Starting phenix.real_space_refine
on Fri Aug 22 14:17:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b1n_44085/08_2025/9b1n_44085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b1n_44085/08_2025/9b1n_44085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b1n_44085/08_2025/9b1n_44085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b1n_44085/08_2025/9b1n_44085.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b1n_44085/08_2025/9b1n_44085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b1n_44085/08_2025/9b1n_44085.map"
  }
  resolution = 3.1
  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=   0.000 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    2578      2.51       5
     N     665      2.21       5
     O     681      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3954
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3931
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 515, 3922
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
      Conformer: "B"
        Number of residues, atoms: 515, 3922
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
          bond proxies already assigned to first conformer: 4010
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'NAG': 1, 'VGL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.61, per 1000 atoms: 0.41
  Number of scatterers: 3954
  At special positions: 0
  Unit cell: (55.165, 88.913, 102.542, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O     681      8.00
     N     665      7.00
     C    2578      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 268.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  952

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 2 sheets defined
      82.5% 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 3 through 11
      removed outlier: 3.849A  pdb=" N   LEU A   7 " --> pdb=" O   PHE A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 37
      removed outlier: 3.540A  pdb=" N   SER A  27 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
    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 97
      removed outlier: 3.715A  pdb=" N   ASP A  97 " --> pdb=" O   GLN A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 3.997A  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: 3.756A  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: 3.585A  pdb=" N   VAL A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE A 189 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 220
      removed outlier: 3.613A  pdb=" N   ALA A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLY A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 226 through 252
      removed outlier: 4.193A  pdb=" N  APHE A 238 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   SER A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 3.829A  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 273
      removed outlier: 4.136A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 286
    Processing helix  chain 'A' and resid 288 through 304
    Processing helix  chain 'A' and resid 305 through 311
      removed outlier: 4.063A  pdb=" N   ALA A 308 " --> pdb=" O   HIS A 305 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LYS A 309 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU A 311 " --> pdb=" O   ALA A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 320
    Processing helix  chain 'A' and resid 320 through 325
    Processing helix  chain 'A' and resid 326 through 329
      removed outlier: 3.769A  pdb=" N   GLU A 329 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 326 through 329'
    Processing helix  chain 'A' and resid 333 through 339
      removed outlier: 3.989A  pdb=" N   PHE A 337 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL A 339 " --> pdb=" O   ASP A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 364
      removed outlier: 4.066A  pdb=" N   ARG A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 373 through 384
      removed outlier: 3.848A  pdb=" N   GLY A 382 " --> pdb=" O   GLN A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 399
    Processing helix  chain 'A' and resid 400 through 422
      removed outlier: 3.520A  pdb=" N   THR A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   THR A 420 " --> pdb=" O   ILE A 416 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU A 421 " --> pdb=" O   LEU A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 453
      removed outlier: 3.560A  pdb=" N   ILE A 450 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   SER A 453 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 482
      removed outlier: 3.528A  pdb=" N   ILE A 477 " --> pdb=" O   ARG A 473 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 478 " --> pdb=" O   GLY A 474 " (cutoff:3.500A)
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'A' and resid 483 through 489
      removed outlier: 3.867A  pdb=" N   VAL A 487 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 509
      removed outlier: 3.715A  pdb=" N   LEU A 494 " --> pdb=" O   PRO A 490 " (cutoff:3.500A)
      Proline residue:  A 501  - end of helix
    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

