Starting phenix.real_space_refine
on Wed Sep 17 04:18:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b1j_44081/09_2025/9b1j_44081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b1j_44081/09_2025/9b1j_44081.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b1j_44081/09_2025/9b1j_44081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b1j_44081/09_2025/9b1j_44081.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b1j_44081/09_2025/9b1j_44081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b1j_44081/09_2025/9b1j_44081.map"
  }
  resolution = 3.0
  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=   0.032
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
     P       1      5.49       5
     S      30      5.16       5
     C    2570      2.51       5
     N     666      2.21       5
     O     686      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3953
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 3922
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 31
          Unusual residues: {'NAG': 1, 'PO4': 1, 'URC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.28, per 1000 atoms: 0.32
  Number of scatterers: 3953
  At special positions: 0
  Unit cell: (57.761, 90.211, 99.946, 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)
     S      30     16.00
     P       1     15.00
     O     686      8.00
     N     666      7.00
     C    2570      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  85 " - pdb=" SG  CYS A 136 " 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 A 601 " - " ASN A  56 "
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 240.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  950

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 2 sheets defined
      81.9% alpha, 1.6% 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 4 through 11
    Processing helix  chain 'A' and resid 14 through 37
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 65 through 74
    Processing helix  chain 'A' and resid 92 through 96
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 3.732A  pdb=" N   TRP A 105 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 127 through 133
    Processing helix  chain 'A' and resid 135 through 139
    Processing helix  chain 'A' and resid 140 through 168
      removed outlier: 3.745A  pdb=" N   GLY A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      Proline residue:  A 162  - end of helix
    Processing helix  chain 'A' and resid 168 through 189
      removed outlier: 3.536A  pdb=" N   VAL A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A 189 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 221
      removed outlier: 3.560A  pdb=" N   ALA A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLY A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLY A 215 " --> pdb=" O   MET A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
      removed outlier: 6.174A  pdb=" N   ARG A 225 " --> pdb=" O   THR A 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 222 through 225'
    Processing helix  chain 'A' and resid 226 through 252
      removed outlier: 4.277A  pdb=" N   PHE A 238 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   SER A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLY A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLY A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 264
    Processing helix  chain 'A' and resid 264 through 274
      removed outlier: 4.102A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   TRP A 274 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 286
    Processing helix  chain 'A' and resid 288 through 303
      removed outlier: 3.603A  pdb=" N   GLN A 294 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL A 299 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 310
      removed outlier: 3.975A  pdb=" N   ALA A 308 " --> pdb=" O   HIS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 319
    Processing helix  chain 'A' and resid 320 through 327
      removed outlier: 3.882A  pdb=" N   VAL A 324 " --> pdb=" O   VAL A 320 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ALA A 325 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 339
      removed outlier: 4.173A  pdb=" N   PHE A 337 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 364
      removed outlier: 4.642A  pdb=" N   PHE A 344 " --> pdb=" O   PRO A 340 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ARG A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE A 356 " --> pdb=" O   CYS A 352 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLY A 357 " --> pdb=" O   TRP A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 373 through 384
    Processing helix  chain 'A' and resid 384 through 399
    Processing helix  chain 'A' and resid 400 through 422
      removed outlier: 4.053A  pdb=" N   THR A 420 " --> pdb=" O   ILE A 416 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A 421 " --> pdb=" O   LEU A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 452
      removed outlier: 3.695A  pdb=" N   THR A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 482
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'A' and resid 483 through 489
      removed outlier: 4.042A  pdb=" N   VAL A 487 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 509
      removed outlier: 4.145A  pdb=" N   LEU A 494 " --> pdb=" O   PRO A 490 " (cutoff:3.500A)
      Proline residue:  A 501  - end of helix
      removed outlier: 3.699A  pdb=" N   LEU A 509 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88

    268 hydrogen bonds defined for protein.
