Starting phenix.real_space_refine
on Sat May 10 07:21:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bvo_44939/05_2025/9bvo_44939.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bvo_44939/05_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_44939/05_2025/9bvo_44939.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bvo_44939/05_2025/9bvo_44939.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bvo_44939/05_2025/9bvo_44939.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bvo_44939/05_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-5687/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: 4.25, 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: 1.54
  Conformation dependent library (CDL) restraints added in 760.3 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: 0.49
  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: 1.35

  Time building geometry restraints manager: 1.72 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:                  0.010
  Normalize map: mean=0, sd=1:             2.460
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.610
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.230
-------------------------------------------------------------------------------
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  : 0.531 
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: 0.2022
  time to fit residues: 59.3209
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  : 0.574 
-------------------------------------------------------------------------------
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 = 0.121621 restraints weight = 9144.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121935 restraints weight = 7379.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.124224 restraints weight = 6055.624|
|-----------------------------------------------------------------------------|
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       1.51885 (    9)
  hydrogen bonds       : bond        0.04575 (  267)
  hydrogen bonds       : angle       4.37741 (  768)
  SS BOND              : bond        0.00148 (    1)
  SS BOND              : angle       5.50800 (    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  : 0.547 
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: 0.3453 (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: 0.6546 (tm-30) cc_final: 0.6042 (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: 0.7745 (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: 0.1701
  time to fit residues: 33.6517
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  : 0.599 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 59 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   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:    0.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.161166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.125036 restraints weight = 8813.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.124763 restraints weight = 7244.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.126761 restraints weight = 6690.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3413
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    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 = 0.3412 r_free = 0.3412    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3412
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.4343

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= 0.161
  Angle     :  0.738  13.215   7652  Z= 0.344
  Chirality :  0.047   0.306    838
  Planarity :  0.005   0.053    944
  Dihedral  : 12.107  87.987    903
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  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:  0.79 (0.34), residues: 636
  helix:  1.38 (0.29), residues: 331
  sheet:  0.94 (0.57), residues: 75
  loop : -0.86 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 390 
 HIS   0.006   0.001   HIS A 160 
 PHE   0.018   0.001   PHE A 535 
 TYR   0.022   0.002   TYR A 397 
 ARG   0.009   0.001   ARG A 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00684 (    4)
  link_NAG-ASN         : angle       7.69800 (   12)
  link_BETA1-4         : bond        0.00877 (    3)
  link_BETA1-4         : angle       1.70684 (    9)
  hydrogen bonds       : bond        0.04231 (  267)
  hydrogen bonds       : angle       4.17221 (  768)
  SS BOND              : bond        0.01111 (    1)
  SS BOND              : angle       3.60113 (    2)
  covalent geometry    : bond        0.00360 ( 5624)
  covalent geometry    : angle       0.66792 ( 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
  136 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.7778 (m-30) cc_final: 0.7059 (p0)
REVERT: A  131 LEU cc_start: 0.8804 (mt) cc_final: 0.8521 (mt)