    267 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: 0.62

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 753
        1.33 -     1.45: 1006
        1.45 -     1.58: 2249
        1.58 -     1.70: 0
        1.70 -     1.83: 47
  Bond restraints: 4055
  Sorted by residual:
  bond pdb=" C   ALA A 355 "
       pdb=" O   ALA A 355 "
    ideal  model  delta    sigma   weight residual
    1.237  1.206  0.031 1.17e-02 7.31e+03 6.90e+00
  bond pdb=" C   PHE A 356 "
       pdb=" O   PHE A 356 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.17e-02 7.31e+03 5.64e+00
  bond pdb=" CA  GLY A 357 "
       pdb=" C   GLY A 357 "
    ideal  model  delta    sigma   weight residual
    1.514  1.483  0.032 1.41e-02 5.03e+03 5.06e+00
  bond pdb=" C1  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.58e+00
  bond pdb=" CA  ALA A 355 "
       pdb=" CB  ALA A 355 "
    ideal  model  delta    sigma   weight residual
    1.528  1.497  0.031 1.56e-02 4.11e+03 4.06e+00
  ... (remaining 4050 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 5172
        1.41 -     2.81: 277
        2.81 -     4.22: 66
        4.22 -     5.63: 16
        5.63 -     7.03: 1
  Bond angle restraints: 5532
  Sorted by residual:
  angle pdb=" CA  TYR A 272 "
        pdb=" CB  TYR A 272 "
        pdb=" CG  TYR A 272 "
      ideal   model   delta    sigma   weight residual
     113.90  120.93   -7.03 1.80e+00 3.09e-01 1.53e+01
  angle pdb=" N   ALA A 355 "
        pdb=" CA  ALA A 355 "
        pdb=" C   ALA A 355 "
      ideal   model   delta    sigma   weight residual
     111.28  115.35   -4.07 1.09e+00 8.42e-01 1.40e+01
  angle pdb=" C   PHE A 358 "
        pdb=" N   THR A 359 "
        pdb=" CA  THR A 359 "
      ideal   model   delta    sigma   weight residual
     120.44  115.91    4.53 1.36e+00 5.41e-01 1.11e+01
  angle pdb=" C   VAL A 264 "
        pdb=" CA  VAL A 264 "
        pdb=" CB  VAL A 264 "
      ideal   model   delta    sigma   weight residual
     114.35  111.16    3.19 1.06e+00 8.90e-01 9.07e+00
  angle pdb=" CA  TYR A 451 "
        pdb=" CB  TYR A 451 "
        pdb=" CG  TYR A 451 "
      ideal   model   delta    sigma   weight residual
     113.90  118.78   -4.88 1.80e+00 3.09e-01 7.34e+00
  ... (remaining 5527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 2265
       17.09 -    34.17: 106
       34.17 -    51.26: 20
       51.26 -    68.35: 4
       68.35 -    85.43: 3
  Dihedral angle restraints: 2398
    sinusoidal: 922
      harmonic: 1476
  Sorted by residual:
  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 -154.61  -25.39     0      5.00e+00 4.00e-02 2.58e+01
  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  157.62   22.38     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  LEU A  54 "
           pdb=" C   LEU A  54 "
           pdb=" N   ASP A  55 "
           pdb=" CA  ASP A  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.84  -18.16     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 2395 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 407
       0.033 -    0.066: 168
       0.066 -    0.099: 49
       0.099 -    0.132: 20
       0.132 -    0.165: 8
  Chirality restraints: 652
  Sorted by residual:
  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    2.35    0.17 2.00e-01 2.50e+01 6.83e-01
  chirality pdb=" CB  ILE A 153 "
            pdb=" CA  ILE A 153 "
            pdb=" CG1 ILE A 153 "
            pdb=" CG2 ILE A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.15 2.00e-01 2.50e+01 5.39e-01
  chirality pdb=" CA  PHE A 361 "
            pdb=" N   PHE A 361 "
            pdb=" C   PHE A 361 "
            pdb=" CB  PHE A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.23e-01
  ... (remaining 649 not shown)

