Starting phenix.real_space_refine
on Sun Apr 27 11:16:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bvo_44939/04_2025/9bvo_44939.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bvo_44939/04_2025/9bvo_44939.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bvo_44939/04_2025/9bvo_44939.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bvo_44939/04_2025/9bvo_44939.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bvo_44939/04_2025/9bvo_44939.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bvo_44939/04_2025/9bvo_44939.cif"
  }
  resolution = 4.4
  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=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      25      5.16       5
     C    3575      2.51       5
     N     904      2.21       5
     O     964      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5469
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 642, 5325
          Classifications: {'peptide': 642}
          Link IDs: {'PTRANS': 30, 'TRANS': 611}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'6PL': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   6PL A 801 " occ=0.60
      ... (44 atoms not shown)
      pdb=" P   6PL A 801 " occ=0.60
  Time building chain proxies: 4.26, per 1000 atoms: 0.78
  Number of scatterers: 5469
  At special positions: 0
  Unit cell: (105.6, 80.3, 95.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     P       1     15.00
     O     964      8.00
     N     904      7.00
     C    3575      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 450 " 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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 802 " - " ASN A 459 "
      " NAG B   1 " - " ASN A 570 "
      " NAG C   1 " - " ASN A 550 "
      " NAG D   1 " - " ASN A 605 "
  Time building additional restraints: 1.43
  Conformation dependent library (CDL) restraints added in 789.4 milliseconds
  

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1216

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 3 sheets defined
      57.8% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 47 through 55
    Processing helix  chain 'A' and resid 61 through 83
      Proline residue:  A  80  - end of helix
      removed outlier: 3.666A  pdb=" N   ARG A  83 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 89
      removed outlier: 3.925A  pdb=" N   LEU A  88 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   ASP A  89 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 85 through 89'
    Processing helix  chain 'A' and resid 111 through 132
    Processing helix  chain 'A' and resid 134 through 153
      Proline residue:  A 145  - end of helix
    Processing helix  chain 'A' and resid 158 through 174
      removed outlier: 3.773A  pdb=" N   TYR A 162 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   PHE A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   MET A 174 " --> pdb=" O   GLN A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 187
      removed outlier: 3.833A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 191
      removed outlier: 3.728A  pdb=" N   ARG A 191 " --> pdb=" O   ALA A 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 188 through 191'
    Processing helix  chain 'A' and resid 197 through 218
      removed outlier: 3.940A  pdb=" N   LEU A 203 " --> pdb=" O   ASN A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 239
      removed outlier: 4.021A  pdb=" N   SER A 233 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A 234 " --> pdb=" O   TYR A 231 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   TRP A 236 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   LEU A 237 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 245
      removed outlier: 3.862A  pdb=" N   LEU A 244 " --> pdb=" O   PRO A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 253
    Processing helix  chain 'A' and resid 256 through 269
    Processing helix  chain 'A' and resid 275 through 294
      removed outlier: 3.519A  pdb=" N   GLY A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 307
    Processing helix  chain 'A' and resid 308 through 311
      removed outlier: 3.650A  pdb=" N   CYS A 311 " --> pdb=" O   PRO A 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 308 through 311'
    Processing helix  chain 'A' and resid 316 through 321
      removed outlier: 3.560A  pdb=" N   VAL A 320 " --> pdb=" O   PRO A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 377
      removed outlier: 3.823A  pdb=" N   GLN A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA A 364 " --> pdb=" O   HIS A 360 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR A 367 " --> pdb=" O   GLY A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 380
      No H-bonds generated for 'chain 'A' and resid 378 through 380'
    Processing helix  chain 'A' and resid 440 through 455
    Processing helix  chain 'A' and resid 456 through 459
      removed outlier: 3.803A  pdb=" N   ASN A 459 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 456 through 459'
    Processing helix  chain 'A' and resid 506 through 510
      removed outlier: 4.054A  pdb=" N   LEU A 509 " --> pdb=" O   LEU A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 521
      removed outlier: 3.590A  pdb=" N   LYS A 515 " --> pdb=" O   PRO A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 625
    Processing helix  chain 'A' and resid 653 through 675
