031A  pdb=" N   ASP A 325 " --> pdb=" O   ASN A 321 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 362
    Processing helix  chain 'A' and resid 372 through 380
      removed outlier: 3.645A  pdb=" N   MET A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 418
      removed outlier: 3.576A  pdb=" N   TRP A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 443
      removed outlier: 3.536A  pdb=" N   ILE A 430 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA A 433 " --> pdb=" O   GLU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 447
    Processing helix  chain 'A' and resid 448 through 449
      No H-bonds generated for 'chain 'A' and resid 448 through 449'
    Processing helix  chain 'A' and resid 450 through 462
      removed outlier: 3.783A  pdb=" N   VAL A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 482
    Processing helix  chain 'A' and resid 484 through 496
      removed outlier: 3.627A  pdb=" N   GLY A 491 " --> pdb=" O   ASN A 487 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASP A 494 " --> pdb=" O   ASP A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 509
    Processing helix  chain 'A' and resid 510 through 526
    Processing helix  chain 'A' and resid 539 through 555
      removed outlier: 3.697A  pdb=" N   SER A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 568
    Processing helix  chain 'A' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532

    273 hydrogen bonds defined for protein.
    807 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: 0.74

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1059
        1.33 -     1.45: 993
        1.45 -     1.57: 2517
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 4615
  Sorted by residual:
  bond pdb=" N   GLU A 591 "
       pdb=" CA  GLU A 591 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.15e-02 7.56e+03 8.53e+00
  bond pdb=" N   ILE A 196 "
       pdb=" CA  ILE A 196 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.59e+00
  bond pdb=" N   VAL A 590 "
       pdb=" CA  VAL A 590 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.19e-02 7.06e+03 7.30e+00
  bond pdb=" N   VAL A 195 "
       pdb=" CA  VAL A 195 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.032 1.19e-02 7.06e+03 7.21e+00
  bond pdb=" N   VAL A 203 "
       pdb=" CA  VAL A 203 "
    ideal  model  delta    sigma   weight residual
    1.460  1.491 -0.031 1.21e-02 6.83e+03 6.74e+00
  ... (remaining 4610 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 6039
        1.55 -     3.09: 173
        3.09 -     4.64: 24
        4.64 -     6.19: 6
        6.19 -     7.73: 4
  Bond angle restraints: 6246
  Sorted by residual:
  angle pdb=" CA  ARG A 583 "
        pdb=" C   ARG A 583 "
        pdb=" O   ARG A 583 "
      ideal   model   delta    sigma   weight residual
     122.41  117.96    4.45 1.21e+00 6.83e-01 1.35e+01
  angle pdb=" N   ARG A 587 "
        pdb=" CA  ARG A 587 "
        pdb=" C   ARG A 587 "
      ideal   model   delta    sigma   weight residual
     113.16  108.65    4.51 1.24e+00 6.50e-01 1.32e+01
  angle pdb=" N   ALA A 589 "
        pdb=" CA  ALA A 589 "
        pdb=" C   ALA A 589 "
      ideal   model   delta    sigma   weight residual
     113.61  108.32    5.29 1.50e+00 4.44e-01 1.24e+01
  angle pdb=" CA  SER A 205 "
        pdb=" C   SER A 205 "
        pdb=" O   SER A 205 "
      ideal   model   delta    sigma   weight residual
     121.84  118.12    3.72 1.16e+00 7.43e-01 1.03e+01
  angle pdb=" N   SER A 205 "
        pdb=" CA  SER A 205 "
        pdb=" C   SER A 205 "
      ideal   model   delta    sigma   weight residual
     111.39  106.98    4.41 1.38e+00 5.25e-01 1.02e+01
  ... (remaining 6241 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.40: 2335
       14.40 -    28.81: 256
       28.81 -    43.21: 70
       43.21 -    57.62: 15
       57.62 -    72.02: 5
  Dihedral angle restraints: 2681
    sinusoidal: 1113
      harmonic: 1568
  Sorted by residual:
  dihedral pdb=" CB  MET A 309 "
           pdb=" CG  MET A 309 "
           pdb=" SD  MET A 309 "
           pdb=" CE  MET A 309 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  125.73   54.27     3      1.50e+01 4.44e-03 9.27e+00
  dihedral pdb=" CB  MET A 452 "
           pdb=" CG  MET A 452 "
           pdb=" SD  MET A 452 "
           pdb=" CE  MET A 452 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.98  -53.02     3      1.50e+01 4.44e-03 9.17e+00
  dihedral pdb=" CA  LYS A 115 "
           pdb=" CB  LYS A 115 "
           pdb=" CG  LYS A 115 "
           pdb=" CD  LYS A 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -127.63  -52.37     3      1.50e+01 4.44e-03 9.11e+00
  ... (remaining 2678 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.310: 684
       0.310 -    0.620: 0
       0.620 -    0.930: 0
       0.930 -    1.240: 0
       1.240 -    1.550: 1
  Chirality restraints: 685
  Sorted by residual:
  chirality pdb=" C1  NAG A 720 "
            pdb=" ND2 ASN A 190 "
            pdb=" C2  NAG A 720 "
            pdb=" O5  NAG A 720 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -3.95    1.55 2.00e-01 2.50e+01 6.01e+01
  chirality pdb=" CA  ILE A 196 "
            pdb=" N   ILE A 196 "
            pdb=" C   ILE A 196 "
            pdb=" CB  ILE A 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.79e-01
  chirality pdb=" C20 CLR A 718 "
            pdb=" C17 CLR A 718 "
            pdb=" C21 CLR A 718 "
            pdb=" C22 CLR A 718 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.41    0.18 2.00e-01 2.50e+01 8.40e-01
  ... (remaining 682 not shown)

