Starting phenix.real_space_refine
on Sat May 10 18:38:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dln_27507/05_2025/8dln_27507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dln_27507/05_2025/8dln_27507.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dln_27507/05_2025/8dln_27507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dln_27507/05_2025/8dln_27507.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dln_27507/05_2025/8dln_27507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dln_27507/05_2025/8dln_27507.cif"
  }
  resolution = 3.04
  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=  -0.001 sd=   0.031
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      37      5.16       5
     C    4190      2.51       5
     N    1078      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6553
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1593
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 5.00, per 1000 atoms: 0.76
  Number of scatterers: 6553
  At special positions: 0
  Unit cell: (77, 85, 123, 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      37     16.00
     O    1248      8.00
     N    1078      7.00
     C    4190      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 530 " - pdb=" SG  CYS E 542 " distance=2.02

  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 B1301 " - " ASN B 343 "
      " NAG E 701 " - " ASN E  53 "
      " NAG E 702 " - " ASN E  90 "
      " NAG E 703 " - " ASN E 103 "
      " NAG E 704 " - " ASN E 322 "
      " NAG E 705 " - " ASN E 432 "
      " NAG E 706 " - " ASN E 546 "
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 922.2 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 7 sheets defined
      57.0% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 4.403A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.725A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.697A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
      removed outlier: 3.563A  pdb=" N   GLN E  81 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.727A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 101
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 4.072A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 147 through 155
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.732A  pdb=" N   VAL E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 218 through 252
      removed outlier: 3.762A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
    Processing helix  chain 'E' and resid 265 through 267
      No H-bonds generated for 'chain 'E' and resid 265 through 267'
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.795A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 300
    Processing helix  chain 'E' and resid 303 through 318
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.585A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.693A  pdb=" N   TYR E 385 " --> pdb=" O   TYR E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.294A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
      removed outlier: 3.526A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.318A  pdb=" N   PHE E 452 " --> pdb=" O   GLY E 448 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 471
      No H-bonds generated for 'chain 'E' and resid 469 through 471'
    Processing helix  chain 'E' and resid 472 through 484
    Processing helix  chain 'E' and resid 499 through 502
      removed outlier: 3.665A  pdb=" N   SER E 502 " --> pdb=" O   ASP E 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 499 through 502'
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 512 through 533
      removed outlier: 4.425A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.877A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.985A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132
      removed outlier: 3.790A  pdb=" N   LEU E 142 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263
      removed outlier: 6.052A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.363A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    912 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: 1.75

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2079
        1.35 -     1.47: 1795
        1.47 -     1.60: 2804
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6736
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.23e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.26e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.72e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.65e+00
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.53e+00
  ... (remaining 6731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 8794
        2.00 -     4.00: 314
        4.00 -     6.00: 35
        6.00 -     8.00: 7
        8.00 -    10.00: 5
  Bond angle restraints: 9155
  Sorted by residual:
  angle pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
        pdb=" CG  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     113.90  123.90  -10.00 1.80e+00 3.09e-01 3.09e+01
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.36  128.33   -5.97 1.42e+00 4.96e-01 1.77e+01
  angle pdb=" CA  CYS E 141 "
        pdb=" CB  CYS E 141 "
        pdb=" SG  CYS E 141 "
      ideal   model   delta    sigma   weight residual
     114.40  123.02   -8.62 2.30e+00 1.89e-01 1.41e+01
  angle pdb=" CA  ASN E 437 "
        pdb=" CB  ASN E 437 "
        pdb=" CG  ASN E 437 "
      ideal   model   delta    sigma   weight residual