    Processing helix  chain 'A' and resid 676 through 709
      removed outlier: 4.379A  pdb=" N   ARG A 680 " --> pdb=" O   PRO A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 725
    Processing sheet with id=AA1, first strand: chain 'A' and resid 423 through 425
      removed outlier: 4.376A  pdb=" N   HIS A 410 " --> pdb=" O   TRP A 470 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   VAL A 471 " --> pdb=" O   GLN A 479 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLN A 479 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 534
      removed outlier: 6.639A  pdb=" N   MET A 600 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   LEU A 555 " --> pdb=" O   MET A 600 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL A 602 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   ILE A 553 " --> pdb=" O   VAL A 602 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 539 through 543
      removed outlier: 3.982A  pdb=" N   VAL A 560 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)

    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: 1.39

  Time building geometry restraints manager: 1.67 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: 975
        1.33 -     1.45: 1556
        1.45 -     1.57: 3049
        1.57 -     1.69: 2
        1.69 -     1.81: 42
  Bond restraints: 5624
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.01e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.36e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.442 -0.036 2.00e-02 2.50e+03 3.22e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.14e+00
  bond pdb=" C   ASN A 427 "
       pdb=" N   PRO A 428 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.021 1.30e-02 5.92e+03 2.71e+00
  ... (remaining 5619 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 7429
        1.65 -     3.30: 164
        3.30 -     4.95: 25
        4.95 -     6.61: 2
        6.61 -     8.26: 9
  Bond angle restraints: 7629
  Sorted by residual:
  angle pdb=" CA  TYR A 397 "
        pdb=" CB  TYR A 397 "
        pdb=" CG  TYR A 397 "
      ideal   model   delta    sigma   weight residual
     113.90  120.20   -6.30 1.80e+00 3.09e-01 1.22e+01
  angle pdb=" N   TRP A 315 "
        pdb=" CA  TRP A 315 "
        pdb=" C   TRP A 315 "
      ideal   model   delta    sigma   weight residual
     109.81  116.95   -7.14 2.21e+00 2.05e-01 1.04e+01
  angle pdb=" N   LEU A 377 "
        pdb=" CA  LEU A 377 "
        pdb=" C   LEU A 377 "
      ideal   model   delta    sigma   weight residual
     112.75  117.00   -4.25 1.36e+00 5.41e-01 9.78e+00
  angle pdb=" CA  TRP A 315 "
        pdb=" C   TRP A 315 "
        pdb=" N   PRO A 316 "
      ideal   model   delta    sigma   weight residual
     118.44  123.27   -4.83 1.59e+00 3.96e-01 9.23e+00
  angle pdb=" N   LEU A 455 "
        pdb=" CA  LEU A 455 "
        pdb=" C   LEU A 455 "
      ideal   model   delta    sigma   weight residual
     113.57  117.58   -4.01 1.38e+00 5.25e-01 8.46e+00
  ... (remaining 7624 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.76: 3227
       24.76 -    49.51: 113
       49.51 -    74.27: 30
       74.27 -    99.02: 10
       99.02 -   123.78: 15
  Dihedral angle restraints: 3395
    sinusoidal: 1507
      harmonic: 1888
  Sorted by residual:
  dihedral pdb=" CA  VAL A 625 "
           pdb=" C   VAL A 625 "
           pdb=" N   GLU A 626 "
           pdb=" CA  GLU A 626 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.57  -33.43     0      5.00e+00 4.00e-02 4.47e+01
  dihedral pdb=" CA  ASN A 605 "
           pdb=" C   ASN A 605 "
           pdb=" N   THR A 606 "
           pdb=" CA  THR A 606 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.44  -30.56     0      5.00e+00 4.00e-02 3.74e+01
  dihedral pdb=" C2  NAG C   1 "
           pdb=" C1  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C5  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   60.82 -123.78     1      3.00e+01 1.11e-03 1.66e+01
  ... (remaining 3392 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.198: 832
       0.198 -    0.396: 0
       0.396 -    0.595: 2
       0.595 -    0.793: 1
       0.793 -    0.991: 3
  Chirality restraints: 838
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.46   -0.94 2.00e-02 2.50e+03 2.23e+03
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.80   -0.60 2.00e-02 2.50e+03 8.98e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-02 2.50e+03 5.22e+02
  ... (remaining 835 not shown)

  Planarity restraints: 948
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 570 "   -0.040 2.00e-02 2.50e+03   2.35e-01 6.92e+02
        pdb=" CG  ASN A 570 "    0.066 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 570 "   -0.170 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 570 "    0.412 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "   -0.268 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 550 "    0.089 2.00e-02 2.50e+03   1.69e-01 3.58e+02
        pdb=" CG  ASN A 550 "   -0.048 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 550 "    0.072 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 550 "   -0.303 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "    0.190 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "   -0.174 2.00e-02 2.50e+03   1.49e-01 2.76e+02
        pdb=" C7  NAG C   2 "    0.036 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "    0.032 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "    0.243 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "   -0.138 2.00e-02 2.50e+03