REVERT: A  198 TRP cc_start: 0.8979 (p-90) cc_final: 0.8203 (p-90)
REVERT: A  235 HIS cc_start: 0.9128 (t-90) cc_final: 0.8329 (t-90)
REVERT: A  293 LEU cc_start: 0.9548 (tp) cc_final: 0.9304 (tp)
REVERT: A  397 TYR cc_start: 0.8917 (p90) cc_final: 0.8713 (p90)
REVERT: A  401 MET cc_start: 0.4174 (ptt) cc_final: 0.3683 (ptt)
REVERT: A  416 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7505 (ttp-110)
REVERT: A  477 PHE cc_start: 0.8587 (m-80) cc_final: 0.8225 (m-80)
REVERT: A  559 GLU cc_start: 0.6802 (tt0) cc_final: 0.6392 (tp30)
REVERT: A  575 GLU cc_start: 0.8705 (mt-10) cc_final: 0.7881 (tm-30)
REVERT: A  615 LEU cc_start: 0.8990 (tt) cc_final: 0.8780 (tt)
REVERT: A  680 ARG cc_start: 0.8329 (ptp-110) cc_final: 0.7410 (ptt180)
REVERT: A  698 MET cc_start: 0.8298 (mmm) cc_final: 0.7971 (mmm)
REVERT: A  705 ASN cc_start: 0.8754 (m-40) cc_final: 0.8245 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1637
  time to fit residues: 29.1316
Evaluate side-chains
  103 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.7518

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.159430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.123920 restraints weight = 9058.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.124270 restraints weight = 7178.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.125991 restraints weight = 6590.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.4728

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= 0.151
  Angle     :  0.667   8.562   7652  Z= 0.324
  Chirality :  0.045   0.261    838
  Planarity :  0.005   0.058    944
  Dihedral  : 10.623  72.994    903
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  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:  1.69 (0.30), residues: 324
  sheet:  0.71 (0.56), residues: 75
  loop : -0.64 (0.43), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 390 
 HIS   0.004   0.001   HIS A 410 
 PHE   0.023   0.002   PHE A 682 
 TYR   0.021   0.002   TYR A 397 
 ARG   0.015   0.001   ARG A 476 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00916 (    4)
  link_NAG-ASN         : angle       4.74694 (   12)
  link_BETA1-4         : bond        0.00776 (    3)
  link_BETA1-4         : angle       1.69633 (    9)
  hydrogen bonds       : bond        0.04094 (  267)
  hydrogen bonds       : angle       4.12575 (  768)
  SS BOND              : bond        0.00848 (    1)
  SS BOND              : angle       2.84892 (    2)
  covalent geometry    : bond        0.00336 ( 5624)
  covalent geometry    : angle       0.63618 ( 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
  131 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.556 
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: 0.7756 (m-30) cc_final: 0.7049 (p0)
REVERT: A  129 MET cc_start: 0.8143 (mtt) cc_final: 0.6946 (ttm)
REVERT: A  235 HIS cc_start: 0.9060 (t-90) cc_final: 0.8143 (t-90)
REVERT: A  237 LEU cc_start: 0.9213 (mt) cc_final: 0.8584 (mt)
REVERT: A  293 LEU cc_start: 0.9534 (tp) cc_final: 0.9246 (tp)
REVERT: A  397 TYR cc_start: 0.8942 (p90) cc_final: 0.8693 (p90)
REVERT: A  401 MET cc_start: 0.4287 (ptt) cc_final: 0.3681 (ptt)
REVERT: A  416 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7568 (ttp-110)
REVERT: A  477 PHE cc_start: 0.8680 (m-80) cc_final: 0.8047 (m-80)
REVERT: A  493 TRP cc_start: 0.7767 (t60) cc_final: 0.7326 (t60)
REVERT: A  559 GLU cc_start: 0.6834 (tt0) cc_final: 0.6383 (tp30)
REVERT: A  615 LEU cc_start: 0.9033 (tt) cc_final: 0.8811 (tt)
REVERT: A  705 ASN cc_start: 0.8906 (m-40) cc_final: 0.8325 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1455
  time to fit residues: 25.5768
Evaluate side-chains
  101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0470
   chunk 43 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 54 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0870
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.5456

-------------------------------------------------------------------------------
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 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 = 0.3890 r_free = 0.3890 target = 0.160537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.126355 restraints weight = 8814.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.123027 restraints weight = 8027.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.124693 restraints weight = 7386.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3385
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.4925

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= 0.127
  Angle     :  0.611   7.754   7652  Z= 0.299
  Chirality :  0.043   0.250    838
  Planarity :  0.004   0.041    944
  Dihedral  :  9.664  63.096    903