    768 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: 0.73

  Time building geometry restraints manager: 0.42 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: 1241
        1.34 -     1.46: 920
        1.46 -     1.58: 1844
        1.58 -     1.70: 0
        1.70 -     1.82: 47
  Bond restraints: 4052
  Sorted by residual:
  bond pdb=" C2  URC A 602 "
       pdb=" O11 URC A 602 "
    ideal  model  delta    sigma   weight residual
    1.213  1.364 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" C8  URC A 602 "
       pdb=" O24 URC A 602 "
    ideal  model  delta    sigma   weight residual
    1.215  1.353 -0.138 2.00e-02 2.50e+03 4.77e+01
  bond pdb=" C4  URC A 602 "
       pdb=" C5  URC A 602 "
    ideal  model  delta    sigma   weight residual
    1.358  1.495 -0.137 2.00e-02 2.50e+03 4.69e+01
  bond pdb=" C6  URC A 602 "
       pdb=" O13 URC A 602 "
    ideal  model  delta    sigma   weight residual
    1.218  1.348 -0.130 2.00e-02 2.50e+03 4.21e+01
  bond pdb=" C8  URC A 602 "
       pdb=" N7  URC A 602 "
    ideal  model  delta    sigma   weight residual
    1.360  1.435 -0.075 2.00e-02 2.50e+03 1.42e+01
  ... (remaining 4047 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 5453
        2.71 -     5.42: 61
        5.42 -     8.13: 8
        8.13 -    10.84: 4
       10.84 -    13.55: 3
  Bond angle restraints: 5529
  Sorted by residual:
  angle pdb=" N1  URC A 602 "
        pdb=" C2  URC A 602 "
        pdb=" N3  URC A 602 "
      ideal   model   delta    sigma   weight residual
     114.62  128.17  -13.55 3.00e+00 1.11e-01 2.04e+01
  angle pdb=" N7  URC A 602 "
        pdb=" C8  URC A 602 "
        pdb=" N9  URC A 602 "
      ideal   model   delta    sigma   weight residual
     104.73  116.67  -11.94 3.00e+00 1.11e-01 1.58e+01
  angle pdb=" C2  URC A 602 "
        pdb=" N1  URC A 602 "
        pdb=" C6  URC A 602 "
      ideal   model   delta    sigma   weight residual
     129.31  117.54   11.77 3.00e+00 1.11e-01 1.54e+01
  angle pdb=" CA  ARG A 473 "
        pdb=" CB  ARG A 473 "
        pdb=" CG  ARG A 473 "
      ideal   model   delta    sigma   weight residual
     114.10  107.00    7.10 2.00e+00 2.50e-01 1.26e+01
  angle pdb=" C5  URC A 602 "
        pdb=" C6  URC A 602 "
        pdb=" N1  URC A 602 "
      ideal   model   delta    sigma   weight residual
     111.19  121.50  -10.31 3.00e+00 1.11e-01 1.18e+01
  ... (remaining 5524 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.05: 2229
       16.05 -    32.11: 131
       32.11 -    48.16: 21
       48.16 -    64.22: 7
       64.22 -    80.27: 3
  Dihedral angle restraints: 2391
    sinusoidal: 919
      harmonic: 1472
  Sorted by residual:
  dihedral pdb=" CA  GLU A  38 "
           pdb=" C   GLU A  38 "
           pdb=" N   ASN A  39 "
           pdb=" CA  ASN A  39 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.07   22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  PHE A 361 "
           pdb=" C   PHE A 361 "
           pdb=" N   GLY A 362 "
           pdb=" CA  GLY A 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.84   20.16     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  PRO A 457 "
           pdb=" C   PRO A 457 "
           pdb=" N   THR A 458 "
           pdb=" CA  THR A 458 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.70  -16.30     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 2388 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 356
       0.026 -    0.051: 176
       0.051 -    0.077: 74
       0.077 -    0.103: 31
       0.103 -    0.128: 14
  Chirality restraints: 651
  Sorted by residual:
  chirality pdb=" CA  PRO A  52 "
            pdb=" N   PRO A  52 "
            pdb=" C   PRO A  52 "
            pdb=" CB  PRO A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  PRO A 501 "
            pdb=" N   PRO A 501 "
            pdb=" C   PRO A 501 "
            pdb=" CB  PRO A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.84e-01
  chirality pdb=" CA  TYR A 272 "
            pdb=" N   TYR A 272 "
            pdb=" C   TYR A 272 "
            pdb=" CB  TYR A 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 648 not shown)

  Planarity restraints: 686