  ... (remaining 945 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1704
        2.84 -     3.35: 4499
        3.35 -     3.87: 8505
        3.87 -     4.38: 8958
        4.38 -     4.90: 15784
  Nonbonded interactions: 39450
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 236 "
            pdb=" OG  SER A 239 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   ARG A 671 "
            pdb=" OG1 THR A 675 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   ASP A 524 "
            pdb=" OG1 THR A 527 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" O   PRO A 654 "
            pdb=" OG1 THR A 658 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" ND2 ASN A 389 "
            pdb=" O   GLY A 393 "
     model   vdw
     2.386 3.120
  ... (remaining 39445 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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=0.60 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             2.130
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.150
  Find NCS groups from input model:        0.060
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   22.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
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      :  0.003   0.040   5632  Z= 0.178
  Angle     :  1.373  46.907   7652  Z= 0.527
  Chirality :  0.077   0.991    838
  Planarity :  0.007   0.149    944
  Dihedral  : 16.826 123.779   2176
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  :  7.06 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.33 %

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: -0.49 (0.31), residues: 636
  helix: -0.07 (0.25), residues: 318
  sheet:  1.24 (0.63), residues: 72
  loop : -1.04 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 501 
 HIS   0.007   0.001   HIS A 160 
 PHE   0.011   0.001   PHE A 299 
 TYR   0.014   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A 276 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00256 (    4)
  link_NAG-ASN         : angle      22.97746 (   12)
  link_BETA1-4         : bond        0.01203 (    3)
  link_BETA1-4         : angle      23.56317 (    9)
  hydrogen bonds       : bond        0.13026 (  267)
  hydrogen bonds       : angle       5.21880 (  768)
  SS BOND              : bond        0.00203 (    1)
  SS BOND              : angle       0.38365 (    2)
  covalent geometry    : bond        0.00325 ( 5624)
  covalent geometry    : angle       0.63574 ( 7629)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 214
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 PRO cc_start: 0.8384 (Cg_exo) cc_final: 0.8084 (Cg_endo)
REVERT: A  101 PHE cc_start: 0.8475 (m-80) cc_final: 0.8244 (m-10)
REVERT: A  143 LEU cc_start: 0.7703 (tp) cc_final: 0.7151 (tt)
REVERT: A  146 TYR cc_start: 0.7632 (t80) cc_final: 0.6434 (t80)
REVERT: A  147 TRP cc_start: 0.5004 (OUTLIER) cc_final: 0.4342 (m100)
REVERT: A  152 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7495 (tt)
REVERT: A  153 ASP cc_start: 0.7957 (t70) cc_final: 0.7565 (t0)
REVERT: A  235 HIS cc_start: 0.8886 (t-90) cc_final: 0.8145 (t-90)
REVERT: A  296 ILE cc_start: 0.9140 (pt) cc_final: 0.8885 (tp)
REVERT: A  376 PHE cc_start: 0.7562 (t80) cc_final: 0.7276 (t80)
REVERT: A  379 TYR cc_start: 0.8767 (m-80) cc_final: 0.8559 (m-80)
REVERT: A  401 MET cc_start: 0.3007 (ptt) cc_final: 0.1948 (ptt)
REVERT: A  402 MET cc_start: 0.7862 (mmt) cc_final: 0.7258 (mtm)
REVERT: A  405 SER cc_start: 0.8906 (m) cc_final: 0.8682 (t)
REVERT: A  416 ARG cc_start: 0.8192 (ttm110) cc_final: 0.7502 (ttp-110)
REVERT: A  427 ASN cc_start: 0.8238 (t0) cc_final: 0.8037 (t0)
REVERT: A  436 ARG cc_start: 0.7505 (tpt170) cc_final: 0.5754 (ttm170)
REVERT: A  443 MET cc_start: 0.8927 (mtp) cc_final: 0.8727 (mtp)
REVERT: A  455 LEU cc_start: 0.7768 (mt) cc_final: 0.7540 (tp)
REVERT: A  468 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8109 (m-30)
REVERT: A  474 ASN cc_start: 0.8011 (m-40) cc_final: 0.7797 (p0)
REVERT: A  477 PHE cc_start: 0.8273 (m-80) cc_final: 0.7971 (m-10)
REVERT: A  503 GLN cc_start: 0.8837 (mm110) cc_final: 0.8476 (mm-40)
REVERT: A  505 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.7889 (tt)
REVERT: A  541 GLU cc_start: 0.7700 (tt0) cc_final: 0.7325 (pp20)
REVERT: A  555 LEU cc_start: 0.8267 (tp) cc_final: 0.7488 (tt)
REVERT: A  559 GLU cc_start: 0.6586 (tt0) cc_final: 0.6003 (tp30)
REVERT: A  563 GLU cc_start: 0.7682 (tt0) cc_final: 0.7449 (tt0)
REVERT: A  574 ARG cc_start: 0.6766 (mpt-90) cc_final: 0.6331 (mmm160)
REVERT: A  575 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7712 (tm-30)
REVERT: A  607 THR cc_start: 0.7968 (m) cc_final: 0.7608 (p)
REVERT: A  609 LEU cc_start: 0.3629 (OUTLIER) cc_final: 0.2115 (tp)
REVERT: A  681 PHE cc_start: 0.8498 (t80) cc_final: 0.8188 (t80)
REVERT: A  689 LEU cc_start: 0.8332 (tp) cc_final: 0.7995 (mt)
REVERT: A  705 ASN cc_start: 0.8622 (m-40) cc_final: 0.8280 (t0)
  outliers start: 33
  outliers final: 5
  residues processed: 238
  average time/residue: 0.2016
  time to fit residues: 58.9755
Evaluate side-chains
  128 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 433 GLN
A 503 GLN