     112.60  116.03   -3.43 1.00e+00 1.00e+00 1.18e+01
  angle pdb=" C   TYR B 495 "
        pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     110.78  105.54    5.24 1.60e+00 3.91e-01 1.07e+01
  ... (remaining 9150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 3688
       17.19 -    34.37: 310
       34.37 -    51.55: 44
       51.55 -    68.74: 12
       68.74 -    85.92: 11
  Dihedral angle restraints: 4065
    sinusoidal: 1726
      harmonic: 2339
  Sorted by residual:
  dihedral pdb=" CB  CYS E 133 "
           pdb=" SG  CYS E 133 "
           pdb=" SG  CYS E 141 "
           pdb=" CB  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -46.48  -39.52     1      1.00e+01 1.00e-02 2.19e+01
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   14.60   64.40     1      2.00e+01 2.50e-03 1.36e+01
  dihedral pdb=" C   ASN B 360 "
           pdb=" N   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.75    8.15     0      2.50e+00 1.60e-01 1.06e+01
  ... (remaining 4062 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 701
       0.052 -    0.105: 197
       0.105 -    0.157: 64
       0.157 -    0.209: 14
       0.209 -    0.261: 2
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  ASN E 437 "
            pdb=" N   ASN E 437 "
            pdb=" C   ASN E 437 "
            pdb=" CB  ASN E 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 975 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "   -0.030 2.00e-02 2.50e+03   1.88e-02 7.09e+00
        pdb=" CG  TYR B 495 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.043 5.00e-02 4.00e+02   6.41e-02 6.58e+00
        pdb=" N   PRO E 590 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 499 "   -0.043 5.00e-02 4.00e+02   6.39e-02 6.53e+00
        pdb=" N   PRO E 500 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO E 500 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E 500 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1941
        2.82 -     3.34: 5987
        3.34 -     3.86: 11373
        3.86 -     4.38: 12873
        4.38 -     4.90: 22360
  Nonbonded interactions: 54534
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD1 ASN B 487 "
            pdb=" OH  TYR E  83 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.366 3.120
  ... (remaining 54529 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.870
  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:             0.010
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
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   0.064   6749  Z= 0.245
  Angle     :  0.892  12.918   9188  Z= 0.488
  Chirality :  0.056   0.261    978
  Planarity :  0.007   0.064   1177
  Dihedral  : 13.351  85.924   2547
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.57 %
    Favored  : 96.14 %
  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: -0.21 (0.26), residues: 793
  helix:  0.33 (0.22), residues: 387
  sheet:  1.07 (0.72), residues: 43
  loop : -0.73 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E  69 
 HIS   0.007   0.001   HIS E  34 
 PHE   0.027   0.003   PHE E 369 
 TYR   0.043   0.002   TYR B 495 
 ARG   0.011   0.001   ARG E 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00985 (    7)
  link_NAG-ASN         : angle       4.70414 (   21)
  hydrogen bonds       : bond        0.13935 (  321)
  hydrogen bonds       : angle       6.07692 (  912)
  SS BOND              : bond        0.00550 (    6)
  SS BOND              : angle       2.50755 (   12)
  covalent geometry    : bond        0.00525 ( 6736)
  covalent geometry    : angle       0.85980 ( 9155)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8276 (m-30) cc_final: 0.7950 (m-30)
REVERT: E  143 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8945 (mp)
REVERT: E  562 LYS cc_start: 0.9196 (tttt) cc_final: 0.8983 (tttp)
REVERT: E  589 GLU cc_start: 0.7916 (tp30) cc_final: 0.7473 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2609
  time to fit residues: 38.1123
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  143 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0070
   chunk 33 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
E 374 HIS
E 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.071188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.054918 restraints weight = 18775.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 3.31
r_work: 0.2768 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6749  Z= 0.137
  Angle     :  0.584   9.217   9188  Z= 0.292
  Chirality :  0.042   0.140    978
  Planarity :  0.005   0.041   1177
  Dihedral  :  5.206  49.543   1015
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.29 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.05 (0.28), residues: 793
  helix:  1.52 (0.25), residues: 383
  sheet:  0.87 (0.72), residues: 43
  loop : -0.15 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.018   0.001   TYR B 495 
 ARG   0.005   0.000   ARG E 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00634 (    7)
  link_NAG-ASN         : angle       3.35454 (   21)
  hydrogen bonds       : bond        0.04446 (  321)
  hydrogen bonds       : angle       4.65332 (  912)
  SS BOND              : bond        0.00539 (    6)
  SS BOND              : angle       2.22947 (   12)
  covalent geometry    : bond        0.00296 ( 6736)
  covalent geometry    : angle       0.55678 ( 9155)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8695 (m-30) cc_final: 0.8174 (m-30)
REVERT: E  143 LEU cc_start: 0.9377 (mp) cc_final: 0.9166 (mt)
