Starting phenix.real_space_refine
on Fri May  9 21:54:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b1n_44085/05_2025/9b1n_44085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b1n_44085/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b1n_44085/05_2025/9b1n_44085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b1n_44085/05_2025/9b1n_44085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b1n_44085/05_2025/9b1n_44085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b1n_44085/05_2025/9b1n_44085.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.42, per 1000 atoms: 1.37
  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: 0.96
  Conformation dependent library (CDL) restraints added in 904.1 milliseconds
  

  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: 0.40
  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: 1.07

  Time building geometry restraints manager: 1.14 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.120
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.610
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.820
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.014   0.002   TRP A  50 
 HIS   0.006   0.001   HIS A 424 
 PHE   0.021   0.003   PHE A 344 
 TYR   0.035   0.003   TYR A 272 
 ARG   0.004   0.001   ARG A 483 

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

*********************** 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  : 0.444 
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: 0.2248
  time to fit residues: 18.4474
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  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.177448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.136728 restraints weight = 4833.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.85
r_work: 0.3223 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3329
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1763

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= 0.139
  Angle     :  0.610   7.233   5539  Z= 0.306
  Chirality :  0.040   0.135    652
  Planarity :  0.005   0.043    689
  Dihedral  :  4.221  17.151    572
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.56 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.37), residues: 515
  helix:  0.86 (0.26), residues: 372
  sheet:  None (None), residues: 0
  loop :  1.47 (0.57), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  50 
 HIS   0.004   0.001   HIS A 139 
 PHE   0.017   0.002   PHE A 344 
 TYR   0.022   0.002   TYR A 272 
 ARG   0.006   0.001   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00262 (    1)
  link_NAG-ASN         : angle       0.83057 (    3)
  hydrogen bonds       : bond        0.05182 (  267)
  hydrogen bonds       : angle       4.41156 (  768)
  SS BOND              : bond        0.00491 (    2)
  SS BOND              : angle       3.25879 (    4)
  covalent geometry    : bond        0.00299 ( 4055)
  covalent geometry    : angle       0.60359 ( 5532)

*********************** 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
  51 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A  165 ASP cc_start: 0.7868 (m-30) cc_final: 0.7606 (m-30)
REVERT: A  281 ARG cc_start: 0.7846 (mtp-110) cc_final: 0.7450 (ttm-80)
REVERT: A  497 TYR cc_start: 0.8485 (m-80) cc_final: 0.8076 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 50
  average time/residue: 0.1410
  time to fit residues: 9.4174
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  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    0.3980
   chunk 49 optimal weight:    0.4980
   chunk 28 optimal weight:    0.7980
   chunk 42 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3985 r_free = 0.3985 target = 0.177211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.139487 restraints weight = 11785.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 4.29
r_work: 0.3070 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3318
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4058  Z= 0.133
  Angle     :  0.575   6.371   5539  Z= 0.283
  Chirality :  0.039   0.126    652
  Planarity :  0.005   0.046    689
  Dihedral  :  3.839  13.825    572
  Min Nonbonded Distance : 2.588

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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.37), residues: 515
  helix:  1.07 (0.26), residues: 373
  sheet:  None (None), residues: 0
  loop :  1.49 (0.57), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.018   0.002   PHE A 344 
 TYR   0.021   0.002   TYR A 272 
 ARG   0.006   0.001   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00233 (    1)
  link_NAG-ASN         : angle       0.77996 (    3)
  hydrogen bonds       : bond        0.04883 (  267)
  hydrogen bonds       : angle       4.24216 (  768)
  SS BOND              : bond        0.00387 (    2)
  SS BOND              : angle       2.50683 (    4)
  covalent geometry    : bond        0.00305 ( 4055)
  covalent geometry    : angle       0.57091 ( 5532)