A 587 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.158545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121623 restraints weight = 9144.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121936 restraints weight = 7378.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.124227 restraints weight = 6055.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3470
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3470 r_free = 0.3470    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   5632  Z= 0.200
  Angle     :  0.772  16.031   7652  Z= 0.367
  Chirality :  0.050   0.446    838
  Planarity :  0.005   0.053    944
  Dihedral  : 13.854  92.901    903
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.93 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  3.96 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  0.57 (0.34), residues: 636
  helix:  1.05 (0.28), residues: 326
  sheet:  1.20 (0.59), residues: 75
  loop : -0.79 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 493 
 HIS   0.008   0.001   HIS A 160 
 PHE   0.016   0.002   PHE A 535 
 TYR   0.022   0.001   TYR A 397 
 ARG   0.013   0.001   ARG A 476 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01088 (    4)
  link_NAG-ASN         : angle       7.05413 (   12)
  link_BETA1-4         : bond        0.00716 (    3)
  link_BETA1-4         : angle       1.51886 (    9)
  hydrogen bonds       : bond        0.04575 (  267)
  hydrogen bonds       : angle       4.37741 (  768)
  SS BOND              : bond        0.00148 (    1)
  SS BOND              : angle       5.50798 (    2)
  covalent geometry    : bond        0.00444 ( 5624)
  covalent geometry    : angle       0.71296 ( 7629)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.7803 (m-30) cc_final: 0.7011 (p0)
REVERT: A  131 LEU cc_start: 0.8726 (mt) cc_final: 0.8371 (mt)
REVERT: A  198 TRP cc_start: 0.8888 (p-90) cc_final: 0.8271 (p-90)
REVERT: A  235 HIS cc_start: 0.9058 (t-90) cc_final: 0.8033 (t-90)
REVERT: A  237 LEU cc_start: 0.9329 (mt) cc_final: 0.8235 (mt)
REVERT: A  293 LEU cc_start: 0.9595 (tp) cc_final: 0.9283 (tp)
REVERT: A  401 MET cc_start: 0.3454 (ptt) cc_final: 0.2421 (ptt)
REVERT: A  416 ARG cc_start: 0.7979 (ttm110) cc_final: 0.7472 (ttp-110)
REVERT: A  436 ARG cc_start: 0.7579 (tpt170) cc_final: 0.5919 (ttm170)
REVERT: A  477 PHE cc_start: 0.8631 (m-80) cc_final: 0.8386 (m-80)
REVERT: A  554 GLN cc_start: 0.6547 (tm-30) cc_final: 0.6043 (tm-30)
REVERT: A  559 GLU cc_start: 0.6611 (tt0) cc_final: 0.6327 (tp30)
REVERT: A  575 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7758 (mm-30)
REVERT: A  680 ARG cc_start: 0.8265 (ptp-110) cc_final: 0.7354 (ptt180)
REVERT: A  698 MET cc_start: 0.7746 (mmm) cc_final: 0.7347 (tpp)
REVERT: A  705 ASN cc_start: 0.8551 (m-40) cc_final: 0.8078 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1723
  time to fit residues: 34.1036
Evaluate side-chains
  111 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 HIS
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.159407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.123730 restraints weight = 8781.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.124159 restraints weight = 7539.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.125714 restraints weight = 7202.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3419
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3419
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.4411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5632  Z= 0.166
  Angle     :  0.736  12.196   7652  Z= 0.346
  Chirality :  0.047   0.277    838
  Planarity :  0.005   0.046    944
  Dihedral  : 11.954  86.823    903
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  0.83 (0.35), residues: 636
  helix:  1.43 (0.29), residues: 331
  sheet:  0.89 (0.57), residues: 75
  loop : -0.83 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 390 
 HIS   0.004   0.001   HIS A 410 
 PHE   0.019   0.002   PHE A 535 
 TYR   0.022   0.002   TYR A 397 
 ARG   0.008   0.001   ARG A 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01305 (    4)
  link_NAG-ASN         : angle       6.59092 (   12)
  link_BETA1-4         : bond        0.00813 (    3)
  link_BETA1-4         : angle       1.70168 (    9)
  hydrogen bonds       : bond        0.04309 (  267)
  hydrogen bonds       : angle       4.19270 (  768)
  SS BOND              : bond        0.00570 (    1)
  SS BOND              : angle       3.07163 (    2)
  covalent geometry    : bond        0.00369 ( 5624)
  covalent geometry    : angle       0.68438 ( 7629)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.7755 (m-30) cc_final: 0.7103 (p0)
REVERT: A  131 LEU cc_start: 0.8816 (mt) cc_final: 0.8549 (mt)
REVERT: A  198 TRP cc_start: 0.8977 (p-90) cc_final: 0.8191 (p-90)
REVERT: A  235 HIS cc_start: 0.9127 (t-90) cc_final: 0.8424 (t-90)
REVERT: A  293 LEU cc_start: 0.9557 (tp) cc_final: 0.9339 (tp)
REVERT: A  397 TYR cc_start: 0.8952 (p90) cc_final: 0.8685 (p90)
REVERT: A  401 MET cc_start: 0.4216 (ptt) cc_final: 0.3678 (ptt)
REVERT: A  416 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7524 (ttp-110)
REVERT: A  477 PHE cc_start: 0.8616 (m-80) cc_final: 0.8232 (m-80)
REVERT: A  505 LEU cc_start: 0.8266 (tt) cc_final: 0.7757 (tt)
REVERT: A  559 GLU cc_start: 0.6837 (tt0) cc_final: 0.6426 (tp30)
REVERT: A  615 LEU cc_start: 0.9009 (tt) cc_final: 0.8804 (tt)
REVERT: A  680 ARG cc_start: 0.8282 (ptp-110) cc_final: 0.7341 (ptt180)
REVERT: A  698 MET cc_start: 0.8266 (mmm) cc_final: 0.7971 (mmt)