  Planarity restraints: 746
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 190 "   -0.050 2.00e-02 2.50e+03   6.22e-02 4.84e+01
        pdb=" CG  ASN A 190 "    0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 190 "    0.087 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 190 "    0.025 2.00e-02 2.50e+03
        pdb=" C1  NAG A 720 "   -0.089 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 720 "   -0.044 2.00e-02 2.50e+03   3.62e-02 1.64e+01
        pdb=" C7  NAG A 720 "    0.012 2.00e-02 2.50e+03
        pdb=" C8  NAG A 720 "   -0.033 2.00e-02 2.50e+03
        pdb=" N2  NAG A 720 "    0.057 2.00e-02 2.50e+03
        pdb=" O7  NAG A 720 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 583 "   -0.258 9.50e-02 1.11e+02   1.16e-01 8.26e+00
        pdb=" NE  ARG A 583 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 583 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 583 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 583 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 743 not shown)

  Histogram of nonbonded interaction distances:
        1.08 -     1.84: 1
        1.84 -     2.61: 43
        2.61 -     3.37: 6096
        3.37 -     4.14: 10811
        4.14 -     4.90: 21046
  Nonbonded interactions: 37997
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 190 "
            pdb=" C1  NAG A 720 "
     model   vdw
     1.080 2.776
  nonbonded pdb=" OG  SER A 301 "
            pdb="CL    CL A 719 "
     model   vdw
     1.951 3.190
  nonbonded pdb=" OH  TYR A  69 "
            pdb=" OD2 ASP A 459 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" OD1 ASN A 190 "
            pdb=" O5  NAG A 720 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" O   PHE A 342 "
            pdb=" OG  SER A 346 "
     model   vdw
     2.207 3.040
  ... (remaining 37992 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:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.330
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
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      :  0.011   0.715   4618  Z= 0.581
  Angle     :  1.225  65.511   6251  Z= 0.497
  Chirality :  0.073   1.550    685
  Planarity :  0.006   0.116    745
  Dihedral  : 13.320  72.021   1686
  Min Nonbonded Distance : 1.080

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.14 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.35), residues: 541
  helix:  0.59 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.27 (0.44), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 583 
 TYR   0.018   0.001   TYR A 137 
 PHE   0.008   0.001   PHE A  79 
 TRP   0.007   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 4615)
  covalent geometry    : angle       0.61764 ( 6246)
  SS BOND              : bond        0.00142 (    1)
  SS BOND              : angle       1.46454 (    2)
  hydrogen bonds       : bond        0.22539 (  273)
  hydrogen bonds       : angle       7.59176 (  807)
  Misc. bond           : bond        0.00004 (    1)
  link_NAG-ASN         : bond        0.71545 (    1)
  link_NAG-ASN         : angle      48.28185 (    3)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  284 ARG cc_start: 0.7029 (mmt-90) cc_final: 0.6680 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0921
  time to fit residues: 9.1135
Evaluate side-chains
  65 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.3980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0970
   chunk 25 optimal weight:    0.0980
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0570
   overall best weight:    0.1496