*********************** 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
  46 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A  120 ASP cc_start: 0.8110 (t70) cc_final: 0.7731 (t0)
REVERT: A  165 ASP cc_start: 0.7901 (m-30) cc_final: 0.7593 (m-30)
REVERT: A  281 ARG cc_start: 0.7930 (mtp-110) cc_final: 0.7550 (ttm-80)
REVERT: A  294 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7310 (tp40)
REVERT: A  497 TYR cc_start: 0.8565 (m-80) cc_final: 0.8065 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 45
  average time/residue: 0.1606
  time to fit residues: 9.6521
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  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 37 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3978 r_free = 0.3978 target = 0.176470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.134021 restraints weight = 5593.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.05
r_work: 0.3346 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3306
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3306
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4058  Z= 0.140
  Angle     :  0.577   7.249   5539  Z= 0.282
  Chirality :  0.039   0.130    652
  Planarity :  0.005   0.046    689
  Dihedral  :  3.712  13.378    572
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  6.71 %
    Favored  : 92.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.37), residues: 515
  helix:  1.41 (0.27), residues: 362
  sheet: -2.16 (1.55), residues: 10
  loop :  1.55 (0.57), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 139 
 PHE   0.018   0.002   PHE A 344 
 TYR   0.019   0.002   TYR A 272 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00150 (    1)
  link_NAG-ASN         : angle       0.81655 (    3)
  hydrogen bonds       : bond        0.04764 (  267)
  hydrogen bonds       : angle       4.16024 (  768)
  SS BOND              : bond        0.00582 (    2)
  SS BOND              : angle       2.26671 (    4)
  covalent geometry    : bond        0.00327 ( 4055)
  covalent geometry    : angle       0.57346 ( 5532)

*********************** 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
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  120 ASP cc_start: 0.8165 (t70) cc_final: 0.7828 (t0)
REVERT: A  165 ASP cc_start: 0.7899 (m-30) cc_final: 0.7596 (m-30)
REVERT: A  281 ARG cc_start: 0.8023 (mtp-110) cc_final: 0.7746 (ttm-80)
REVERT: A  294 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7492 (tp40)
REVERT: A  497 TYR cc_start: 0.8688 (m-80) cc_final: 0.8248 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 52
  average time/residue: 0.1416
  time to fit residues: 9.7554
Evaluate side-chains
  48 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  447 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 31 optimal weight:    9.9990
   chunk 22 optimal weight:    0.1980
   chunk 1 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.178020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.143557 restraints weight = 10881.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 3.37
r_work: 0.3158 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
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 = 0.45   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: 0.7926
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4058  Z= 0.126
  Angle     :  0.570   8.462   5539  Z= 0.274
  Chirality :  0.038   0.133    652
  Planarity :  0.004   0.044    689
  Dihedral  :  3.594  13.406    572
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  9.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.37), residues: 515
  helix:  1.53 (0.27), residues: 364
  sheet: -2.24 (1.51), residues: 10
  loop :  1.57 (0.57), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  93 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.016   0.002   PHE A 344 
 TYR   0.018   0.002   TYR A 272 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00183 (    1)
  link_NAG-ASN         : angle       0.76819 (    3)
  hydrogen bonds       : bond        0.04443 (  267)
  hydrogen bonds       : angle       4.07149 (  768)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       2.04892 (    4)
  covalent geometry    : bond        0.00290 ( 4055)
  covalent geometry    : angle       0.56781 ( 5532)

*********************** 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: 2
    poor density    : 46
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 ASP cc_start: 0.8022 (t70) cc_final: 0.7691 (t0)
REVERT: A  165 ASP cc_start: 0.7841 (m-30) cc_final: 0.7544 (m-30)
REVERT: A  281 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7658 (ttm-80)
REVERT: A  294 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7462 (tp40)
REVERT: A  497 TYR cc_start: 0.8644 (m-80) cc_final: 0.8263 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 46
  average time/residue: 0.1610
  time to fit residues: 9.7139
Evaluate side-chains
  43 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
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 1 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.177245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.140657 restraints weight = 6909.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.07
r_work: 0.3376 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4058  Z= 0.137
  Angle     :  0.583   8.773   5539  Z= 0.281
  Chirality :  0.039   0.133    652
  Planarity :  0.004   0.043    689
  Dihedral  :  3.578  13.374    572
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  9.83 %
    Favored  : 89.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.38), residues: 515
  helix:  1.43 (0.27), residues: 368
  sheet: -2.18 (1.58), residues: 10
  loop :  1.59 (0.58), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.016   0.002   PHE A 344 
 TYR   0.018   0.002   TYR A 272 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00139 (    1)
  link_NAG-ASN         : angle       0.80323 (    3)
  hydrogen bonds       : bond        0.04580 (  267)
  hydrogen bonds       : angle       4.05913 (  768)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       2.05288 (    4)
  covalent geometry    : bond        0.00323 ( 4055)
  covalent geometry    : angle       0.58091 ( 5532)