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  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:  1.25 (0.36), residues: 636
  helix:  1.77 (0.30), residues: 326
  sheet:  0.68 (0.57), residues: 75
  loop : -0.43 (0.46), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 678 
 PHE   0.018   0.001   PHE A 366 
 TYR   0.022   0.001   TYR A 397 
 ARG   0.005   0.000   ARG A 476 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00740 (    4)
  link_NAG-ASN         : angle       3.39888 (   12)
  link_BETA1-4         : bond        0.00647 (    3)
  link_BETA1-4         : angle       1.37940 (    9)
  hydrogen bonds       : bond        0.03831 (  267)
  hydrogen bonds       : angle       4.00399 (  768)
  SS BOND              : bond        0.01096 (    1)
  SS BOND              : angle       2.25297 (    2)
  covalent geometry    : bond        0.00280 ( 5624)
  covalent geometry    : angle       0.59364 ( 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  : 0.604 
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: 0.7151 (mmt180) cc_final: 0.6267 (mmm160)
REVERT: A  113 ASP cc_start: 0.7659 (m-30) cc_final: 0.7050 (p0)
REVERT: A  153 ASP cc_start: 0.8586 (t0) cc_final: 0.8368 (t0)
REVERT: A  235 HIS cc_start: 0.9029 (t-90) cc_final: 0.8165 (t-90)
REVERT: A  237 LEU cc_start: 0.9280 (mt) cc_final: 0.8563 (mt)
REVERT: A  293 LEU cc_start: 0.9522 (tp) cc_final: 0.9232 (tp)
REVERT: A  397 TYR cc_start: 0.8952 (p90) cc_final: 0.8583 (p90)
REVERT: A  401 MET cc_start: 0.4276 (ptt) cc_final: 0.3630 (ptt)
REVERT: A  402 MET cc_start: 0.5955 (mtm) cc_final: 0.5216 (mtm)
REVERT: A  416 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7753 (ttp-110)
REVERT: A  443 MET cc_start: 0.8876 (ptp) cc_final: 0.8545 (ptp)
REVERT: A  477 PHE cc_start: 0.8575 (m-80) cc_final: 0.8009 (m-80)
REVERT: A  559 GLU cc_start: 0.6777 (tt0) cc_final: 0.6275 (tp30)
REVERT: A  615 LEU cc_start: 0.9065 (tt) cc_final: 0.8799 (tt)
REVERT: A  705 ASN cc_start: 0.8935 (m-40) cc_final: 0.8427 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1626
  time to fit residues: 26.9583
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  : 0.565 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0970
   chunk 57 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0170
   chunk 12 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5016

-------------------------------------------------------------------------------
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 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 = 0.3888 r_free = 0.3888 target = 0.160104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.125537 restraints weight = 8786.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.123113 restraints weight = 8215.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.124836 restraints weight = 7367.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3397
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.5093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5632  Z= 0.126
  Angle     :  0.648  12.006   7652  Z= 0.307
  Chirality :  0.044   0.238    838
  Planarity :  0.004   0.038    944
  Dihedral  :  9.322  58.891    903
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  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:  1.28 (0.35), residues: 636
  helix:  1.77 (0.30), residues: 325
  sheet:  0.71 (0.55), residues: 78
  loop : -0.37 (0.46), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 678 
 PHE   0.014   0.001   PHE A 366 
 TYR   0.018   0.001   TYR A 397 
 ARG   0.004   0.000   ARG A 476 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01009 (    4)
  link_NAG-ASN         : angle       5.96016 (   12)
  link_BETA1-4         : bond        0.00671 (    3)
  link_BETA1-4         : angle       1.49551 (    9)
  hydrogen bonds       : bond        0.03758 (  267)
  hydrogen bonds       : angle       3.96938 (  768)
  SS BOND              : bond        0.00760 (    1)
  SS BOND              : angle       2.13411 (    2)
  covalent geometry    : bond        0.00275 ( 5624)
  covalent geometry    : angle       0.60084 ( 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
  126 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.580 
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: 0.8607 (tmm-80) cc_final: 0.8124 (tmm-80)
REVERT: A  100 ARG cc_start: 0.7017 (mmt180) cc_final: 0.6678 (mmm160)
REVERT: A  113 ASP cc_start: 0.7718 (m-30) cc_final: 0.7045 (p0)
REVERT: A  235 HIS cc_start: 0.9175 (t-90) cc_final: 0.8377 (t-90)
REVERT: A  236 TRP cc_start: 0.8200 (p-90) cc_final: 0.7986 (p-90)
REVERT: A  237 LEU cc_start: 0.9275 (mt) cc_final: 0.8784 (mt)
REVERT: A  292 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8512 (mm-40)
REVERT: A  293 LEU cc_start: 0.9507 (tp) cc_final: 0.9279 (tp)