REVERT: A  705 ASN cc_start: 0.8776 (m-40) cc_final: 0.8259 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1691
  time to fit residues: 30.5075
Evaluate side-chains
  105 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 11 optimal weight:    0.1980
   chunk 10 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0000
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.4784

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.161239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.126236 restraints weight = 8812.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.125188 restraints weight = 6956.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.125940 restraints weight = 6189.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3407
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3407
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.4659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5632  Z= 0.131
  Angle     :  0.654  10.483   7652  Z= 0.313
  Chirality :  0.045   0.269    838
  Planarity :  0.005   0.057    944
  Dihedral  : 10.704  73.988    903
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  1.07 (0.35), residues: 636
  helix:  1.68 (0.30), residues: 324
  sheet:  0.70 (0.56), residues: 75
  loop : -0.64 (0.43), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.024   0.001   PHE A 682 
 TYR   0.020   0.001   TYR A 397 
 ARG   0.016   0.001   ARG A 476 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00817 (    4)
  link_NAG-ASN         : angle       5.29829 (   12)
  link_BETA1-4         : bond        0.00205 (    3)
  link_BETA1-4         : angle       1.59436 (    9)
  hydrogen bonds       : bond        0.03922 (  267)
  hydrogen bonds       : angle       4.10889 (  768)
  SS BOND              : bond        0.00843 (    1)
  SS BOND              : angle       2.25468 (    2)
  covalent geometry    : bond        0.00281 ( 5624)
  covalent geometry    : angle       0.61671 ( 7629)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.7762 (m-30) cc_final: 0.7094 (p0)
REVERT: A  131 LEU cc_start: 0.8713 (mt) cc_final: 0.8430 (mt)
REVERT: A  235 HIS cc_start: 0.9015 (t-90) cc_final: 0.8450 (t-90)
REVERT: A  237 LEU cc_start: 0.9277 (mt) cc_final: 0.8858 (mt)
REVERT: A  292 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8479 (mm-40)
REVERT: A  293 LEU cc_start: 0.9537 (tp) cc_final: 0.9324 (tp)
REVERT: A  397 TYR cc_start: 0.8886 (p90) cc_final: 0.8669 (p90)
REVERT: A  401 MET cc_start: 0.4197 (ptt) cc_final: 0.3612 (ptt)
REVERT: A  416 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7548 (ttp-110)
REVERT: A  477 PHE cc_start: 0.8680 (m-80) cc_final: 0.8151 (m-80)
REVERT: A  559 GLU cc_start: 0.6700 (tt0) cc_final: 0.6251 (tp30)
REVERT: A  575 GLU cc_start: 0.8675 (mt-10) cc_final: 0.7724 (tm-30)
REVERT: A  615 LEU cc_start: 0.9071 (tt) cc_final: 0.8847 (tt)
REVERT: A  680 ARG cc_start: 0.8283 (ptp-110) cc_final: 0.7432 (ptt180)
REVERT: A  705 ASN cc_start: 0.8898 (m-40) cc_final: 0.8327 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1646
  time to fit residues: 29.1870
Evaluate side-chains
  99 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    0.3980
   chunk 43 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 2 optimal weight:    0.4980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 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 = 0.3881 r_free = 0.3881 target = 0.159160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.123496 restraints weight = 8890.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.120710 restraints weight = 7964.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.122470 restraints weight = 7548.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5632  Z= 0.143
  Angle     :  0.627   7.698   7652  Z= 0.309
  Chirality :  0.044   0.254    838
  Planarity :  0.004   0.041    944
  Dihedral  :  9.864  65.192    903
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  1.21 (0.36), residues: 636
  helix:  1.73 (0.30), residues: 327
  sheet:  0.55 (0.56), residues: 75
  loop : -0.39 (0.46), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 410 
 PHE   0.016   0.001   PHE A 535 
 TYR   0.021   0.001   TYR A 397 
 ARG   0.006   0.000   ARG A 476 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00717 (    4)
  link_NAG-ASN         : angle       3.49364 (   12)
  link_BETA1-4         : bond        0.00612 (    3)
  link_BETA1-4         : angle       1.42943 (    9)
  hydrogen bonds       : bond        0.04013 (  267)
  hydrogen bonds       : angle       4.09218 (  768)
  SS BOND              : bond        0.00940 (    1)
  SS BOND              : angle       2.63034 (    2)
  covalent geometry    : bond        0.00321 ( 5624)
  covalent geometry    : angle       0.60947 ( 7629)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7143 (mmt180) cc_final: 0.6270 (mmm160)
REVERT: A  113 ASP cc_start: 0.7709 (m-30) cc_final: 0.7078 (p0)
REVERT: A  235 HIS cc_start: 0.9129 (t-90) cc_final: 0.8416 (t-90)
REVERT: A  237 LEU cc_start: 0.9231 (mt) cc_final: 0.8840 (mt)
REVERT: A  293 LEU cc_start: 0.9540 (tp) cc_final: 0.9270 (tp)
REVERT: A  397 TYR cc_start: 0.8937 (p90) cc_final: 0.8619 (p90)
REVERT: A  401 MET cc_start: 0.4323 (ptt) cc_final: 0.3723 (ptt)
REVERT: A  416 ARG cc_start: 0.8126 (ttm110) cc_final: 0.7752 (ttp-110)
REVERT: A  477 PHE cc_start: 0.8703 (m-80) cc_final: 0.8086 (m-80)
REVERT: A  559 GLU cc_start: 0.6801 (tt0) cc_final: 0.6408 (tp30)