  Planarity restraints: 690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 272 "   -0.022 2.00e-02 2.50e+03   1.47e-02 4.30e+00
        pdb=" CG  TYR A 272 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 272 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 272 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 272 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 272 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 272 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 272 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 264 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO A 265 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 265 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 265 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 479 "   -0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO A 480 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 480 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 480 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 687 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 1811
        2.94 -     3.43: 4064
        3.43 -     3.92: 6454
        3.92 -     4.41: 7589
        4.41 -     4.90: 12114
  Nonbonded interactions: 32032
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 239 "
            pdb=" OD2 ASP A 385 "
     model   vdw
     2.454 3.040
  nonbonded pdb=" N   ASP A 290 "
            pdb=" OD1 ASP A 290 "
     model   vdw
     2.522 3.120
  nonbonded pdb=" OE1 GLU A 220 "
            pdb=" OG  SER A 279 "
     model   vdw
     2.525 3.040
  nonbonded pdb=" O   ASP A 366 "
            pdb=" OD1 ASP A 366 "
     model   vdw
     2.530 3.040
  nonbonded pdb=" O   LEU A 417 "
            pdb=" OG1 THR A 420 "
     model   vdw
     2.534 3.040
  ... (remaining 32027 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=0.42 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     6.270
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   4058  Z= 0.246
  Angle     :  0.792   7.034   5539  Z= 0.435
  Chirality :  0.044   0.165    652
  Planarity :  0.006   0.059    689
  Dihedral  : 11.087  85.433   1440
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 0.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  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: -0.18 (0.35), residues: 515
  helix: -0.24 (0.24), residues: 374
  sheet: -0.97 (1.44), residues: 10
  loop :  0.96 (0.59), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 483 
 TYR   0.035   0.003   TYR A 272 
 PHE   0.021   0.003   PHE A 344 
 TRP   0.014   0.002   TRP A  50 
 HIS   0.006   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 4055)
  covalent geometry    : angle       0.78835 ( 5532)
  SS BOND              : bond        0.00174 (    2)
  SS BOND              : angle       2.63698 (    4)
  hydrogen bonds       : bond        0.12426 (  267)
  hydrogen bonds       : angle       5.90331 (  768)
  link_NAG-ASN         : bond        0.01338 (    1)
  link_NAG-ASN         : angle       1.23255 (    3)

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   89 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7257 (ttm110)
REVERT: A   94 GLN cc_start: 0.8386 (pt0) cc_final: 0.8022 (pp30)
REVERT: A  165 ASP cc_start: 0.7938 (m-30) cc_final: 0.7639 (m-30)
REVERT: A  183 MET cc_start: 0.8551 (mmt) cc_final: 0.8278 (mmt)
REVERT: A  281 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.7557 (ttm-80)
REVERT: A  379 MET cc_start: 0.8414 (ttp) cc_final: 0.8208 (ttt)
REVERT: A  497 TYR cc_start: 0.8436 (m-80) cc_final: 0.8153 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0899
  time to fit residues: 7.2636
Evaluate side-chains
  51 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0050
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0370
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.3872

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.178844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.140565 restraints weight = 9890.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 3.11
r_work: 0.3238 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4058  Z= 0.132
  Angle     :  0.601   7.361   5539  Z= 0.300
  Chirality :  0.040   0.131    652
  Planarity :  0.005   0.052    689
  Dihedral  :  4.169  16.455    572
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  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:  1.44 (0.37), residues: 515
  helix:  0.91 (0.26), residues: 373
  sheet:  None (None), residues: 0
  loop :  1.54 (0.57), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 301 
 TYR   0.022   0.002   TYR A 272 
 PHE   0.016   0.002   PHE A 344 
 TRP   0.014   0.001   TRP A  50 
 HIS   0.004   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4055)
  covalent geometry    : angle       0.59539 ( 5532)
  SS BOND              : bond        0.00878 (    2)
  SS BOND              : angle       3.02889 (    4)
  hydrogen bonds       : bond        0.04907 (  267)
  hydrogen bonds       : angle       4.36683 (  768)
  link_NAG-ASN         : bond        0.00320 (    1)
  link_NAG-ASN         : angle       0.71345 (    3)

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  165 ASP cc_start: 0.8014 (m-30) cc_final: 0.7765 (m-30)
REVERT: A  281 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7594 (ttm-80)
REVERT: A  294 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7291 (tp40)
REVERT: A  497 TYR cc_start: 0.8568 (m-80) cc_final: 0.8131 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0613
  time to fit residues: 3.9060
Evaluate side-chains
  43 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 7 optimal weight:    0.0020
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.4388

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.178639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.142957 restraints weight = 10699.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 3.69
r_work: 0.3186 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3391
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3391
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4058  Z= 0.122
  Angle     :  0.560   6.533   5539  Z= 0.276
  Chirality :  0.038   0.135    652
  Planarity :  0.005   0.044    689
  Dihedral  :  3.714  13.000    572
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  6.24 %
    Favored  : 93.53 %
  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:  1.95 (0.37), residues: 515
  helix:  1.31 (0.27), residues: 364
  sheet:  None (None), residues: 0
  loop :  1.62 (0.56), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 169 
 TYR   0.021   0.002   TYR A 272 
 PHE   0.018   0.002   PHE A 344 
 TRP   0.012   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4055)
  covalent geometry    : angle       0.55647 ( 5532)
  SS BOND              : bond        0.00159 (    2)
  SS BOND              : angle       2.33179 (    4)
  hydrogen bonds       : bond        0.04607 (  267)
  hydrogen bonds       : angle       4.18600 (  768)
  link_NAG-ASN         : bond        0.00279 (    1)
  link_NAG-ASN         : angle       0.66872 (    3)