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 358 "    0.008 2.00e-02 2.50e+03   1.57e-02 2.48e+00
        pdb=" C   PHE A 358 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   PHE A 358 "    0.010 2.00e-02 2.50e+03
        pdb=" N   THR A 359 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 297 "   -0.008 2.00e-02 2.50e+03   1.51e-02 2.29e+00
        pdb=" C   ARG A 297 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ARG A 297 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A 298 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 483 "   -0.116 9.50e-02 1.11e+02   5.18e-02 1.65e+00
        pdb=" NE  ARG A 483 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 483 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 483 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 483 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 683 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1557
        2.89 -     3.39: 3985
        3.39 -     3.90: 6535
        3.90 -     4.40: 7587
        4.40 -     4.90: 12585
  Nonbonded interactions: 32249
  Sorted by model distance:
  nonbonded pdb=" O   TRP A  30 "
            pdb=" OG1 THR A  33 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" OG  SER A 239 "
            pdb=" OD2 ASP A 385 "
     model   vdw
     2.409 3.040
  nonbonded pdb=" OE1 GLU A 220 "
            pdb=" OG  SER A 279 "
     model   vdw
     2.450 3.040
  nonbonded pdb=" NE  ARG A 473 "
            pdb=" O3  PO4 A 603 "
     model   vdw
     2.467 3.120
  nonbonded pdb=" OD1 ASN A  56 "
            pdb=" OG1 THR A  58 "
     model   vdw
     2.494 3.040
  ... (remaining 32244 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:             4.080
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.010
  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:11.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
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      :  0.006   0.151   4055  Z= 0.322
  Angle     :  0.836  13.548   5536  Z= 0.410
  Chirality :  0.040   0.128    651
  Planarity :  0.005   0.052    685
  Dihedral  : 11.220  80.271   1435
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 1.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  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:  0.31 (0.36), residues: 513
  helix:  0.01 (0.26), residues: 358
  sheet: -1.68 (1.59), residues: 10
  loop :  1.41 (0.55), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 430 
 TYR   0.020   0.002   TYR A 272 
 PHE   0.015   0.002   PHE A 356 
 TRP   0.014   0.001   TRP A  50 
 HIS   0.004   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00646 ( 4052)
  covalent geometry    : angle       0.83327 ( 5529)
  SS BOND              : bond        0.00286 (    2)
  SS BOND              : angle       2.51881 (    4)
  hydrogen bonds       : bond        0.13468 (  268)
  hydrogen bonds       : angle       5.75888 (  768)
  link_NAG-ASN         : bond        0.00805 (    1)
  link_NAG-ASN         : angle       0.30345 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  115 ASP cc_start: 0.8474 (m-30) cc_final: 0.8099 (m-30)
REVERT: A  126 SER cc_start: 0.8831 (t) cc_final: 0.8425 (m)
REVERT: A  144 MET cc_start: 0.7503 (ttm) cc_final: 0.7286 (ttt)
REVERT: A  225 ARG cc_start: 0.6953 (ptt180) cc_final: 0.6463 (ptp-170)
REVERT: A  285 ILE cc_start: 0.7800 (mt) cc_final: 0.7474 (mp)
REVERT: A  295 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6880 (mm-30)
REVERT: A  390 MET cc_start: 0.7370 (mmm) cc_final: 0.7162 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.4645
  time to fit residues: 29.4489
Evaluate side-chains
  53 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    0.0670
   chunk 25 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.4318

-------------------------------------------------------------------------------
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 = 0.4127 r_free = 0.4127 target = 0.195639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.145373 restraints weight = 4082.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.93
r_work: 0.3447 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4055  Z= 0.136
  Angle     :  0.559   6.660   5536  Z= 0.286