REVERT: E  149 ASN cc_start: 0.9285 (m-40) cc_final: 0.9060 (m-40)
REVERT: E  152 MET cc_start: 0.8269 (mmp) cc_final: 0.7930 (mmt)
REVERT: E  249 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8838 (mtm)
REVERT: E  471 ASP cc_start: 0.8611 (p0) cc_final: 0.8117 (t0)
REVERT: E  474 MET cc_start: 0.8504 (mmt) cc_final: 0.7987 (mmt)
REVERT: E  577 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8667 (mttm)
  outliers start: 6
  outliers final: 3
  residues processed: 73
  average time/residue: 0.2694
  time to fit residues: 24.7262
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  458 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0970
   chunk 39 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.6978

-------------------------------------------------------------------------------
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 = 0.3297 r_free = 0.3297 target = 0.070123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.053895 restraints weight = 18936.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 3.26
r_work: 0.2748 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6749  Z= 0.134
  Angle     :  0.540   8.050   9188  Z= 0.269
  Chirality :  0.041   0.132    978
  Planarity :  0.004   0.043   1177
  Dihedral  :  4.801  50.534   1013
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.43 %
    Favored  : 90.14 %
  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:  1.44 (0.29), residues: 793
  helix:  1.76 (0.26), residues: 389
  sheet:  0.77 (0.73), residues: 43
  loop :  0.17 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.013   0.001   TYR B 495 
 ARG   0.004   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00530 (    7)
  link_NAG-ASN         : angle       2.82998 (   21)
  hydrogen bonds       : bond        0.04160 (  321)
  hydrogen bonds       : angle       4.43852 (  912)
  SS BOND              : bond        0.00401 (    6)
  SS BOND              : angle       1.89138 (   12)
  covalent geometry    : bond        0.00292 ( 6736)
  covalent geometry    : angle       0.51878 ( 9155)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8711 (m-30) cc_final: 0.8169 (m-30)
REVERT: E  145 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8477 (tm-30)
REVERT: E  149 ASN cc_start: 0.9298 (m-40) cc_final: 0.9082 (m110)
REVERT: E  249 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8876 (mtm)
REVERT: E  471 ASP cc_start: 0.8621 (p0) cc_final: 0.8175 (t0)
REVERT: E  577 LYS cc_start: 0.9008 (mtpt) cc_final: 0.8710 (mttm)
  outliers start: 10
  outliers final: 5
  residues processed: 66
  average time/residue: 0.2546
  time to fit residues: 21.2203
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  458 LYS
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0020
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0010
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
E  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.070620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.054042 restraints weight = 19230.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 3.40
r_work: 0.2758 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6749  Z= 0.109
  Angle     :  0.522   7.170   9188  Z= 0.259
  Chirality :  0.040   0.130    978
  Planarity :  0.004   0.043   1177
  Dihedral  :  4.681  51.529   1013
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.71 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.60 (0.29), residues: 793
  helix:  1.83 (0.26), residues: 389
  sheet:  0.83 (0.75), residues: 43
  loop :  0.34 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.012   0.001   PHE E 369 
 TYR   0.011   0.001   TYR B 495 
 ARG   0.002   0.000   ARG E 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00463 (    7)
  link_NAG-ASN         : angle       2.56210 (   21)
  hydrogen bonds       : bond        0.03867 (  321)
  hydrogen bonds       : angle       4.32953 (  912)
  SS BOND              : bond        0.00376 (    6)
  SS BOND              : angle       1.74318 (   12)
  covalent geometry    : bond        0.00234 ( 6736)
  covalent geometry    : angle       0.50409 ( 9155)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 MET cc_start: 0.9067 (ttm) cc_final: 0.8592 (ttm)
REVERT: E  145 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8440 (tm-30)
REVERT: E  149 ASN cc_start: 0.9289 (m-40) cc_final: 0.9068 (m110)
REVERT: E  152 MET cc_start: 0.8260 (mmp) cc_final: 0.7825 (mmt)
REVERT: E  249 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8900 (mtm)
REVERT: E  471 ASP cc_start: 0.8576 (p0) cc_final: 0.8006 (t0)
REVERT: E  577 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8725 (mmtm)
  outliers start: 10
  outliers final: 2
  residues processed: 68
  average time/residue: 0.2798
  time to fit residues: 23.9121
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 26 optimal weight:    0.2980
   chunk 49 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.069247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.053099 restraints weight = 19030.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 3.25
r_work: 0.2759 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6749  Z= 0.145
  Angle     :  0.533   6.941   9188  Z= 0.267
  Chirality :  0.040   0.127    978
  Planarity :  0.004   0.043   1177
  Dihedral  :  4.681  52.262   1013
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  9.29 %
    Favored  : 89.71 %
  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:  1.65 (0.29), residues: 793
  helix:  1.79 (0.25), residues: 402