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  165 ASP cc_start: 0.7845 (m-30) cc_final: 0.7541 (m-30)
REVERT: A  281 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7609 (ttm-80)
REVERT: A  294 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7264 (tp40)
REVERT: A  497 TYR cc_start: 0.8579 (m-80) cc_final: 0.8099 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0655
  time to fit residues: 3.8915
Evaluate side-chains
  42 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 31 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 49 optimal weight:    0.3980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 378 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.177378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.140946 restraints weight = 7199.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.29
r_work: 0.3419 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4058  Z= 0.132
  Angle     :  0.570   6.956   5539  Z= 0.279
  Chirality :  0.039   0.131    652
  Planarity :  0.005   0.045    689
  Dihedral  :  3.656  13.173    572
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  7.43 %
    Favored  : 92.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.38), residues: 515
  helix:  1.40 (0.27), residues: 365
  sheet: -1.82 (1.61), residues: 10
  loop :  1.64 (0.58), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 301 
 TYR   0.019   0.002   TYR A 272 
 PHE   0.018   0.002   PHE A 344 
 TRP   0.012   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4055)
  covalent geometry    : angle       0.56717 ( 5532)
  SS BOND              : bond        0.00216 (    2)
  SS BOND              : angle       2.19901 (    4)
  hydrogen bonds       : bond        0.04556 (  267)
  hydrogen bonds       : angle       4.09128 (  768)
  link_NAG-ASN         : bond        0.00112 (    1)
  link_NAG-ASN         : angle       0.82266 (    3)

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  165 ASP cc_start: 0.7965 (m-30) cc_final: 0.7665 (m-30)
REVERT: A  294 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7720 (tp40)
REVERT: A  497 TYR cc_start: 0.8632 (m-80) cc_final: 0.8196 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 51
  average time/residue: 0.0654
  time to fit residues: 4.3774
Evaluate side-chains
  48 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 16 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 = 0.3983 r_free = 0.3983 target = 0.177210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.140921 restraints weight = 7960.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.38
r_work: 0.3277 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4058  Z= 0.139
  Angle     :  0.585   8.324   5539  Z= 0.283
  Chirality :  0.039   0.130    652
  Planarity :  0.004   0.045    689
  Dihedral  :  3.609  13.284    572
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  9.35 %
    Favored  : 90.41 %
  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:  1.94 (0.38), residues: 515
  helix:  1.41 (0.27), residues: 366
  sheet: -1.84 (1.66), residues: 10
  loop :  1.57 (0.57), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 169 
 TYR   0.018   0.002   TYR A 272 
 PHE   0.017   0.002   PHE A 344 
 TRP   0.012   0.001   TRP A  93 
 HIS   0.002   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4055)
  covalent geometry    : angle       0.58206 ( 5532)
  SS BOND              : bond        0.00210 (    2)
  SS BOND              : angle       2.18322 (    4)
  hydrogen bonds       : bond        0.04646 (  267)
  hydrogen bonds       : angle       4.08773 (  768)
  link_NAG-ASN         : bond        0.00147 (    1)
  link_NAG-ASN         : angle       0.76708 (    3)

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  165 ASP cc_start: 0.7970 (m-30) cc_final: 0.7671 (m-30)
REVERT: A  294 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7504 (tp40)
REVERT: A  497 TYR cc_start: 0.8695 (m-80) cc_final: 0.8250 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 47
  average time/residue: 0.0637
  time to fit residues: 3.9232
Evaluate side-chains
  46 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 16 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0870
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.3994 r_free = 0.3994 target = 0.178359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.142747 restraints weight = 8198.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.48
r_work: 0.3430 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4058  Z= 0.123
  Angle     :  0.567   8.746   5539  Z= 0.273
  Chirality :  0.038   0.135    652
  Planarity :  0.004   0.042    689
  Dihedral  :  3.518  13.079    572
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  9.35 %
    Favored  : 90.17 %
  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:  2.11 (0.38), residues: 515
  helix:  1.52 (0.27), residues: 367
  sheet: -2.08 (1.59), residues: 10
  loop :  1.71 (0.58), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 169 
 TYR   0.017   0.002   TYR A 272 
 PHE   0.015   0.001   PHE A 344 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4055)
  covalent geometry    : angle       0.56444 ( 5532)
  SS BOND              : bond        0.00199 (    2)
  SS BOND              : angle       1.94729 (    4)
  hydrogen bonds       : bond        0.04276 (  267)
  hydrogen bonds       : angle       3.99464 (  768)
  link_NAG-ASN         : bond        0.00185 (    1)
  link_NAG-ASN         : angle       0.72797 (    3)