  Chirality :  0.041   0.127    651
  Planarity :  0.005   0.040    685
  Dihedral  :  4.235  16.441    569
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.17 %
    Favored  : 90.62 %
  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:  1.67 (0.37), residues: 513
  helix:  1.04 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop :  1.66 (0.54), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 461 
 TYR   0.021   0.002   TYR A 272 
 PHE   0.013   0.002   PHE A 354 
 TRP   0.011   0.001   TRP A  50 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4052)
  covalent geometry    : angle       0.55778 ( 5529)
  SS BOND              : bond        0.00044 (    2)
  SS BOND              : angle       1.72836 (    4)
  hydrogen bonds       : bond        0.04968 (  268)
  hydrogen bonds       : angle       4.49101 (  768)
  link_NAG-ASN         : bond        0.00472 (    1)
  link_NAG-ASN         : angle       0.38850 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  115 ASP cc_start: 0.8284 (m-30) cc_final: 0.8067 (m-30)
REVERT: A  126 SER cc_start: 0.8890 (t) cc_final: 0.8404 (m)
REVERT: A  225 ARG cc_start: 0.7080 (ptt180) cc_final: 0.6524 (ptp-170)
REVERT: A  285 ILE cc_start: 0.7879 (mt) cc_final: 0.7540 (mt)
REVERT: A  295 GLU cc_start: 0.7255 (mt-10) cc_final: 0.7040 (mm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 54
  average time/residue: 0.4443
  time to fit residues: 25.1929
Evaluate side-chains
  47 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  272 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0980
   chunk 19 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.188774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.140407 restraints weight = 4122.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.82
r_work: 0.3408 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4055  Z= 0.189
  Angle     :  0.615   6.654   5536  Z= 0.310
  Chirality :  0.042   0.122    651
  Planarity :  0.005   0.042    685
  Dihedral  :  4.064  14.574    569
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  :  8.89 %
    Favored  : 88.46 %
  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:  1.20 (0.37), residues: 513
  helix:  0.92 (0.27), residues: 356
  sheet: -2.00 (1.72), residues: 10
  loop :  1.08 (0.55), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 473 
 TYR   0.016   0.003   TYR A 497 
 PHE   0.018   0.002   PHE A 354 
 TRP   0.012   0.001   TRP A  50 
 HIS   0.004   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 4052)
  covalent geometry    : angle       0.61382 ( 5529)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       1.61207 (    4)
  hydrogen bonds       : bond        0.05673 (  268)
  hydrogen bonds       : angle       4.55799 (  768)
  link_NAG-ASN         : bond        0.00221 (    1)
  link_NAG-ASN         : angle       1.01081 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8906 (t) cc_final: 0.8401 (m)
REVERT: A  183 MET cc_start: 0.8558 (mmt) cc_final: 0.8294 (mmt)
REVERT: A  225 ARG cc_start: 0.7178 (ptt180) cc_final: 0.6602 (ptp-170)
REVERT: A  285 ILE cc_start: 0.7873 (mt) cc_final: 0.7529 (mt)
REVERT: A  401 ARG cc_start: 0.4051 (OUTLIER) cc_final: 0.3280 (mmt180)
  outliers start: 11
  outliers final: 6
  residues processed: 47
  average time/residue: 0.4592
  time to fit residues: 22.6013
Evaluate side-chains
  49 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  401 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 49 optimal weight:    0.3980
   chunk 25 optimal weight:    0.2980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.4103 r_free = 0.4103 target = 0.193012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.144882 restraints weight = 4068.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.84
r_work: 0.3434 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4055  Z= 0.119
  Angle     :  0.523   6.155   5536  Z= 0.261
  Chirality :  0.039   0.119    651
  Planarity :  0.004   0.037    685
  Dihedral  :  3.801  14.798    569
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.82 %
    Favored  : 87.74 %
  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 aren not related in a simple way.