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 135 ASN
A 297 GLN
A 316 ASN
A 355 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.148205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.114907 restraints weight = 5468.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.19
r_work: 0.3138 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4618  Z= 0.114
  Angle     :  0.554   7.478   6251  Z= 0.277
  Chirality :  0.041   0.275    685
  Planarity :  0.004   0.039    745
  Dihedral  :  6.165  45.780    760
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  6.09 %
    Favored  : 93.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.35), residues: 541
  helix:  1.29 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.10 (0.43), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 201 
 TYR   0.015   0.001   TYR A  69 
 PHE   0.019   0.001   PHE A 338 
 TRP   0.017   0.001   TRP A 470 
 HIS   0.002   0.000   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 4615)
  covalent geometry    : angle       0.54869 ( 6246)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       1.48281 (    2)
  hydrogen bonds       : bond        0.04487 (  273)
  hydrogen bonds       : angle       4.83229 (  807)
  Misc. bond           : bond        0.00009 (    1)
  link_NAG-ASN         : bond        0.00068 (    1)
  link_NAG-ASN         : angle       3.39522 (    3)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8446 (pttm) cc_final: 0.7964 (ptmt)
REVERT: A  168 THR cc_start: 0.8958 (m) cc_final: 0.8737 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 87
  average time/residue: 0.0560
  time to fit residues: 6.8783
Evaluate side-chains
  74 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0010
   chunk 44 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 16 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0000
   overall best weight:    0.3190

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

Flipped N/Q/H residues before XYZ refinement:
A 135 ASN
A 355 GLN
A 567 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.147551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.114157 restraints weight = 5448.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.17
r_work: 0.3145 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4618  Z= 0.114
  Angle     :  0.536   7.276   6251  Z= 0.263
  Chirality :  0.040   0.177    685
  Planarity :  0.004   0.040    745
  Dihedral  :  5.587  42.077    760
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.00 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.35), residues: 541
  helix:  1.41 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.99 (0.44), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 201 
 TYR   0.018   0.001   TYR A 323 
 PHE   0.020   0.001   PHE A 338 
 TRP   0.016   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 4615)
  covalent geometry    : angle       0.53451 ( 6246)
  SS BOND              : bond        0.00184 (    1)
  SS BOND              : angle       1.17814 (    2)
  hydrogen bonds       : bond        0.04031 (  273)
  hydrogen bonds       : angle       4.57900 (  807)
  Misc. bond           : bond        0.00011 (    1)
  link_NAG-ASN         : bond        0.00120 (    1)
  link_NAG-ASN         : angle       1.75278 (    3)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8270 (pttm) cc_final: 0.7278 (mmtt)
REVERT: A  311 SER cc_start: 0.8419 (t) cc_final: 0.8163 (m)
REVERT: A  434 PHE cc_start: 0.8436 (t80) cc_final: 0.8233 (t80)
  outliers start: 6
  outliers final: 2
  residues processed: 80
  average time/residue: 0.0617
  time to fit residues: 6.6421
Evaluate side-chains
  76 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  422 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 355 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.144424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.110939 restraints weight = 5529.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.19
r_work: 0.3067 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4618  Z= 0.161
  Angle     :  0.554   7.194   6251  Z= 0.270
  Chirality :  0.041   0.178    685
  Planarity :  0.004   0.041    745
  Dihedral  :  5.750  41.852    760
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.52 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.35), residues: 541
  helix:  1.42 (0.26), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.05 (0.44), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.018   0.001   TYR A  69 
 PHE   0.017   0.001   PHE A 338 
 TRP   0.015   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 4615)
  covalent geometry    : angle       0.55312 ( 6246)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       1.21410 (    2)
  hydrogen bonds       : bond        0.04027 (  273)
  hydrogen bonds       : angle       4.59530 (  807)
  Misc. bond           : bond        0.00007 (    1)
  link_NAG-ASN         : bond        0.00047 (    1)
  link_NAG-ASN         : angle       1.22557 (    3)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8340 (pttm) cc_final: 0.7901 (ptmt)
REVERT: A  168 THR cc_start: 0.8935 (m) cc_final: 0.8718 (m)
REVERT: A  434 PHE cc_start: 0.8486 (t80) cc_final: 0.8273 (t80)
  outliers start: 4
  outliers final: 1
  residues processed: 74
  average time/residue: 0.0576
  time to fit residues: 5.9556
Evaluate side-chains
  71 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   chunk 36 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0270
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.4838