  sheet:  0.99 (0.78), residues: 43
  loop :  0.40 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00431 (    7)
  link_NAG-ASN         : angle       2.32511 (   21)
  hydrogen bonds       : bond        0.03987 (  321)
  hydrogen bonds       : angle       4.30738 (  912)
  SS BOND              : bond        0.00347 (    6)
  SS BOND              : angle       1.66223 (   12)
  covalent geometry    : bond        0.00323 ( 6736)
  covalent geometry    : angle       0.51835 ( 9155)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8661 (m-30) cc_final: 0.8134 (m-30)
REVERT: E   22 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8450 (tm-30)
REVERT: E   62 MET cc_start: 0.9119 (ttm) cc_final: 0.8719 (ttm)
REVERT: E  152 MET cc_start: 0.8365 (mmp) cc_final: 0.7873 (mmt)
REVERT: E  249 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8901 (mtm)
REVERT: E  471 ASP cc_start: 0.8636 (p0) cc_final: 0.8066 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 65
  average time/residue: 0.2683
  time to fit residues: 22.1929
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0980
   chunk 56 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.068843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.052436 restraints weight = 18978.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 3.32
r_work: 0.2720 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6749  Z= 0.135
  Angle     :  0.529   6.607   9188  Z= 0.265
  Chirality :  0.040   0.127    978
  Planarity :  0.003   0.043   1177
  Dihedral  :  4.637  52.574   1013
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.29 %
    Favored  : 89.57 %
  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:  1.73 (0.29), residues: 793
  helix:  1.83 (0.25), residues: 402
  sheet:  1.08 (0.80), residues: 43
  loop :  0.47 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00403 (    7)
  link_NAG-ASN         : angle       2.20923 (   21)
  hydrogen bonds       : bond        0.03895 (  321)
  hydrogen bonds       : angle       4.31471 (  912)
  SS BOND              : bond        0.00411 (    6)
  SS BOND              : angle       1.57013 (   12)
  covalent geometry    : bond        0.00300 ( 6736)
  covalent geometry    : angle       0.51643 ( 9155)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   22 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8496 (tm-30)
REVERT: E  249 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8877 (mtm)
REVERT: E  471 ASP cc_start: 0.8723 (p0) cc_final: 0.8226 (t0)
REVERT: E  480 MET cc_start: 0.9233 (mtp) cc_final: 0.8973 (mtp)
  outliers start: 8
  outliers final: 4
  residues processed: 66
  average time/residue: 0.2789
  time to fit residues: 23.7230
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.068575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.052388 restraints weight = 19021.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 3.29
r_work: 0.2705 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6749  Z= 0.153
  Angle     :  0.558  10.387   9188  Z= 0.277
  Chirality :  0.041   0.185    978
  Planarity :  0.004   0.041   1177
  Dihedral  :  4.686  52.918   1013
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.86 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.76 (0.29), residues: 793
  helix:  1.82 (0.25), residues: 403
  sheet:  1.08 (0.80), residues: 43
  loop :  0.53 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.001   0.000   ARG E 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00386 (    7)
  link_NAG-ASN         : angle       2.11558 (   21)
  hydrogen bonds       : bond        0.03990 (  321)
  hydrogen bonds       : angle       4.31844 (  912)
  SS BOND              : bond        0.00408 (    6)
  SS BOND              : angle       1.53498 (   12)
  covalent geometry    : bond        0.00345 ( 6736)
  covalent geometry    : angle       0.54713 ( 9155)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  152 MET cc_start: 0.8266 (mmp) cc_final: 0.7670 (mmt)
REVERT: E  249 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8889 (mtm)
REVERT: E  471 ASP cc_start: 0.8734 (p0) cc_final: 0.8235 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 60
  average time/residue: 0.2930
  time to fit residues: 22.0931
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
E 522 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.068678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.052289 restraints weight = 19138.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 3.30
r_work: 0.2680 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6749  Z= 0.175
  Angle     :  0.566   9.717   9188  Z= 0.282
  Chirality :  0.042   0.169    978
  Planarity :  0.004   0.040   1177
  Dihedral  :  4.797  52.971   1013
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 10.14 %
    Favored  : 88.71 %
  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:  1.75 (0.29), residues: 793
  helix:  1.80 (0.25), residues: 403
  sheet:  0.93 (0.78), residues: 43
  loop :  0.57 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.014   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 273 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00383 (    7)
  link_NAG-ASN         : angle       2.12330 (   21)
  hydrogen bonds       : bond        0.04146 (  321)
  hydrogen bonds       : angle       4.39352 (  912)
  SS BOND              : bond        0.00431 (    6)
  SS BOND              : angle       1.53592 (   12)
  covalent geometry    : bond        0.00392 ( 6736)