REVERT: A  615 LEU cc_start: 0.9106 (tt) cc_final: 0.8858 (tt)
REVERT: A  681 PHE cc_start: 0.8517 (t80) cc_final: 0.8121 (t80)
REVERT: A  705 ASN cc_start: 0.8981 (m-40) cc_final: 0.8448 (t0)
REVERT: A  725 LEU cc_start: 0.8833 (pp) cc_final: 0.8625 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1657
  time to fit residues: 27.5861
Evaluate side-chains
  100 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0030
   chunk 57 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 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 = 0.3884 r_free = 0.3884 target = 0.159186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.123890 restraints weight = 8745.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.121559 restraints weight = 7810.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.123356 restraints weight = 7287.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.5061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5632  Z= 0.133
  Angle     :  0.651  12.668   7652  Z= 0.310
  Chirality :  0.044   0.257    838
  Planarity :  0.004   0.046    944
  Dihedral  :  9.486  59.121    903
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  1.26 (0.35), residues: 636
  helix:  1.80 (0.30), residues: 325
  sheet:  0.51 (0.57), residues: 75
  loop : -0.37 (0.45), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 678 
 PHE   0.014   0.001   PHE A 150 
 TYR   0.019   0.001   TYR A 397 
 ARG   0.003   0.000   ARG A 476 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01009 (    4)
  link_NAG-ASN         : angle       6.01509 (   12)
  link_BETA1-4         : bond        0.00748 (    3)
  link_BETA1-4         : angle       1.60802 (    9)
  hydrogen bonds       : bond        0.03853 (  267)
  hydrogen bonds       : angle       4.00838 (  768)
  SS BOND              : bond        0.00626 (    1)
  SS BOND              : angle       2.66862 (    2)
  covalent geometry    : bond        0.00294 ( 5624)
  covalent geometry    : angle       0.60287 ( 7629)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ARG cc_start: 0.8732 (tmm-80) cc_final: 0.8247 (tmm-80)
REVERT: A  100 ARG cc_start: 0.7126 (mmt180) cc_final: 0.6745 (mmm160)
REVERT: A  113 ASP cc_start: 0.7636 (m-30) cc_final: 0.7037 (p0)
REVERT: A  235 HIS cc_start: 0.9019 (t-90) cc_final: 0.8357 (t-90)
REVERT: A  237 LEU cc_start: 0.9282 (mt) cc_final: 0.8847 (mt)
REVERT: A  293 LEU cc_start: 0.9530 (tp) cc_final: 0.9252 (tp)
REVERT: A  397 TYR cc_start: 0.8934 (p90) cc_final: 0.8599 (p90)
REVERT: A  401 MET cc_start: 0.4356 (ptt) cc_final: 0.3713 (ptt)
REVERT: A  416 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7746 (ttp-110)
REVERT: A  477 PHE cc_start: 0.8653 (m-80) cc_final: 0.8160 (m-80)
REVERT: A  559 GLU cc_start: 0.6807 (tt0) cc_final: 0.6325 (tp30)
REVERT: A  615 LEU cc_start: 0.9040 (tt) cc_final: 0.8772 (tt)
REVERT: A  681 PHE cc_start: 0.8418 (t80) cc_final: 0.8037 (t80)
REVERT: A  705 ASN cc_start: 0.8925 (m-40) cc_final: 0.8412 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1637
  time to fit residues: 26.3785
Evaluate side-chains
  98 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 31 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 580 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.156869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121445 restraints weight = 8878.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121792 restraints weight = 7309.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.123526 restraints weight = 6414.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3455
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3455 r_free = 0.3455    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.5225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5632  Z= 0.152
  Angle     :  0.662  11.891   7652  Z= 0.319
  Chirality :  0.043   0.232    838
  Planarity :  0.004   0.040    944
  Dihedral  :  9.089  58.235    903
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  1.23 (0.35), residues: 636
  helix:  1.87 (0.30), residues: 319
  sheet:  0.28 (0.57), residues: 75
  loop : -0.38 (0.45), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 390 
 HIS   0.003   0.001   HIS A 410 
 PHE   0.029   0.001   PHE A 682 
 TYR   0.020   0.001   TYR A 397 
 ARG   0.003   0.000   ARG A  83 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00861 (    4)
  link_NAG-ASN         : angle       5.16794 (   12)
  link_BETA1-4         : bond        0.00611 (    3)
  link_BETA1-4         : angle       1.50861 (    9)
  hydrogen bonds       : bond        0.04109 (  267)
  hydrogen bonds       : angle       4.11284 (  768)
  SS BOND              : bond        0.00917 (    1)
  SS BOND              : angle       2.30453 (    2)
  covalent geometry    : bond        0.00343 ( 5624)
  covalent geometry    : angle       0.62680 ( 7629)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ARG cc_start: 0.8749 (tmm-80) cc_final: 0.8282 (tmm-80)
REVERT: A  100 ARG cc_start: 0.7080 (mmt180) cc_final: 0.6697 (mmm160)
REVERT: A  113 ASP cc_start: 0.7709 (m-30) cc_final: 0.7057 (p0)
REVERT: A  129 MET cc_start: 0.8375 (mmm) cc_final: 0.7765 (ttm)
REVERT: A  153 ASP cc_start: 0.8603 (t0) cc_final: 0.8361 (t0)
REVERT: A  235 HIS cc_start: 0.9020 (t-90) cc_final: 0.8183 (t-90)
REVERT: A  237 LEU cc_start: 0.9292 (mt) cc_final: 0.8652 (mt)
REVERT: A  293 LEU cc_start: 0.9540 (tp) cc_final: 0.9217 (tp)
REVERT: A  397 TYR cc_start: 0.8976 (p90) cc_final: 0.8590 (p90)