  whole:  1.53 (0.37), residues: 513
  helix:  1.17 (0.27), residues: 364
  sheet: -2.36 (1.55), residues: 10
  loop :  1.21 (0.57), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.015   0.002   TYR A 272 
 PHE   0.014   0.001   PHE A 354 
 TRP   0.010   0.001   TRP A 175 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4052)
  covalent geometry    : angle       0.52142 ( 5529)
  SS BOND              : bond        0.00116 (    2)
  SS BOND              : angle       1.39930 (    4)
  hydrogen bonds       : bond        0.04405 (  268)
  hydrogen bonds       : angle       4.27203 (  768)
  link_NAG-ASN         : bond        0.00253 (    1)
  link_NAG-ASN         : angle       0.78238 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8866 (t) cc_final: 0.8360 (m)
REVERT: A  219 MET cc_start: 0.7205 (mtp) cc_final: 0.6991 (mtp)
REVERT: A  225 ARG cc_start: 0.7150 (ptt180) cc_final: 0.6614 (ptp-170)
REVERT: A  285 ILE cc_start: 0.7774 (mt) cc_final: 0.7466 (mt)
REVERT: A  312 THR cc_start: 0.7003 (OUTLIER) cc_final: 0.6760 (t)
REVERT: A  446 THR cc_start: 0.6710 (m) cc_final: 0.6361 (p)
  outliers start: 6
  outliers final: 2
  residues processed: 45
  average time/residue: 0.4101
  time to fit residues: 19.4175
Evaluate side-chains
  41 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  384 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0980
   chunk 24 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0050
   chunk 0 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0570
   chunk 34 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.2712

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.194668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.148402 restraints weight = 4115.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 1.77
r_work: 0.3539 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4055  Z= 0.108
  Angle     :  0.507   7.538   5536  Z= 0.249
  Chirality :  0.038   0.121    651
  Planarity :  0.004   0.036    685
  Dihedral  :  3.565  13.072    569
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.10 %
    Favored  : 87.74 %
  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 aren not related in a simple way.
  whole:  2.24 (0.37), residues: 513
  helix:  1.83 (0.27), residues: 344
  sheet: -2.57 (1.50), residues: 10
  loop :  1.24 (0.54), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.021   0.002   TYR A 272 
 PHE   0.013   0.001   PHE A 354 
 TRP   0.008   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 4052)
  covalent geometry    : angle       0.50604 ( 5529)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       1.24984 (    4)
  hydrogen bonds       : bond        0.03975 (  268)
  hydrogen bonds       : angle       4.13204 (  768)
  link_NAG-ASN         : bond        0.00198 (    1)
  link_NAG-ASN         : angle       0.77804 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8834 (t) cc_final: 0.8326 (m)
REVERT: A  219 MET cc_start: 0.7116 (mtp) cc_final: 0.6898 (mtp)
REVERT: A  225 ARG cc_start: 0.7166 (ptt180) cc_final: 0.6588 (ptp-170)
REVERT: A  312 THR cc_start: 0.6994 (OUTLIER) cc_final: 0.6750 (t)
REVERT: A  401 ARG cc_start: 0.4001 (OUTLIER) cc_final: 0.3237 (mpt180)
REVERT: A  446 THR cc_start: 0.6705 (m) cc_final: 0.6335 (p)
  outliers start: 9
  outliers final: 4
  residues processed: 50
  average time/residue: 0.4473
  time to fit residues: 23.3383
Evaluate side-chains
  42 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  401 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   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 = 0.4106 r_free = 0.4106 target = 0.193441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.147138 restraints weight = 4176.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.77
r_work: 0.3431 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4055  Z= 0.143
  Angle     :  0.545   7.938   5536  Z= 0.269
  Chirality :  0.040   0.118    651
  Planarity :  0.004   0.037    685
  Dihedral  :  3.609  13.055    569
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 10.58 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.37), residues: 513
  helix:  1.60 (0.27), residues: 350
  sheet: -2.64 (1.57), residues: 10
  loop :  1.36 (0.55), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 473 
 TYR   0.015   0.002   TYR A 272 
 PHE   0.015   0.002   PHE A 354 
 TRP   0.008   0.001   TRP A  50 
 HIS   0.003   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4052)
  covalent geometry    : angle       0.54453 ( 5529)
  SS BOND              : bond        0.00200 (    2)
  SS BOND              : angle       1.20542 (    4)
  hydrogen bonds       : bond        0.04625 (  268)
  hydrogen bonds       : angle       4.21866 (  768)
  link_NAG-ASN         : bond        0.00199 (    1)
  link_NAG-ASN         : angle       0.83714 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8870 (t) cc_final: 0.8338 (m)
REVERT: A  219 MET cc_start: 0.7096 (mtp) cc_final: 0.6858 (mtp)