*********************** 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
  48 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7983 (m-30) cc_final: 0.7693 (m-30)
REVERT: A  219 MET cc_start: 0.6220 (mmp) cc_final: 0.5352 (mtp)
REVERT: A  294 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7734 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 47
  average time/residue: 0.1425
  time to fit residues: 9.0793
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  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 11 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 49 optimal weight:    0.1980
   chunk 40 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3988 r_free = 0.3988 target = 0.177609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.143795 restraints weight = 12998.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 4.16
r_work: 0.3271 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
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 = 0.49   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: 0.8171
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      :  0.003   0.034   4058  Z= 0.132
  Angle     :  0.579   9.176   5539  Z= 0.279
  Chirality :  0.039   0.132    652
  Planarity :  0.004   0.042    689
  Dihedral  :  3.538  13.128    572
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 10.55 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.38), residues: 515
  helix:  1.47 (0.27), residues: 369
  sheet: -2.17 (1.62), residues: 10
  loop :  1.71 (0.58), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.015   0.001   PHE A 344 
 TYR   0.017   0.002   TYR A 272 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00163 (    1)
  link_NAG-ASN         : angle       0.78026 (    3)
  hydrogen bonds       : bond        0.04438 (  267)
  hydrogen bonds       : angle       4.01974 (  768)
  SS BOND              : bond        0.00198 (    2)
  SS BOND              : angle       2.03090 (    4)
  covalent geometry    : bond        0.00306 ( 4055)
  covalent geometry    : angle       0.57630 ( 5532)

*********************** 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
  49 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7993 (m-30) cc_final: 0.7705 (m-30)
REVERT: A  219 MET cc_start: 0.6311 (mmp) cc_final: 0.5430 (mtp)
REVERT: A  294 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7771 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 48
  average time/residue: 0.1404
  time to fit residues: 8.9280
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  : 0.382 
-------------------------------------------------------------------------------
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 9 optimal weight:    0.0270
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   chunk 48 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.5438

-------------------------------------------------------------------------------
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 = 0.181780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.145679 restraints weight = 9393.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 3.09
r_work: 0.3233 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2903

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= 0.125
  Angle     :  0.566   7.740   5539  Z= 0.272
  Chirality :  0.039   0.135    652
  Planarity :  0.004   0.042    689
  Dihedral  :  3.489  13.024    572
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 10.31 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.38), residues: 515
  helix:  1.54 (0.27), residues: 369
  sheet: -2.44 (1.58), residues: 10
  loop :  1.72 (0.58), residues: 136

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

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00181 (    1)
  link_NAG-ASN         : angle       0.73912 (    3)
  hydrogen bonds       : bond        0.04254 (  267)
  hydrogen bonds       : angle       3.95129 (  768)
  SS BOND              : bond        0.00199 (    2)
  SS BOND              : angle       1.93553 (    4)
  covalent geometry    : bond        0.00283 ( 4055)
  covalent geometry    : angle       0.56401 ( 5532)