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.147230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.114498 restraints weight = 5512.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.14
r_work: 0.3082 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4618  Z= 0.122
  Angle     :  0.529   7.027   6251  Z= 0.255
  Chirality :  0.040   0.180    685
  Planarity :  0.004   0.041    745
  Dihedral  :  5.399  39.751    760
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.87 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.35), residues: 541
  helix:  1.50 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.94 (0.44), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 201 
 TYR   0.016   0.001   TYR A  69 
 PHE   0.015   0.001   PHE A 338 
 TRP   0.015   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4615)
  covalent geometry    : angle       0.52797 ( 6246)
  SS BOND              : bond        0.00156 (    1)
  SS BOND              : angle       1.06503 (    2)
  hydrogen bonds       : bond        0.03778 (  273)
  hydrogen bonds       : angle       4.46119 (  807)
  Misc. bond           : bond        0.00002 (    1)
  link_NAG-ASN         : bond        0.00001 (    1)
  link_NAG-ASN         : angle       1.14074 (    3)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8409 (pttm) cc_final: 0.7896 (ptmt)
REVERT: A  168 THR cc_start: 0.8879 (m) cc_final: 0.8640 (m)
REVERT: A  324 ARG cc_start: 0.7378 (mmt-90) cc_final: 0.7093 (mmt-90)
REVERT: A  395 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8411 (mt)
  outliers start: 7
  outliers final: 3
  residues processed: 80
  average time/residue: 0.0579
  time to fit residues: 6.3466
Evaluate side-chains
  72 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  552 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.146677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.114071 restraints weight = 5570.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.13
r_work: 0.3096 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4618  Z= 0.150
  Angle     :  0.551   6.489   6251  Z= 0.267
  Chirality :  0.041   0.180    685
  Planarity :  0.004   0.042    745
  Dihedral  :  5.471  38.833    760
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.52 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.35), residues: 541
  helix:  1.45 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.96 (0.45), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.018   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A 338 
 TRP   0.014   0.001   TRP A 470 
 HIS   0.001   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4615)
  covalent geometry    : angle       0.54948 ( 6246)
  SS BOND              : bond        0.00246 (    1)
  SS BOND              : angle       1.53788 (    2)
  hydrogen bonds       : bond        0.03831 (  273)
  hydrogen bonds       : angle       4.49353 (  807)
  Misc. bond           : bond        0.00003 (    1)
  link_NAG-ASN         : bond        0.00024 (    1)
  link_NAG-ASN         : angle       1.14305 (    3)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8442 (pttm) cc_final: 0.7909 (ptmt)
REVERT: A  168 THR cc_start: 0.8920 (m) cc_final: 0.8668 (m)
REVERT: A  395 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8437 (mt)
  outliers start: 6
  outliers final: 4
  residues processed: 74
  average time/residue: 0.0575
  time to fit residues: 5.9662
Evaluate side-chains
  74 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  552 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.144094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.111002 restraints weight = 5608.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.17
r_work: 0.3088 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4618  Z= 0.149
  Angle     :  0.543   6.409   6251  Z= 0.262
  Chirality :  0.040   0.181    685
  Planarity :  0.004   0.042    745
  Dihedral  :  5.481  37.564    760
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.39 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.35), residues: 541
  helix:  1.46 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.00 (0.45), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.018   0.001   TYR A  69 
 PHE   0.011   0.001   PHE A 338 
 TRP   0.014   0.001   TRP A 470 
 HIS   0.001   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4615)
  covalent geometry    : angle       0.54173 ( 6246)
  SS BOND              : bond        0.00227 (    1)
  SS BOND              : angle       1.39096 (    2)
  hydrogen bonds       : bond        0.03791 (  273)
  hydrogen bonds       : angle       4.46086 (  807)
  Misc. bond           : bond        0.00001 (    1)
  link_NAG-ASN         : bond        0.00003 (    1)
  link_NAG-ASN         : angle       1.15957 (    3)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8451 (pttm) cc_final: 0.7902 (ptmt)
REVERT: A  395 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8419 (mt)
  outliers start: 8
  outliers final: 7
  residues processed: 75
  average time/residue: 0.0554
  time to fit residues: 5.8378
Evaluate side-chains
  76 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  552 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.144544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.110845 restraints weight = 5626.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.19
r_work: 0.3097 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4618  Z= 0.154
  Angle     :  0.559   7.250   6251  Z= 0.268
  Chirality :  0.041   0.181    685
  Planarity :  0.004   0.042    745
  Dihedral  :  5.523  37.250    760
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.26 %
    Favored  : 85.00 %
  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 aren not related in a simple way.
  whole:  1.03 (0.35), residues: 541
  helix:  1.43 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.01 (0.45), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.019   0.001   TYR A  69 
 PHE   0.010   0.001   PHE A 338 
 TRP   0.014   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 4615)
  covalent geometry    : angle       0.55828 ( 6246)
  SS BOND              : bond        0.00183 (    1)
  SS BOND              : angle       1.48735 (    2)
  hydrogen bonds       : bond        0.03833 (  273)
  hydrogen bonds       : angle       4.49421 (  807)
  Misc. bond           : bond        0.00003 (    1)
  link_NAG-ASN         : bond        0.00005 (    1)
  link_NAG-ASN         : angle       1.09571 (    3)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8385 (pttm) cc_final: 0.7915 (ptmt)
REVERT: A  395 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8391 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0579
  time to fit residues: 6.3298
Evaluate side-chains
  77 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  552 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    0.0570
   chunk 48 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.5098