REVERT: A  391 THR cc_start: 0.7874 (p) cc_final: 0.7647 (p)
REVERT: A  397 TYR cc_start: 0.8968 (p90) cc_final: 0.8626 (p90)
REVERT: A  401 MET cc_start: 0.4160 (ptt) cc_final: 0.3564 (ptt)
REVERT: A  402 MET cc_start: 0.6017 (mtm) cc_final: 0.5272 (mtm)
REVERT: A  416 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7825 (ttp-110)
REVERT: A  443 MET cc_start: 0.8845 (ptp) cc_final: 0.8575 (ptm)
REVERT: A  477 PHE cc_start: 0.8598 (m-80) cc_final: 0.8163 (m-80)
REVERT: A  559 GLU cc_start: 0.6696 (tt0) cc_final: 0.6232 (tp30)
REVERT: A  615 LEU cc_start: 0.9101 (tt) cc_final: 0.8859 (tt)
REVERT: A  681 PHE cc_start: 0.8538 (t80) cc_final: 0.8148 (t80)
REVERT: A  705 ASN cc_start: 0.8952 (m-40) cc_final: 0.8474 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1552
  time to fit residues: 25.9203
Evaluate side-chains
  101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 49 optimal weight:    0.4980
   chunk 56 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.154996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.119746 restraints weight = 8963.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.119958 restraints weight = 7634.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.121345 restraints weight = 7134.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.5256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5632  Z= 0.134
  Angle     :  0.640  11.442   7652  Z= 0.307
  Chirality :  0.043   0.234    838
  Planarity :  0.004   0.043    944
  Dihedral  :  8.843  58.814    903
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  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:  1.84 (0.30), residues: 319
  sheet:  0.67 (0.56), residues: 78
  loop : -0.35 (0.45), residues: 239

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   0.029   0.001   PHE A 682 
 TYR   0.019   0.001   TYR A 397 
 ARG   0.003   0.000   ARG A  83 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00862 (    4)
  link_NAG-ASN         : angle       5.12908 (   12)
  link_BETA1-4         : bond        0.00626 (    3)
  link_BETA1-4         : angle       1.46044 (    9)
  hydrogen bonds       : bond        0.03887 (  267)
  hydrogen bonds       : angle       4.02113 (  768)
  SS BOND              : bond        0.01608 (    1)
  SS BOND              : angle       1.88326 (    2)
  covalent geometry    : bond        0.00297 ( 5624)
  covalent geometry    : angle       0.60450 ( 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
  125 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.649 
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: 0.8658 (tmm-80) cc_final: 0.8183 (tmm-80)
REVERT: A  100 ARG cc_start: 0.7064 (mmt180) cc_final: 0.6668 (mmm160)
REVERT: A  113 ASP cc_start: 0.7732 (m-30) cc_final: 0.7070 (p0)
REVERT: A  235 HIS cc_start: 0.9094 (t-90) cc_final: 0.8369 (t-90)
REVERT: A  237 LEU cc_start: 0.9237 (mt) cc_final: 0.8839 (mt)
REVERT: A  293 LEU cc_start: 0.9533 (tp) cc_final: 0.9236 (tp)
REVERT: A  397 TYR cc_start: 0.8980 (p90) cc_final: 0.8580 (p90)
REVERT: A  401 MET cc_start: 0.4093 (ptt) cc_final: 0.3488 (ptt)
REVERT: A  402 MET cc_start: 0.5982 (mtm) cc_final: 0.5305 (mtm)
REVERT: A  416 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7736 (ttp-110)
REVERT: A  443 MET cc_start: 0.8783 (ptp) cc_final: 0.8500 (ptm)
REVERT: A  505 LEU cc_start: 0.8202 (tt) cc_final: 0.7874 (mt)
REVERT: A  559 GLU cc_start: 0.6686 (tt0) cc_final: 0.6229 (tp30)
REVERT: A  615 LEU cc_start: 0.9053 (tt) cc_final: 0.8771 (tt)
REVERT: A  681 PHE cc_start: 0.8364 (t80) cc_final: 0.8013 (t80)
REVERT: A  705 ASN cc_start: 0.8925 (m-40) cc_final: 0.8432 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1577
  time to fit residues: 26.2613
Evaluate side-chains
  97 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 14 optimal weight:    0.2980
   chunk 60 optimal weight:    5.9990
   chunk 41 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0370
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.3857 r_free = 0.3857 target = 0.157306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.121941 restraints weight = 9026.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.119243 restraints weight = 7995.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.120967 restraints weight = 8508.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3393
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3393
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.5381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5632  Z= 0.123
  Angle     :  0.623  10.676   7652  Z= 0.300
  Chirality :  0.042   0.240    838
  Planarity :  0.004   0.040    944
  Dihedral  :  8.304  57.325    903
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  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:  1.40 (0.35), residues: 636