REVERT: A  401 MET cc_start: 0.4168 (ptt) cc_final: 0.3480 (ptt)
REVERT: A  416 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7728 (ttp-110)
REVERT: A  427 ASN cc_start: 0.8047 (m110) cc_final: 0.7835 (m-40)
REVERT: A  477 PHE cc_start: 0.8681 (m-80) cc_final: 0.8139 (m-80)
REVERT: A  559 GLU cc_start: 0.6849 (tt0) cc_final: 0.6298 (tp30)
REVERT: A  615 LEU cc_start: 0.9015 (tt) cc_final: 0.8744 (tt)
REVERT: A  681 PHE cc_start: 0.8312 (t80) cc_final: 0.7951 (t80)
REVERT: A  705 ASN cc_start: 0.8949 (m-40) cc_final: 0.8418 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1581
  time to fit residues: 25.8296
Evaluate side-chains
  98 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0870
   chunk 14 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 12 optimal weight:    0.1980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 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 = 0.3851 r_free = 0.3851 target = 0.157119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.122172 restraints weight = 9015.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.121608 restraints weight = 8788.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.123080 restraints weight = 7757.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3435
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3435
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.5327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5632  Z= 0.126
  Angle     :  0.640  10.991   7652  Z= 0.304
  Chirality :  0.043   0.240    838
  Planarity :  0.004   0.042    944
  Dihedral  :  8.570  57.373    903
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  1.26 (0.35), residues: 636
  helix:  1.87 (0.30), residues: 319
  sheet:  0.33 (0.57), residues: 75
  loop : -0.35 (0.45), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 390 
 HIS   0.004   0.001   HIS A 287 
 PHE   0.021   0.001   PHE A 682 
 TYR   0.018   0.001   TYR A 397 
 ARG   0.005   0.000   ARG A  83 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00897 (    4)
  link_NAG-ASN         : angle       4.78571 (   12)
  link_BETA1-4         : bond        0.00657 (    3)
  link_BETA1-4         : angle       1.52235 (    9)
  hydrogen bonds       : bond        0.03836 (  267)
  hydrogen bonds       : angle       4.00997 (  768)
  SS BOND              : bond        0.00770 (    1)
  SS BOND              : angle       1.67605 (    2)
  covalent geometry    : bond        0.00279 ( 5624)
  covalent geometry    : angle       0.60920 ( 7629)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7210 (mmt180) cc_final: 0.6750 (mmm160)
REVERT: A  113 ASP cc_start: 0.7661 (m-30) cc_final: 0.7102 (p0)
REVERT: A  235 HIS cc_start: 0.9098 (t-90) cc_final: 0.8143 (t-90)
REVERT: A  237 LEU cc_start: 0.9245 (mt) cc_final: 0.8602 (mt)
REVERT: A  272 PHE cc_start: 0.7388 (m-80) cc_final: 0.7156 (m-80)
REVERT: A  293 LEU cc_start: 0.9522 (tp) cc_final: 0.9199 (tp)
REVERT: A  397 TYR cc_start: 0.9028 (p90) cc_final: 0.8639 (p90)
REVERT: A  401 MET cc_start: 0.4181 (ptt) cc_final: 0.3477 (ptt)
REVERT: A  443 MET cc_start: 0.8793 (ptp) cc_final: 0.8475 (ptp)
REVERT: A  477 PHE cc_start: 0.8668 (m-80) cc_final: 0.8119 (m-80)
REVERT: A  559 GLU cc_start: 0.6646 (tt0) cc_final: 0.6199 (tp30)
REVERT: A  615 LEU cc_start: 0.9020 (tt) cc_final: 0.8684 (tt)
REVERT: A  681 PHE cc_start: 0.8390 (t80) cc_final: 0.8070 (t80)
REVERT: A  705 ASN cc_start: 0.8928 (m-40) cc_final: 0.8435 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1618
  time to fit residues: 25.4452
Evaluate side-chains
  96 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 8 optimal weight:    0.4980
   chunk 25 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 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 = 0.3869 r_free = 0.3869 target = 0.158471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.123580 restraints weight = 8966.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.123089 restraints weight = 8506.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.125089 restraints weight = 8096.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3459
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3459 r_free = 0.3459    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3459 r_free = 0.3459    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3459
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.5407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5632  Z= 0.131
  Angle     :  0.636  10.416   7652  Z= 0.306
  Chirality :  0.043   0.245    838
  Planarity :  0.004   0.041    944
  Dihedral  :  8.163  59.061    903
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  1.31 (0.35), residues: 636
  helix:  1.89 (0.30), residues: 319
  sheet:  0.44 (0.57), residues: 74
  loop : -0.31 (0.45), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 390 
 HIS   0.004   0.001   HIS A 287 
 PHE   0.020   0.001   PHE A 682 
 TYR   0.018   0.001   TYR A 397 
 ARG   0.006   0.000   ARG A  68 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00851 (    4)
  link_NAG-ASN         : angle       4.57364 (   12)
  link_BETA1-4         : bond        0.00530 (    3)
  link_BETA1-4         : angle       1.45562 (    9)
  hydrogen bonds       : bond        0.03975 (  267)
  hydrogen bonds       : angle       4.04204 (  768)
  SS BOND              : bond        0.00433 (    1)
  SS BOND              : angle       1.84501 (    2)