  covalent geometry    : angle       0.55485 ( 9155)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8794 (m-30) cc_final: 0.8245 (m-30)
REVERT: B  471 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8936 (mm-30)
REVERT: E  152 MET cc_start: 0.8242 (mmp) cc_final: 0.7723 (mmt)
REVERT: E  249 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8860 (mtm)
  outliers start: 8
  outliers final: 5
  residues processed: 60
  average time/residue: 0.2734
  time to fit residues: 20.8142
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    0.2980
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   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 = 0.3250 r_free = 0.3250 target = 0.068434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.051921 restraints weight = 19213.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 3.33
r_work: 0.2765 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6749  Z= 0.135
  Angle     :  0.559   9.432   9188  Z= 0.278
  Chirality :  0.041   0.153    978
  Planarity :  0.003   0.040   1177
  Dihedral  :  4.722  53.772   1013
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.71 %
    Favored  : 88.57 %
  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:  1.71 (0.29), residues: 793
  helix:  1.75 (0.25), residues: 411
  sheet:  0.95 (0.80), residues: 43
  loop :  0.52 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.001   0.000   ARG E 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00361 (    7)
  link_NAG-ASN         : angle       2.15969 (   21)
  hydrogen bonds       : bond        0.03892 (  321)
  hydrogen bonds       : angle       4.36132 (  912)
  SS BOND              : bond        0.00396 (    6)
  SS BOND              : angle       1.49696 (   12)
  covalent geometry    : bond        0.00307 ( 6736)
  covalent geometry    : angle       0.54802 ( 9155)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  471 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8905 (mm-30)
REVERT: E  152 MET cc_start: 0.8225 (mmp) cc_final: 0.7703 (mmt)
REVERT: E  249 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8854 (mtm)
REVERT: E  344 CYS cc_start: 0.8576 (p) cc_final: 0.8296 (t)
REVERT: E  471 ASP cc_start: 0.8861 (p0) cc_final: 0.8242 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 59
  average time/residue: 0.2765
  time to fit residues: 20.7161
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   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 = 0.3264 r_free = 0.3264 target = 0.068600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.052484 restraints weight = 19197.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 3.22
r_work: 0.2730 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6749  Z= 0.147
  Angle     :  0.578  11.392   9188  Z= 0.286
  Chirality :  0.041   0.150    978
  Planarity :  0.003   0.039   1177
  Dihedral  :  4.704  53.733   1013
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.86 %
    Favored  : 88.29 %
  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:  1.70 (0.30), residues: 793
  helix:  1.75 (0.25), residues: 411
  sheet:  0.80 (0.78), residues: 43
  loop :  0.52 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.001   0.000   ARG E 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00352 (    7)
  link_NAG-ASN         : angle       2.13405 (   21)
  hydrogen bonds       : bond        0.03978 (  321)
  hydrogen bonds       : angle       4.37574 (  912)
  SS BOND              : bond        0.00392 (    6)
  SS BOND              : angle       1.45500 (   12)
  covalent geometry    : bond        0.00334 ( 6736)
  covalent geometry    : angle       0.56717 ( 9155)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8774 (m-30) cc_final: 0.8251 (m-30)
REVERT: B  471 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8926 (mm-30)
REVERT: E  152 MET cc_start: 0.8235 (mmp) cc_final: 0.7712 (mmt)
REVERT: E  249 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8862 (mtm)
REVERT: E  344 CYS cc_start: 0.8601 (p) cc_final: 0.8302 (t)
REVERT: E  471 ASP cc_start: 0.8890 (p0) cc_final: 0.8262 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 58
  average time/residue: 0.2700
  time to fit residues: 19.9071
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0370
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.5858

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.069287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.053100 restraints weight = 19395.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 3.29
r_work: 0.2785 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6749  Z= 0.130
  Angle     :  0.575  11.204   9188  Z= 0.282
  Chirality :  0.040   0.147    978
  Planarity :  0.003   0.040   1177
  Dihedral  :  4.659  54.021   1013
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.29 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.66 (0.29), residues: 793
  helix:  1.73 (0.25), residues: 410
  sheet:  0.74 (0.78), residues: 43
  loop :  0.51 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00349 (    7)
  link_NAG-ASN         : angle       2.12893 (   21)
  hydrogen bonds       : bond        0.03874 (  321)
  hydrogen bonds       : angle       4.38372 (  912)
  SS BOND              : bond        0.00377 (    6)
  SS BOND              : angle       1.43508 (   12)
  covalent geometry    : bond        0.00294 ( 6736)
  covalent geometry    : angle       0.56446 ( 9155)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3305.62 seconds
wall clock time: 58 minutes 10.18 seconds (3490.18 seconds total)