  helix:  1.95 (0.30), residues: 319
  sheet:  0.66 (0.56), residues: 78
  loop : -0.34 (0.45), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 678 
 PHE   0.020   0.001   PHE A 682 
 TYR   0.017   0.001   TYR A 397 
 ARG   0.006   0.000   ARG A  83 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00869 (    4)
  link_NAG-ASN         : angle       4.68289 (   12)
  link_BETA1-4         : bond        0.00641 (    3)
  link_BETA1-4         : angle       1.50421 (    9)
  hydrogen bonds       : bond        0.03790 (  267)
  hydrogen bonds       : angle       3.96068 (  768)
  SS BOND              : bond        0.00814 (    1)
  SS BOND              : angle       1.62773 (    2)
  covalent geometry    : bond        0.00270 ( 5624)
  covalent geometry    : angle       0.59304 ( 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
  120 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.622 
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: 0.7257 (mmt180) cc_final: 0.6701 (mmm160)
REVERT: A  113 ASP cc_start: 0.7652 (m-30) cc_final: 0.7100 (p0)
REVERT: A  235 HIS cc_start: 0.9079 (t-90) cc_final: 0.8381 (t-90)
REVERT: A  237 LEU cc_start: 0.9293 (mt) cc_final: 0.8834 (mt)
REVERT: A  272 PHE cc_start: 0.7351 (m-80) cc_final: 0.7125 (m-80)
REVERT: A  293 LEU cc_start: 0.9509 (tp) cc_final: 0.9225 (tp)
REVERT: A  397 TYR cc_start: 0.9041 (p90) cc_final: 0.8640 (p90)
REVERT: A  401 MET cc_start: 0.4084 (ptt) cc_final: 0.3444 (ptt)
REVERT: A  402 MET cc_start: 0.6016 (mtm) cc_final: 0.5312 (mtm)
REVERT: A  443 MET cc_start: 0.8828 (ptp) cc_final: 0.8580 (ptp)
REVERT: A  505 LEU cc_start: 0.8251 (tt) cc_final: 0.7885 (tt)
REVERT: A  506 LEU cc_start: 0.6560 (pt) cc_final: 0.6269 (pt)
REVERT: A  559 GLU cc_start: 0.6573 (tt0) cc_final: 0.6149 (tp30)
REVERT: A  615 LEU cc_start: 0.9108 (tt) cc_final: 0.8813 (tt)
REVERT: A  681 PHE cc_start: 0.8464 (t80) cc_final: 0.8115 (t80)
REVERT: A  705 ASN cc_start: 0.8955 (m-40) cc_final: 0.8500 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1649
  time to fit residues: 26.0569
Evaluate side-chains
  103 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   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 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 = 0.3859 r_free = 0.3859 target = 0.157612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.122451 restraints weight = 9058.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.120447 restraints weight = 7885.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.121966 restraints weight = 7530.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3360
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.5560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5632  Z= 0.155
  Angle     :  0.661   9.965   7652  Z= 0.319
  Chirality :  0.043   0.248    838
  Planarity :  0.004   0.037    944
  Dihedral  :  8.175  58.130    903
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  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:  1.27 (0.35), residues: 636
  helix:  1.86 (0.30), residues: 320
  sheet:  0.13 (0.57), residues: 81
  loop : -0.27 (0.45), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 287 
 PHE   0.020   0.001   PHE A 682 
 TYR   0.018   0.001   TYR A 397 
 ARG   0.003   0.000   ARG A  83 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00863 (    4)
  link_NAG-ASN         : angle       4.48464 (   12)
  link_BETA1-4         : bond        0.00745 (    3)
  link_BETA1-4         : angle       2.01000 (    9)
  hydrogen bonds       : bond        0.04214 (  267)
  hydrogen bonds       : angle       4.10714 (  768)
  SS BOND              : bond        0.00463 (    1)
  SS BOND              : angle       2.06185 (    2)
  covalent geometry    : bond        0.00352 ( 5624)
  covalent geometry    : angle       0.63349 ( 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
  117 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.628 
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: 0.7269 (mmt180) cc_final: 0.6814 (mmm160)
REVERT: A  113 ASP cc_start: 0.7693 (m-30) cc_final: 0.7123 (p0)
REVERT: A  129 MET cc_start: 0.7875 (mmt) cc_final: 0.7627 (mmp)
REVERT: A  235 HIS cc_start: 0.9196 (t-90) cc_final: 0.8426 (t-90)
REVERT: A  237 LEU cc_start: 0.9247 (mt) cc_final: 0.8845 (mt)
REVERT: A  293 LEU cc_start: 0.9533 (tp) cc_final: 0.9245 (tp)
REVERT: A  319 LEU cc_start: 0.8443 (mp) cc_final: 0.8169 (mt)
REVERT: A  401 MET cc_start: 0.4203 (ptt) cc_final: 0.3451 (ptt)
REVERT: A  559 GLU cc_start: 0.6722 (tt0) cc_final: 0.6202 (tp30)
REVERT: A  615 LEU cc_start: 0.9142 (tt) cc_final: 0.8864 (tt)
REVERT: A  705 ASN cc_start: 0.8930 (m-40) cc_final: 0.8531 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1565
  time to fit residues: 24.5845