  covalent geometry    : bond        0.00295 ( 5624)
  covalent geometry    : angle       0.60734 ( 7629)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7217 (mmt180) cc_final: 0.6823 (mmm160)
REVERT: A  113 ASP cc_start: 0.7687 (m-30) cc_final: 0.7131 (p0)
REVERT: A  235 HIS cc_start: 0.9107 (t-90) cc_final: 0.8124 (t-90)
REVERT: A  237 LEU cc_start: 0.9274 (mt) cc_final: 0.8575 (mt)
REVERT: A  293 LEU cc_start: 0.9529 (tp) cc_final: 0.9188 (tp)
REVERT: A  319 LEU cc_start: 0.8324 (mp) cc_final: 0.7989 (mt)
REVERT: A  401 MET cc_start: 0.4225 (ptt) cc_final: 0.3546 (ptt)
REVERT: A  477 PHE cc_start: 0.8673 (m-80) cc_final: 0.8174 (m-80)
REVERT: A  559 GLU cc_start: 0.6603 (tt0) cc_final: 0.6146 (tp30)
REVERT: A  615 LEU cc_start: 0.9055 (tt) cc_final: 0.8728 (tt)
REVERT: A  705 ASN cc_start: 0.8897 (m-40) cc_final: 0.8496 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.2023
  time to fit residues: 32.8080
Evaluate side-chains
  95 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0170
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 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 = 0.3863 r_free = 0.3863 target = 0.157498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.122554 restraints weight = 8957.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.121587 restraints weight = 7882.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.123200 restraints weight = 7023.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3390
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.5535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5632  Z= 0.122
  Angle     :  0.636   9.902   7652  Z= 0.303
  Chirality :  0.042   0.251    838
  Planarity :  0.004   0.041    944
  Dihedral  :  7.720  54.910    903
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  1.43 (0.35), residues: 636
  helix:  1.96 (0.30), residues: 320
  sheet:  0.58 (0.56), residues: 77
  loop : -0.27 (0.45), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 390 
 HIS   0.004   0.001   HIS A 287 
 PHE   0.020   0.001   PHE A 682 
 TYR   0.039   0.001   TYR A 397 
 ARG   0.006   0.000   ARG A  68 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00815 (    4)
  link_NAG-ASN         : angle       4.33489 (   12)
  link_BETA1-4         : bond        0.00665 (    3)
  link_BETA1-4         : angle       1.75920 (    9)
  hydrogen bonds       : bond        0.03769 (  267)
  hydrogen bonds       : angle       3.95356 (  768)
  SS BOND              : bond        0.00340 (    1)
  SS BOND              : angle       1.46325 (    2)
  covalent geometry    : bond        0.00269 ( 5624)
  covalent geometry    : angle       0.60988 ( 7629)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ARG cc_start: 0.8811 (tmm160) cc_final: 0.8145 (tmm160)
REVERT: A  100 ARG cc_start: 0.7165 (mmt180) cc_final: 0.6784 (mmm160)
REVERT: A  113 ASP cc_start: 0.7670 (m-30) cc_final: 0.7155 (p0)
REVERT: A  235 HIS cc_start: 0.9158 (t-90) cc_final: 0.8082 (t-90)
REVERT: A  237 LEU cc_start: 0.9282 (mt) cc_final: 0.8506 (mt)
REVERT: A  293 LEU cc_start: 0.9521 (tp) cc_final: 0.9183 (tp)
REVERT: A  319 LEU cc_start: 0.8401 (mp) cc_final: 0.8082 (mt)
REVERT: A  401 MET cc_start: 0.4241 (ptt) cc_final: 0.3531 (ptt)
REVERT: A  477 PHE cc_start: 0.8664 (m-80) cc_final: 0.8109 (m-80)
REVERT: A  559 GLU cc_start: 0.6551 (tt0) cc_final: 0.6088 (tp30)
REVERT: A  689 LEU cc_start: 0.8070 (tp) cc_final: 0.7739 (mt)
REVERT: A  705 ASN cc_start: 0.8881 (m-40) cc_final: 0.8492 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1625
  time to fit residues: 26.3726
Evaluate side-chains
  98 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 14 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   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 479 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 = 0.3839 r_free = 0.3839 target = 0.155145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.120360 restraints weight = 9157.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.118978 restraints weight = 7416.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.120303 restraints weight = 7870.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.5678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5632  Z= 0.139
  Angle     :  0.637   9.357   7652  Z= 0.309
  Chirality :  0.043   0.262    838
  Planarity :  0.004   0.040    944
  Dihedral  :  7.665  54.644    903
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  1.42 (0.35), residues: 636
  helix:  2.03 (0.30), residues: 319
  sheet: -0.04 (0.55), residues: 81
  loop : -0.15 (0.45), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 678 
 PHE   0.018   0.002   PHE A 682 
 TYR   0.033   0.001   TYR A 397 
 ARG   0.004   0.000   ARG A  68 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00804 (    4)
  link_NAG-ASN         : angle       4.15399 (   12)
  link_BETA1-4         : bond        0.00619 (    3)
  link_BETA1-4         : angle       1.63471 (    9)
  hydrogen bonds       : bond        0.04028 (  267)
  hydrogen bonds       : angle       3.98268 (  768)
  SS BOND              : bond        0.00410 (    1)
  SS BOND              : angle       1.81697 (    2)
  covalent geometry    : bond        0.00313 ( 5624)
  covalent geometry    : angle       0.61298 ( 7629)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2222.64 seconds
wall clock time: 39 minutes 24.97 seconds (2364.97 seconds total)