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7940 (m-30) cc_final: 0.7651 (m-30)
REVERT: A  294 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7761 (tp40)
REVERT: A  497 TYR cc_start: 0.8629 (m-80) cc_final: 0.8276 (m-80)
  outliers start: 2
  outliers final: 2
  residues processed: 44
  average time/residue: 0.0641
  time to fit residues: 3.7613
Evaluate side-chains
  44 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  446 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 32 optimal weight:    8.9990
   chunk 46 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.176018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.135047 restraints weight = 8002.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.36
r_work: 0.3128 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3239
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4058  Z= 0.148
  Angle     :  0.585   7.545   5539  Z= 0.284
  Chirality :  0.039   0.133    652
  Planarity :  0.004   0.043    689
  Dihedral  :  3.553  13.284    572
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  9.59 %
    Favored  : 90.17 %
  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:  1.99 (0.38), residues: 515
  helix:  1.39 (0.27), residues: 369
  sheet: -2.39 (1.46), residues: 10
  loop :  1.83 (0.58), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 169 
 TYR   0.017   0.002   TYR A 272 
 PHE   0.016   0.002   PHE A 344 
 TRP   0.011   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4055)
  covalent geometry    : angle       0.58270 ( 5532)
  SS BOND              : bond        0.00225 (    2)
  SS BOND              : angle       2.11638 (    4)
  hydrogen bonds       : bond        0.04681 (  267)
  hydrogen bonds       : angle       4.03246 (  768)
  link_NAG-ASN         : bond        0.00121 (    1)
  link_NAG-ASN         : angle       0.79223 (    3)

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7834 (m-30) cc_final: 0.7560 (m-30)
REVERT: A  294 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7202 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 47
  average time/residue: 0.0648
  time to fit residues: 3.9747
Evaluate side-chains
  46 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 42 optimal weight:    0.2980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0000
   chunk 38 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.4384

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.179186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.147202 restraints weight = 13024.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 3.99
r_work: 0.3293 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4058  Z= 0.117
  Angle     :  0.571   9.744   5539  Z= 0.271
  Chirality :  0.038   0.132    652
  Planarity :  0.004   0.041    689
  Dihedral  :  3.439  12.240    572
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 10.07 %
    Favored  : 89.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.38), residues: 515
  helix:  1.58 (0.27), residues: 368
  sheet: -2.60 (1.34), residues: 10
  loop :  1.86 (0.57), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 169 
 TYR   0.016   0.001   TYR A 272 
 PHE   0.014   0.001   PHE A 344 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4055)
  covalent geometry    : angle       0.56864 ( 5532)
  SS BOND              : bond        0.00162 (    2)
  SS BOND              : angle       1.86549 (    4)
  hydrogen bonds       : bond        0.04068 (  267)
  hydrogen bonds       : angle       3.91750 (  768)
  link_NAG-ASN         : bond        0.00221 (    1)
  link_NAG-ASN         : angle       0.70730 (    3)