*********************** 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
  49 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7961 (m-30) cc_final: 0.7684 (m-30)
REVERT: A  219 MET cc_start: 0.6210 (mmp) cc_final: 0.5172 (mtp)
REVERT: A  294 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7577 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 48
  average time/residue: 0.1564
  time to fit residues: 9.7263
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  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 25 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   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 = 0.3977 r_free = 0.3977 target = 0.176497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.146278 restraints weight = 14695.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 3.87
r_work: 0.3254 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4058  Z= 0.142
  Angle     :  0.589   8.357   5539  Z= 0.285
  Chirality :  0.039   0.130    652
  Planarity :  0.004   0.043    689
  Dihedral  :  3.525  12.163    572
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 10.55 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.38), residues: 515
  helix:  1.46 (0.27), residues: 369
  sheet: -2.66 (1.41), residues: 10
  loop :  1.82 (0.58), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.015   0.002   PHE A 344 
 TYR   0.017   0.002   TYR A 272 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00127 (    1)
  link_NAG-ASN         : angle       0.77839 (    3)
  hydrogen bonds       : bond        0.04571 (  267)
  hydrogen bonds       : angle       3.99266 (  768)
  SS BOND              : bond        0.00226 (    2)
  SS BOND              : angle       2.04864 (    4)
  covalent geometry    : bond        0.00335 ( 4055)
  covalent geometry    : angle       0.58629 ( 5532)

*********************** 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
  49 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.8012 (m-30) cc_final: 0.7723 (m-30)
REVERT: A  219 MET cc_start: 0.6351 (mmp) cc_final: 0.5439 (mtp)
REVERT: A  294 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7790 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 48
  average time/residue: 0.1426
  time to fit residues: 9.0616
Evaluate side-chains
  49 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.2980
   chunk 18 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0770
   chunk 2 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 47 optimal weight:    0.4980
   chunk 37 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.4138

-------------------------------------------------------------------------------
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 = 0.4048 r_free = 0.4048 target = 0.183447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.146561 restraints weight = 7366.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.34
r_work: 0.3228 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3356
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3356
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.3067

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= 0.116
  Angle     :  0.561   8.550   5539  Z= 0.270
  Chirality :  0.038   0.135    652
  Planarity :  0.004   0.040    689
  Dihedral  :  3.412  12.154    572
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 10.55 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.38), residues: 515
  helix:  1.63 (0.27), residues: 368
  sheet: -2.70 (1.32), residues: 10
  loop :  1.84 (0.58), residues: 137

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

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00188 (    1)
  link_NAG-ASN         : angle       0.71481 (    3)
  hydrogen bonds       : bond        0.03983 (  267)
  hydrogen bonds       : angle       3.90491 (  768)
  SS BOND              : bond        0.00195 (    2)
  SS BOND              : angle       1.81979 (    4)
  covalent geometry    : bond        0.00254 ( 4055)
  covalent geometry    : angle       0.55903 ( 5532)

********************** 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
  47 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7786 (m-30) cc_final: 0.7513 (m-30)
REVERT: A  219 MET cc_start: 0.6013 (mmp) cc_final: 0.5005 (mtp)
REVERT: A  294 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7411 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 46
  average time/residue: 0.1550
  time to fit residues: 9.4137
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  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 32 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   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 = 0.4021 r_free = 0.4021 target = 0.180583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.144661 restraints weight = 11350.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 3.91
r_work: 0.3248 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4058  Z= 0.149
  Angle     :  0.601   8.911   5539  Z= 0.290
  Chirality :  0.040   0.134    652
  Planarity :  0.004   0.043    689
  Dihedral  :  3.484  11.818    572
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 10.79 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.38), residues: 515
  helix:  1.52 (0.27), residues: 368
  sheet: -2.86 (1.33), residues: 10
  loop :  1.76 (0.58), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A 242 
 PHE   0.015   0.002   PHE A 344 
 TYR   0.017   0.002   TYR A 272 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00116 (    1)
  link_NAG-ASN         : angle       0.77627 (    3)
  hydrogen bonds       : bond        0.04557 (  267)
  hydrogen bonds       : angle       3.99315 (  768)
  SS BOND              : bond        0.00231 (    2)
  SS BOND              : angle       1.98081 (    4)
  covalent geometry    : bond        0.00356 ( 4055)
  covalent geometry    : angle       0.59899 ( 5532)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2778.24 seconds
wall clock time: 48 minutes 36.88 seconds (2916.88 seconds total)