Evaluate side-chains
  94 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 16 optimal weight:    0.3980
   chunk 60 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0470
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.155800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.121178 restraints weight = 8976.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.117522 restraints weight = 7791.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.119117 restraints weight = 8278.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.5642

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= 0.129
  Angle     :  0.648   9.578   7652  Z= 0.312
  Chirality :  0.042   0.253    838
  Planarity :  0.004   0.049    944
  Dihedral  :  7.842  55.296    903
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  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:  1.90 (0.29), residues: 320
  sheet:  0.35 (0.59), residues: 77
  loop : -0.11 (0.46), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 390 
 HIS   0.005   0.001   HIS A 287 
 PHE   0.020   0.001   PHE A 682 
 TYR   0.038   0.001   TYR A 397 
 ARG   0.019   0.001   ARG A  68 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00838 (    4)
  link_NAG-ASN         : angle       4.31090 (   12)
  link_BETA1-4         : bond        0.00666 (    3)
  link_BETA1-4         : angle       1.69782 (    9)
  hydrogen bonds       : bond        0.03961 (  267)
  hydrogen bonds       : angle       4.05120 (  768)
  SS BOND              : bond        0.00340 (    1)
  SS BOND              : angle       1.60099 (    2)
  covalent geometry    : bond        0.00287 ( 5624)
  covalent geometry    : angle       0.62323 ( 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
  119 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7177 (mmt180) cc_final: 0.6796 (mmm160)
REVERT: A  113 ASP cc_start: 0.7647 (m-30) cc_final: 0.7160 (p0)
REVERT: A  235 HIS cc_start: 0.9135 (t-90) cc_final: 0.8170 (t-90)
REVERT: A  237 LEU cc_start: 0.9308 (mt) cc_final: 0.8706 (mt)
REVERT: A  293 LEU cc_start: 0.9526 (tp) cc_final: 0.9186 (tp)
REVERT: A  319 LEU cc_start: 0.8427 (mp) cc_final: 0.8143 (mt)
REVERT: A  401 MET cc_start: 0.4174 (ptt) cc_final: 0.3434 (ptt)
REVERT: A  402 MET cc_start: 0.5922 (mtm) cc_final: 0.5183 (mtm)
REVERT: A  507 MET cc_start: 0.7002 (tmm) cc_final: 0.5590 (ttt)
REVERT: A  559 GLU cc_start: 0.6600 (tt0) cc_final: 0.6136 (tp30)
REVERT: A  615 LEU cc_start: 0.9163 (tt) cc_final: 0.8849 (tt)
REVERT: A  705 ASN cc_start: 0.8871 (m-40) cc_final: 0.8513 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1456
  time to fit residues: 23.6542
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  : 0.573 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 14 optimal weight:    0.3980
   chunk 28 optimal weight:    0.4980
   chunk 13 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0170
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
A 479 GLN
** A 580 GLN ** 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 = 0.3836 r_free = 0.3836 target = 0.154329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.119283 restraints weight = 9013.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.118185 restraints weight = 7631.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.119816 restraints weight = 7348.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3400
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3400
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.5760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5632  Z= 0.134
  Angle     :  0.732  18.161   7652  Z= 0.336
  Chirality :  0.058   1.055    838
  Planarity :  0.004   0.045    944
  Dihedral  :  7.890  55.396    903
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  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:  1.48 (0.35), residues: 636
  helix:  1.94 (0.29), residues: 320
  sheet:  0.35 (0.57), residues: 80
  loop : -0.04 (0.46), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 390 
 HIS   0.004   0.001   HIS A 287 
 PHE   0.019   0.001   PHE A 682 
 TYR   0.034   0.001   TYR A 397 
 ARG   0.012   0.000   ARG A  68 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01036 (    4)
  link_NAG-ASN         : angle       6.69572 (   12)
  link_BETA1-4         : bond        0.02096 (    3)
  link_BETA1-4         : angle       3.61640 (    9)
  hydrogen bonds       : bond        0.03875 (  267)
  hydrogen bonds       : angle       3.99989 (  768)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       1.43346 (    2)
  covalent geometry    : bond        0.00285 ( 5624)
  covalent geometry    : angle       0.67179 ( 7629)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2060.35 seconds
wall clock time: 36 minutes 43.84 seconds (2203.84 seconds total)