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7960 (m-30) cc_final: 0.7671 (m-30)
REVERT: A  219 MET cc_start: 0.6180 (mmp) cc_final: 0.5313 (mtm)
REVERT: A  294 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7693 (tp40)
  outliers start: 2
  outliers final: 2
  residues processed: 43
  average time/residue: 0.0656
  time to fit residues: 3.7179
Evaluate side-chains
  44 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  446 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0670
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.3986 r_free = 0.3986 target = 0.177560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.139853 restraints weight = 6867.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.95
r_work: 0.3351 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4058  Z= 0.130
  Angle     :  0.577   8.320   5539  Z= 0.276
  Chirality :  0.038   0.130    652
  Planarity :  0.004   0.042    689
  Dihedral  :  3.435  11.735    572
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  9.83 %
    Favored  : 89.69 %
  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:  2.14 (0.38), residues: 515
  helix:  1.53 (0.27), residues: 369
  sheet: -2.68 (1.33), residues: 10
  loop :  1.84 (0.57), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 169 
 TYR   0.017   0.002   TYR A 272 
 PHE   0.014   0.001   PHE A 344 
 TRP   0.010   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4055)
  covalent geometry    : angle       0.57508 ( 5532)
  SS BOND              : bond        0.00186 (    2)
  SS BOND              : angle       1.92326 (    4)
  hydrogen bonds       : bond        0.04337 (  267)
  hydrogen bonds       : angle       3.93361 (  768)
  link_NAG-ASN         : bond        0.00152 (    1)
  link_NAG-ASN         : angle       0.74993 (    3)

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7824 (m-30) cc_final: 0.7515 (m-30)
REVERT: A  219 MET cc_start: 0.6112 (mmp) cc_final: 0.5202 (mtp)
REVERT: A  294 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7414 (tp40)
  outliers start: 2
  outliers final: 2
  residues processed: 45
  average time/residue: 0.0688
  time to fit residues: 4.0522
Evaluate side-chains
  47 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  446 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0070
   chunk 23 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0980
   chunk 43 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0670
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.3736

-------------------------------------------------------------------------------
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 = 0.4051 r_free = 0.4051 target = 0.184020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.148060 restraints weight = 9157.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 3.06
r_work: 0.3235 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3308
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3308 r_free = 0.3308    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3308 r_free = 0.3308    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3308
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4058  Z= 0.111
  Angle     :  0.558   8.629   5539  Z= 0.265
  Chirality :  0.038   0.134    652
  Planarity :  0.004   0.040    689
  Dihedral  :  3.342  11.866    572
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  9.83 %
    Favored  : 89.69 %
  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:  2.35 (0.38), residues: 515
  helix:  1.69 (0.27), residues: 368
  sheet: -2.64 (1.31), residues: 10
  loop :  1.88 (0.57), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 169 
 TYR   0.016   0.001   TYR A 272 
 PHE   0.013   0.001   PHE A 344 
 TRP   0.009   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 4055)
  covalent geometry    : angle       0.55587 ( 5532)
  SS BOND              : bond        0.00146 (    2)
  SS BOND              : angle       1.73324 (    4)
  hydrogen bonds       : bond        0.03881 (  267)
  hydrogen bonds       : angle       3.85266 (  768)
  link_NAG-ASN         : bond        0.00199 (    1)
  link_NAG-ASN         : angle       0.69695 (    3)

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7980 (m-30) cc_final: 0.7692 (m-30)
REVERT: A  219 MET cc_start: 0.6198 (mmp) cc_final: 0.5330 (mtp)
REVERT: A  294 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7604 (tp40)
  outliers start: 2
  outliers final: 2
  residues processed: 42
  average time/residue: 0.0656
  time to fit residues: 3.6496
Evaluate side-chains
  43 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  446 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0970
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.182192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.146284 restraints weight = 10346.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 3.35
r_work: 0.3260 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4058  Z= 0.127
  Angle     :  0.589   8.714   5539  Z= 0.282
  Chirality :  0.039   0.143    652
  Planarity :  0.004   0.041    689
  Dihedral  :  3.369  11.618    572
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  9.83 %
    Favored  : 89.69 %
  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:  2.26 (0.38), residues: 515
  helix:  1.62 (0.27), residues: 369
  sheet: -2.69 (1.35), residues: 10
  loop :  1.86 (0.57), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 169 
 TYR   0.016   0.002   TYR A 272 
 PHE   0.014   0.001   PHE A 344 
 TRP   0.009   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4055)
  covalent geometry    : angle       0.58678 ( 5532)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       1.81897 (    4)
  hydrogen bonds       : bond        0.04211 (  267)
  hydrogen bonds       : angle       3.93881 (  768)
  link_NAG-ASN         : bond        0.00151 (    1)
  link_NAG-ASN         : angle       0.75196 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1471.06 seconds
wall clock time: 25 minutes 47.74 seconds (1547.74 seconds total)