REVERT: A  225 ARG cc_start: 0.7187 (ptt180) cc_final: 0.6845 (ptp-170)
REVERT: A  401 ARG cc_start: 0.3923 (OUTLIER) cc_final: 0.3230 (mmt180)
  outliers start: 11
  outliers final: 6
  residues processed: 43
  average time/residue: 0.4550
  time to fit residues: 20.3707
Evaluate side-chains
  40 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  401 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 28 optimal weight:    0.3980
   chunk 37 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.191977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.146462 restraints weight = 4216.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.75
r_work: 0.3460 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4055  Z= 0.133
  Angle     :  0.533   7.605   5536  Z= 0.263
  Chirality :  0.039   0.119    651
  Planarity :  0.004   0.036    685
  Dihedral  :  3.575  13.140    569
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 11.06 %
    Favored  : 86.54 %
  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:  2.09 (0.38), residues: 513
  helix:  1.63 (0.27), residues: 350
  sheet: -2.56 (1.70), residues: 10
  loop :  1.39 (0.55), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 473 
 TYR   0.016   0.002   TYR A 272 
 PHE   0.014   0.001   PHE A 354 
 TRP   0.008   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4052)
  covalent geometry    : angle       0.53238 ( 5529)
  SS BOND              : bond        0.00143 (    2)
  SS BOND              : angle       1.27366 (    4)
  hydrogen bonds       : bond        0.04467 (  268)
  hydrogen bonds       : angle       4.18957 (  768)
  link_NAG-ASN         : bond        0.00200 (    1)
  link_NAG-ASN         : angle       0.82832 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8884 (t) cc_final: 0.8352 (m)
REVERT: A  219 MET cc_start: 0.7186 (mtp) cc_final: 0.6942 (mtp)
REVERT: A  401 ARG cc_start: 0.4000 (OUTLIER) cc_final: 0.3220 (mmt180)
REVERT: A  446 THR cc_start: 0.6745 (m) cc_final: 0.6367 (p)
REVERT: A  454 GLU cc_start: 0.4792 (OUTLIER) cc_final: 0.4580 (mm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 44
  average time/residue: 0.3903
  time to fit residues: 18.0103
Evaluate side-chains
  39 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  401 ARG
Chi-restraints excluded: chain A residue  454 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 48 optimal weight:    0.2980
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4084 r_free = 0.4084 target = 0.191312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.145847 restraints weight = 4190.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.74
r_work: 0.3439 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4055  Z= 0.142
  Angle     :  0.551   8.926   5536  Z= 0.271
  Chirality :  0.040   0.118    651
  Planarity :  0.004   0.036    685
  Dihedral  :  3.589  13.158    569
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.78 %
    Favored  : 86.54 %
  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:  2.04 (0.38), residues: 513
  helix:  1.59 (0.27), residues: 350
  sheet: -2.60 (1.70), residues: 10
  loop :  1.37 (0.56), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 473 
 TYR   0.020   0.002   TYR A 272 
 PHE   0.014   0.002   PHE A 354 
 TRP   0.009   0.001   TRP A  50 
 HIS   0.003   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 4052)
  covalent geometry    : angle       0.54994 ( 5529)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       1.28859 (    4)
  hydrogen bonds       : bond        0.04624 (  268)
  hydrogen bonds       : angle       4.22463 (  768)
  link_NAG-ASN         : bond        0.00188 (    1)
  link_NAG-ASN         : angle       0.84987 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8891 (t) cc_final: 0.8362 (m)
REVERT: A  219 MET cc_start: 0.7210 (mtp) cc_final: 0.6964 (mtp)
REVERT: A  401 ARG cc_start: 0.3998 (OUTLIER) cc_final: 0.3284 (mmt180)
  outliers start: 7
  outliers final: 6
  residues processed: 38
  average time/residue: 0.4269
  time to fit residues: 17.0523
Evaluate side-chains
  37 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  401 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:    0.1980
   chunk 41 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0980
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0000
   chunk 26 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0870
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.1562

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.196310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.151212 restraints weight = 4111.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 1.75
r_work: 0.3557 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4055  Z= 0.102
  Angle     :  0.505   8.395   5536  Z= 0.246
  Chirality :  0.037   0.122    651
  Planarity :  0.004   0.034    685
  Dihedral  :  3.446  12.982    569
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 12.74 %
    Favored  : 86.54 %
  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:  2.49 (0.38), residues: 513