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.145451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.112327 restraints weight = 5533.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.16
r_work: 0.3104 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4618  Z= 0.126
  Angle     :  0.551   7.465   6251  Z= 0.264
  Chirality :  0.040   0.182    685
  Planarity :  0.004   0.042    745
  Dihedral  :  5.300  34.892    760
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.04 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.35), residues: 541
  helix:  1.50 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.03 (0.44), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  66 
 TYR   0.015   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A 338 
 TRP   0.014   0.001   TRP A 470 
 HIS   0.001   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4615)
  covalent geometry    : angle       0.55028 ( 6246)
  SS BOND              : bond        0.00206 (    1)
  SS BOND              : angle       1.27559 (    2)
  hydrogen bonds       : bond        0.03659 (  273)
  hydrogen bonds       : angle       4.42293 (  807)
  Misc. bond           : bond        0.00003 (    1)
  link_NAG-ASN         : bond        0.00093 (    1)
  link_NAG-ASN         : angle       1.03345 (    3)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8331 (pttm) cc_final: 0.7885 (ptmt)
REVERT: A  395 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8382 (mt)
  outliers start: 8
  outliers final: 7
  residues processed: 79
  average time/residue: 0.0573
  time to fit residues: 6.3569
Evaluate side-chains
  79 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  552 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    0.0170
   chunk 45 optimal weight:    0.0870
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
A 355 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.146916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.113363 restraints weight = 5579.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.19
r_work: 0.3085 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4618  Z= 0.118
  Angle     :  0.555   8.220   6251  Z= 0.265
  Chirality :  0.040   0.182    685
  Planarity :  0.004   0.041    745
  Dihedral  :  5.129  34.800    760
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.04 %
    Favored  : 85.00 %
  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 aren not related in a simple way.
  whole:  1.14 (0.35), residues: 541
  helix:  1.52 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.01 (0.45), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  66 
 TYR   0.015   0.001   TYR A  69 
 PHE   0.014   0.001   PHE A 338 
 TRP   0.014   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4615)
  covalent geometry    : angle       0.55383 ( 6246)
  SS BOND              : bond        0.00112 (    1)
  SS BOND              : angle       1.43273 (    2)
  hydrogen bonds       : bond        0.03620 (  273)
  hydrogen bonds       : angle       4.38518 (  807)
  Misc. bond           : bond        0.00004 (    1)
  link_NAG-ASN         : bond        0.00077 (    1)
  link_NAG-ASN         : angle       1.02318 (    3)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8315 (pttm) cc_final: 0.7850 (ptmt)
REVERT: A  395 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8343 (mt)
  outliers start: 9
  outliers final: 6
  residues processed: 78
  average time/residue: 0.0557
  time to fit residues: 6.0420
Evaluate side-chains
  77 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  355 GLN
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  552 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 21 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0030
   chunk 43 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0030
   chunk 24 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0980
   chunk 8 optimal weight:    0.3980
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0170
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.0416

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

Flipped N/Q/H residues before XYZ refinement:
A 321 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.151221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.118484 restraints weight = 5489.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.18
r_work: 0.3160 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4618  Z= 0.099
  Angle     :  0.530   8.433   6251  Z= 0.255
  Chirality :  0.038   0.184    685
  Planarity :  0.004   0.040    745
  Dihedral  :  4.627  35.123    760
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.83 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.35), residues: 541
  helix:  1.69 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.96 (0.45), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.012   0.001   TYR A 137 
 PHE   0.018   0.001   PHE A 338 
 TRP   0.016   0.001   TRP A 470 
 HIS   0.001   0.000   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 4615)
  covalent geometry    : angle       0.52982 ( 6246)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       1.17264 (    2)
  hydrogen bonds       : bond        0.03379 (  273)
  hydrogen bonds       : angle       4.24384 (  807)
  Misc. bond           : bond        0.00016 (    1)
  link_NAG-ASN         : bond        0.00161 (    1)
  link_NAG-ASN         : angle       0.88779 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1265.01 seconds
wall clock time: 22 minutes 29.03 seconds (1349.03 seconds total)