  helix:  2.00 (0.28), residues: 344
  sheet: -2.19 (1.75), residues: 10
  loop :  1.37 (0.55), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.025   0.002   TYR A 272 
 PHE   0.009   0.001   PHE A 354 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 4052)
  covalent geometry    : angle       0.50428 ( 5529)
  SS BOND              : bond        0.00099 (    2)
  SS BOND              : angle       1.18365 (    4)
  hydrogen bonds       : bond        0.03755 (  268)
  hydrogen bonds       : angle       4.04881 (  768)
  link_NAG-ASN         : bond        0.00207 (    1)
  link_NAG-ASN         : angle       0.71914 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  219 MET cc_start: 0.7141 (mtp) cc_final: 0.6903 (mtp)
REVERT: A  312 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6790 (t)
REVERT: A  401 ARG cc_start: 0.4146 (OUTLIER) cc_final: 0.3340 (mmt180)
REVERT: A  446 THR cc_start: 0.6657 (m) cc_final: 0.6277 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 38
  average time/residue: 0.4825
  time to fit residues: 19.1763
Evaluate side-chains
  34 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  401 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0470
   chunk 22 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0270
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.4936

-------------------------------------------------------------------------------
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 = 0.4109 r_free = 0.4109 target = 0.193817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.148449 restraints weight = 4107.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.75
r_work: 0.3461 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4055  Z= 0.121
  Angle     :  0.538   9.515   5536  Z= 0.261
  Chirality :  0.039   0.131    651
  Planarity :  0.004   0.035    685
  Dihedral  :  3.444  12.369    569
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.50 %
    Favored  : 86.30 %
  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:  2.32 (0.38), residues: 513
  helix:  1.87 (0.27), residues: 346
  sheet: -2.50 (1.68), residues: 10
  loop :  1.31 (0.56), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.020   0.002   TYR A 272 
 PHE   0.013   0.001   PHE A 354 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4052)
  covalent geometry    : angle       0.53718 ( 5529)
  SS BOND              : bond        0.00118 (    2)
  SS BOND              : angle       1.19829 (    4)
  hydrogen bonds       : bond        0.04179 (  268)
  hydrogen bonds       : angle       4.09997 (  768)
  link_NAG-ASN         : bond        0.00167 (    1)
  link_NAG-ASN         : angle       0.75243 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   54 LEU cc_start: 0.6841 (mp) cc_final: 0.6608 (mt)
REVERT: A  126 SER cc_start: 0.8899 (t) cc_final: 0.8388 (m)
REVERT: A  219 MET cc_start: 0.7066 (mtp) cc_final: 0.6837 (mtp)
REVERT: A  401 ARG cc_start: 0.3965 (OUTLIER) cc_final: 0.3205 (mmt180)
REVERT: A  446 THR cc_start: 0.6690 (m) cc_final: 0.6290 (p)
  outliers start: 5
  outliers final: 3
  residues processed: 37
  average time/residue: 0.4625
  time to fit residues: 17.9645
Evaluate side-chains
  36 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  401 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0770
   chunk 34 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    0.2980
   overall best weight:    1.0744

-------------------------------------------------------------------------------
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 = 0.4076 r_free = 0.4076 target = 0.190003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.143869 restraints weight = 4158.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.76
r_work: 0.3409 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4055  Z= 0.182
  Angle     :  0.602   9.156   5536  Z= 0.296
  Chirality :  0.042   0.142    651
  Planarity :  0.005   0.037    685
  Dihedral  :  3.668  13.798    569
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.74 %
    Favored  : 86.30 %
  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:  2.00 (0.38), residues: 513
  helix:  1.53 (0.27), residues: 349
  sheet: -2.74 (1.69), residues: 10
  loop :  1.46 (0.56), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 473 
 TYR   0.016   0.002   TYR A 272 
 PHE   0.017   0.002   PHE A 354 
 TRP   0.009   0.001   TRP A  50 
 HIS   0.003   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 4052)
  covalent geometry    : angle       0.60131 ( 5529)
  SS BOND              : bond        0.00192 (    2)
  SS BOND              : angle       1.36586 (    4)
  hydrogen bonds       : bond        0.05123 (  268)
  hydrogen bonds       : angle       4.30013 (  768)
  link_NAG-ASN         : bond        0.00140 (    1)
  link_NAG-ASN         : angle       0.89940 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1681.52 seconds
wall clock time: 29 minutes 30.89 seconds (1770.89 seconds total)